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https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Leah+Novinger Proteopedia - User contributions [en] 2026-09-13T09:15:57Z User contributions MediaWiki 1.43.8 https://proteopedia.org/index.php?title=G3p&diff=951602 G3p 2009-04-28T17:44:20Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='350' frame='true' align='right' caption='D1 and D2 domains of g3p(1g3p)' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> Finally, two papers <ref name="lubkowski 99"> PMID: 10404600 </ref> <ref name="deprez"> PMID:15701516 </ref> were later published described interactions between g3p and TolA protein (located on the host cell, see [[#Infectivity]]. <br /> <br /> ===D1 Domain===<br /> <applet load='2g3p' size='350' frame='true' align='left' caption='(2g3p) Representation is a dimer of two molecules of D1 and D2 domains of g3p' /><br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> <br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing <scene name='G3p/Hydrophobic/1'>hydrophobic molecules </scene> facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> ===D3 Domain===<br /> Upon review of the literature, no structural analyses of this domain were identified. <br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> <applet load='1tol' size='350' frame='true' align='right' caption='D1 of g3p interacting with D3 of TolA' /><br /> The function of the protein has a close correlation with its structural domains. The <scene name='G3p/D1_and_tola/1'>D1 domain (blue) interacts with TolA protein (orange)</scene> in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. <br /> <br /> <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus and is necessary for phage packaging<ref name="holliger 99"/>.<br /> <br /> <br /> <br /> ===Phage Display=== <br /> Infection with filamentous phage does not cause host cell lysis or death <ref name="gailus"> PMID:8026502 </ref>. The N terminus of g3p can be truncated and the peptide of choice can be inserted <ref name="cabilly"/>. Insertions can also be made between D2 and D3 <ref name="h and r"> PMID: 9032075 </ref>. Specifically, fusions to ther N terminus have no affect on infectivity, between D12 and D3 have 100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides <ref name="chatellier"/>.<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> While the N terminus domain is necessary for infection, the full protein does not need to exist for all five particles on the surface <ref name="cabilly"/>.<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951601 G3p 2009-04-28T17:43:27Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='350' frame='true' align='right' caption='D1 and D2 domains of g3p(1g3p)' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> Finally, two papers <ref name="lubkowski 99"> PMID: 10404600 </ref> <ref name="deprez"> PMID:15701516 </ref> were later published described interactions between g3p and TolA protein (located on the host cell, see [[#Infectivity]]. <br /> <br /> ===D1 Domain===<br /> <applet load='2g3p' size='350' frame='true' align='right' caption='(2g3p) Representation is a dimer of two molecules of D1 and D2 domains of g3p' /><br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> <br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing <scene name='G3p/Hydrophobic/1'>hydrophobic molecules </scene> facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> ===D3 Domain===<br /> Upon review of the literature, no structural analyses of this domain were identified. <br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> <applet load='1tol' size='350' frame='true' align='right' caption='D1 of g3p interacting with D3 of TolA' /><br /> The function of the protein has a close correlation with its structural domains. The <scene name='G3p/D1_and_tola/1'>D1 domain (blue) interacts with TolA protein (orange)</scene> in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. <br /> <br /> <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus and is necessary for phage packaging<ref name="holliger 99"/>.<br /> <br /> <br /> <br /> ===Phage Display=== <br /> Infection with filamentous phage does not cause host cell lysis or death <ref name="gailus"> PMID:8026502 </ref>. The N terminus of g3p can be truncated and the peptide of choice can be inserted <ref name="cabilly"/>. Insertions can also be made between D2 and D3 <ref name="h and r"> PMID: 9032075 </ref>. Specifically, fusions to ther N terminus have no affect on infectivity, between D12 and D3 have 100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides <ref name="chatellier"/>.<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> While the N terminus domain is necessary for infection, the full protein does not need to exist for all five particles on the surface <ref name="cabilly"/>.<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951600 G3p 2009-04-28T17:42:03Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p(1g3p)' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> Finally, two papers <ref name="lubkowski 99"> PMID: 10404600 </ref> <ref name="deprez"> PMID:15701516 </ref> were later published described interactions between g3p and TolA protein (located on the host cell, see [[#Infectivity]]. <br /> <br /> ===D1 Domain===<br /> <applet load='2g3p' size='200' frame='true' align='right' caption='(2g3p) Representation is a dimer of two molecules of D1 and D2 domains of g3p' /><br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> <br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing <scene name='G3p/Hydrophobic/1'>hydrophobic molecules </scene> facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> ===D3 Domain===<br /> Upon review of the literature, no structural analyses of this domain were identified. <br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> <applet load='1tol' size='300' frame='true' align='right' caption='D1 of g3p interacting with D3 of TolA' /><br /> The function of the protein has a close correlation with its structural domains. The <scene name='G3p/D1_and_tola/1'>D1 domain (blue) interacts with TolA protein (orange)</scene> in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. <br /> <br /> <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus and is necessary for phage packaging<ref name="holliger 99"/>.<br /> <br /> <br /> <br /> ===Phage Display=== <br /> Infection with filamentous phage does not cause host cell lysis or death <ref name="gailus"> PMID:8026502 </ref>. The N terminus of g3p can be truncated and the peptide of choice can be inserted <ref name="Cabilly"/>. Insertions can also be made between D2 and D3 <ref name="h and r"> PMID: 9032075 </ref>. Specifically, fusions to ther N terminus have no affect on infectivity, between D12 and D3 have 100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides <ref name="chatellier"/>.<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> While the N terminus domain is necessary for infection, the full protein does not need to exist for all five particles on the surface <ref name="cabilly"/>.<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951599 G3p 2009-04-28T17:10:02Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p(1g3p)' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> Finally, two papers <ref name="lubkowski 99"> PMID: 10404600 </ref> <ref name="deprez"> PMID:15701516 </ref> were later published described interactions between g3p and TolA protein (located on the host cell, see [[#Infectivity]]. <br /> <br /> ===D1 Domain===<br /> <applet load='2g3p' size='200' frame='true' align='right' caption='(2g3p) Representation is a dimer of two molecules of D1 and D2 domains of g3p' /><br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> <br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing <scene name='G3p/Hydrophobic/1'>hydrophobic molecules </scene> facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> ===D3 Domain===<br /> Upon review of the literature, no structural analyses of this domain were identified. <br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> <applet load='1tol' size='300' frame='true' align='right' caption='D1 of g3p interacting with D3 of TolA' /><br /> The function of the protein has a close correlation with its structural domains. The <scene name='G3p/D1_and_tola/1'>D1 domain (blue) interacts with TolA protein (orange)</scene> in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. <br /> <br /> <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus and is necessary for phage packaging<ref name="holliger 99"/>.<br /> <br /> <br /> <br /> ===Phage Display=== <br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951598 G3p 2009-04-28T17:03:30Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p(1g3p)' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> Finally, two papers <ref name="lubkowski 99"> PMID: 10404600 </ref> <ref name="deprez"> PMID:15701516 </ref> were later published described interactions between g3p and TolA protein (located on the host cell, see [[#Infectivity]]. <br /> <br /> ===D1 Domain===<br /> <applet load='{{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}' size='200' frame='true' align='right' caption='(2g3p) Representation is a dimer of two molecules of D1 and D2 domains of g3p' /><br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> <br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing <scene name='G3p/Hydrophobic/1'>hydrophobic molecules </scene> facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> ===D3 Domain===<br /> Upon review of the literature, no structural analyses of this domain were identified. <br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> <applet load='{{STRUCTURE_1tol | PDB=1tol | SCENE= }}' size='300' frame='true' align='right' caption='Insert caption here' /><br /> The function of the protein has a close correlation with its structural domains. The <scene name='G3p/D1_and_tola/1'>D1 domain (blue) interacts with TolA protein (orange)</scene> in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. <br /> <br /> <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus and is necessary for phage packaging<ref name="holliger 99"/>.<br /> <br /> <br /> <br /> ===Phage Display=== <br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951597 G3p 2009-04-28T16:55:09Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p(1g3p)' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> Finally, two papers <ref name="lubkowski 99"> PMID: 10404600 </ref> <ref name="deprez"> PMID:15701516 </ref> were later published described interactions between g3p and TolA protein (located on the host cell, see [[Infectivity]]. <br /> <br /> ===D1 Domain===<br /> <applet load='{{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}' size='200' frame='true' align='right' caption='(2g3p) Representation is a dimer of two molecules of D1 and D2 domains of g3p' /><br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> <br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing <scene name='G3p/Hydrophobic/1'>hydrophobic molecules </scene> facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> ===D3 Domain===<br /> Upon review of the literature, no structural analyses of this domain were identified. <br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> {{STRUCTURE_1tol | PDB=1tol | SCENE= }}<br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. <br /> <br /> <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus and is necessary for phage packaging<ref name="holliger 99"/>.<br /> <br /> <br /> <br /> ===Phage Display=== <br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951596 G3p 2009-04-28T16:45:55Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='350' frame='true' align='right' caption='D1 and D2 domains of g3p(1g3p)' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> Finally, two papers <ref name="lubkowski 99" PMID: 10404600 </ref><ref name="deprez" PMID:15701516</ref> were later published described interactions between g3p and TolA protein (located on the host cell, see ||Infectivity||. <br /> <br /> ===D1 Domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Further elaboration on the interactions between the domains is described in [[#Infectivity]] <br /> <br /> ===D3 Domain===<br /> Upon review of the literature, no structural analyses of this domain were identified. <br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> {{STRUCTURE_1tol | PDB=1tol | SCENE= }}<br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing <scene name='G3p/Hydrophobic/1'>hydrophobic molecules </scene> facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus and is necessary for phage packaging<ref name="holliger 99"/>.<br /> <br /> <br /> <br /> ===Phage Display=== <br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951592 G3p 2009-04-28T16:07:59Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='350' frame='true' align='right' caption='D1 and D2 domains of g3p(1g3p)' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> ===D1 Domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The <scene name='G3p/D1_in_blue_spin/1'>D1 domain</scene> consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Further elaboration on the interactions between the domains is described in [[#Infectivity]] <br /> <br /> ===D3 Domain===<br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing <scene name='G3p/Hydrophobic/1'>hydrophobic molecules </scene> facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> {{STRUCTURE_1tol | PDB=1tol | SCENE= }}<br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951571 G3p 2009-04-28T12:51:02Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='350' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> ===D1 Domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Further elaboration on the interactions between the domains is described in [[#Infectivity]] <br /> <br /> ===D3 Domain===<br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing hydrophobic molecules facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> {{STRUCTURE_1tol | PDB=1tol | SCENE= }}<br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951570 G3p 2009-04-28T12:50:13Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='400' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> ===D1 Domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Further elaboration on the interactions between the domains is described in [[#Infectivity]] <br /> <br /> ===D3 Domain===<br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing hydrophobic molecules facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> {{STRUCTURE_1tol | PDB=1tol | SCENE= }}<br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951568 G3p 2009-04-28T12:46:27Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> ===D1 Domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Further elaboration on the interactions between the domains is described in [[#Infectivity]] <br /> <br /> ===D3 Domain===<br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing hydrophobic molecules facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> {{STRUCTURE_1tol | PDB=1tol | SCENE= }}<br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=951567 User talk:Eran Hodis 2009-04-28T12:34:43Z

<p>Leah Novinger: </p> <hr /> <div>==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.<br/><br /> my best<br/><br /> Tom<br/><br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <nowiki><scene>...<scene/></nowiki> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the <img src="www.filename.jpg"> code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making "metalloprotease" as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says "calcium atoms (yellow)" but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)<br /> <br /> ==Image Issue==<br /> Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah</div>

Leah Novinger https://proteopedia.org/index.php?title=User_talk:Eran_Hodis&diff=951566 User talk:Eran Hodis 2009-04-28T12:33:25Z

<p>Leah Novinger: </p> <hr /> <div>Hi Eran, <br /> I got your message and will take care of it. I think modified images were okay. <br /> Thanks!<br /> Leah<br /> <br /> ==News from Greece==<br /> Hi Eran,<br /> actually I was on vacation after the summer school of Erice! <br /> The last days I'm back in the lab and try to find the rythm of the experiments ;)<br /> I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.<br /> We'll be in contact..you'll see the progress of my page!<br /> <br /> best wishes<br /> Maria<br /> ---------<br /> <br /> <br /> Hi Eran,<br /> Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.<br /> best regards<br /> Trevor<br /> ---------<br /> <br /> <br /> == Bad green link ==<br /> Eran,<br /> I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?<br /> <br /> Karl<br /> <br /> ---------<br /> After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.<br /> <br /> Karl<br /> <br /> <br /> == PDBsum site ==<br /> Eran,<br /> After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.<br /> <br /> By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.<br /> <br /> Karl<br /> <br /> Eran,<br /> I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.<br /> <br /> Karl<br /> <br /> == Proteopedia for teaching ==<br /> Hi Eran<br /> <br /> I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:<br /> <br /> 1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)<br /> <br /> 2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.<br /> <br /> cheers!<br /> <br /> Shaun<br /> <br /> == What to do with my students contributions ==<br /> <br /> Hi Eran,<br /> <br /> I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?<br /> <br /> Tom<br /> <br /> == Surfaces ==<br /> <br /> Hi Eran,<br /> <br /> I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.<br /> <br /> Tom<br /> <br /> == more on surfaces ==<br /> <br /> Hi<br /> <br /> Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces.<br/><br /> my best<br/><br /> Tom<br/><br /> PS. So, what is the Israeli greetings/salutation during Hannukah?<br /> <br /> == Cheers Eran! ==<br /> <br /> Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific. <br /> <br /> <br /> BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)<br /> <br /> == RE: ==<br /> <br /> <br /> Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST) <br /> <br /> : With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)<br /> <br /> :: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)<br /> <br /> ==RE: Models==<br /> <br /> Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!<br /> <br /> -Mark<br /> <br /> == Moving scenes from one page to another ==<br /> <br /> Hi Eran,<br /> <br /> I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <nowiki><scene>...<scene/></nowiki> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.<br /> <br /> Tom<br /> <br /> ==Other Media in Proteopedia?==<br /> <br /> Hi Eran,<br /> <br /> I have a question about the potential for additional media on pages. I know we can easily load and display images on Proteopedia, but is there any way to upload other file varieties - for example, simple flash animations (.swf) or something similar to that? Or, if we can't actually upload them to the Proteopedia webspace, is there any way to have files uploaded on our own server and just displayed on the proteopedia page - perhaps by using some html similar to the <img src="www.filename.jpg"> code you can use for linking to images)?<br /> <br /> -Mark<br /> <br /> ===tilman ===<br /> Eran, you are right. That page <br /> Http://proteopedia.org/wiki/index.php/User:Tilman_Schirmer/Sandbox_10<br /> is obsolete. I've saved the content to the proper Sandbox_10.<br /> <br /> You can delete it. Thanks,<br /> Tilman<br /> ==References==<br /> <br /> Thanks for the tip Eran. I seem to stumble across cool built in features for Proteopedia like that every time I use it! Keep up the good work.<br /> <br /> -Mark<br /> <br /> == good enough? ==<br /> <br /> Would you say, [[User:Ralf Stephan/Sandbox 2|this]] is good enough to replace [[2a7g]]? What more does it need for a page 'Thermolysin'? --[[User:Ralf Stephan|Ralf Stephan]] 16:57, 7 February 2009 (IST)<br /> <br /> :It's certainly enough to replace [[2a7g]], and a great start! (please do replace it) The automatically added abstract here doesn't seem to have anything to do with the structure. Is this indeed the primary publication for the structure? Some questions/comments about your additions: Consider making "metalloprotease" as a interwiki link. We have a not-so-well developed page on [[Matrix_metalloproteinases]], but none on metalloproteases, so the reader may wonder what is a metalloprotease and what is its enzymatic function. It says "calcium atoms (yellow)" but I don't see any calcium atoms in yellow, they are green for me (as they usually are by default). It's not made entirely clear what the HEXHH motif is, could you clarify? I feel the reader would also wonder why is it important to mention in the first sentence that the protein contains zinc and several calcium atoms. Also, what is the substrate usually? The green links look just spectacular, and I'm glad to see you've quickly gotten the hang of the Scene Authoring Tools. <br /> <br /> :A page called 'Thermolysin' is a great idea, are there any other structures? We could transclude a section from your new [[2a7g]] page as well as elaborate more -- especially if there are other structures. --[[User:Eran Hodis|Eran Hodis]] 02:34, 8 February 2009 (IST)<br /> ::*There are lots of other thermolysin structures, mostly inhibitors docking and soaked with different solvent concentrations (why these?).<br /> :::Just thinking that a topic page on thermolysin could use the other structures as well to present a fuller picture.<br /> ::*So, a topic has a set of structures, ideally of all structures, with the structures pointing to 'their' nearest topic?<br /> :::That's the current mode of thinking. Of course better ideas will be adopted.<br /> ::*Regarding yellow/green, that's an example of me unconsciously giving away personal genetic data ;) Really, if I have that problem, other R/G blind people would have, too, so I'd suggest a different color for calcium.<br /> :::Hmm, yes we actually were wondering if that would be a problem when we made the scene links green -- is it a problem? Unfortunately it would be quite unfeasible to change from green scene links at this point. As far as changing calcium to a color other than green -- green might be part of a big coloring scheme that we might want to stick with. We can have a discussion on this if need be. <br /> ::*/Wrt the paper, that paper is given by PDBsum, too, one of those where the protein is just an example in a technical presentation. I should have used a different one.<br /> :::Ok, in this case then it is probably acceptable to leave out the publication abstract. If we use a more fitting abstract, but one from authors that did not solve that structure, it might send the wrong impression to readers that the wrong set of authors solved the structure. If you choose to do this, I would make it clear that the abstract is not the official one for this structure, and list the authors that did solve the structure with the appropriate reference.<br /> ::*Yes, MMPs are only a small subset of metalloproteases and should link to that WP article, too. <br /> :::Ok good.<br /> ::Thanks also for the other hints. Is there a list of all structure pages that have been enhanced manually? I know there's a manually maintained list as part of the topic page list but I think there should be something automatical such that enhancements are not lost. --[[User:Ralf Stephan|Ralf Stephan]] 10:16, 8 February 2009 (IST)<br /> :::Agreed, but the way to do this has slipped my mind at the moment. Let's see if Jaime Prilusky knows and will respond on the mailing list. --[[User:Eran Hodis|Eran Hodis]] 12:27, 8 February 2009 (IST)<br /> <br /> == java.io.File not found ==<br /> <br /> Do you understand why the applet can't find the PDB file in [[Helix-turn-helix motif]]? --[[User:Ralf Stephan|Ralf Stephan]] 17:57, 8 February 2009 (IST)<br /> :Never mind, I found it out myself: I forgot to provide a scene. --[[User:Ralf Stephan|Ralf Stephan]] 18:14, 8 February 2009 (IST)</div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951560 G3p 2009-04-28T06:53:31Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> ===D1 Domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Further elaboration on the interactions between the domains is described in [[#Infectivity]] <br /> <br /> ===D3 Domain===<br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] {{STRUCTURE_1tol | PDB=1tol | SCENE= }}<br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing hydrophobic molecules facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951559 G3p 2009-04-28T06:49:04Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID: 10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution <ref name="holliger 99"/>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> ===D1 Domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubkowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Further elaboration on the interactions between the domains is described in [[#Infectivity]] <br /> <br /> ===D3 Domain===<br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubkowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubkowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing hydrophobic molecules facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951558 G3p 2009-04-28T06:42:31Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1997, Lubkowski et al crystallized the first two domains of g3p from M13 phage to 1.46Å resolution. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> One year later, another structure containing D1 and D2 (albeit from the filamentous phage, fd, containing a two residue difference) was published using x-ray crystallography to 1.9Å resolution<ref name="holliger 99" PMID: 10329170 </ref>. Dimer formation was observed, but was attributed to the experimental conditions. <br /> <br /> ===D1 Domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Further elaboration on the interactions between the domains is described in [[#Infectivity]] <br /> <br /> ===D3 Domain===<br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>. In both Lubowski et al and Holliger et al, these regions were not observed through crystallography study <ref name="lubowski"/><ref name="holliger 99"/>. <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein in the periplasm of the bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/><ref name="holliger 99"/>. (The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli(Cell 90, 351-360 (1997)). The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <ref name="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low<ref name="lubkowski"/>. It has been speculated that D2 interacts with the F pilus first, drawing the phage closer to the bacterial cell, thus allowing D1-TolA interactions to occur<ref name="holliger 99"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<ref name="chatellier"/>. Lubkowski et al like the interaction between D1 and D2 to a horseshoe shaped molecule attributing hydrophobic molecules facing toward the center as stabilizing factors <ref name="lubkowski"/>. <br /> <br /> The function of D3 was elicited last. D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> <br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951557 G3p 2009-04-28T06:16:07Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. Differences from the first paper published were mainly attributed to turns in the structure, the orientation of the C terminus, and interacting amino acids between the two domains. In addition, the authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 Domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 Domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> Further elaboration on the interactions between the domains is described in [[#Infectivity]] <br /> <br /> ===D3 Domain===<br /> <br /> ===Linkers===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The function of the protein has a close correlation with its structural domains. The D1 domain interacts with TolA protein on bacterial cell. <ref name="lubkowski"/><ref name="cabilly"/>. The D2 domain binds to F pilus on the outer membrane of ''Escherichia coli'', however, it is also blocks TolA binding to D1 in the absence of the F pilus <refname="chatellier"> PMID:10606756 </ref>. In fact, without the D2 domain, infectivity is very low despite the initial contact being attributed to the D1 domain<ref name="lubkowski"/>. Chatellier et al suggest that the complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, and upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria<refname="chatellier"/>.<br /> <br /> The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> <br /> <br /> <br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched).<br /> <br /> <br /> <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> <br /> <br /> <br /> <br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> <br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> <br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> <br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951555 G3p 2009-04-28T05:57:46Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID: 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. Differences from the first paper published were mainly attributed to turns in the structure and the orientation of the C terminus. The authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951554 G3p 2009-04-28T05:57:21Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997 <ref name="holliger 97"> PMID 9032075 </ref>.They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. Differences from the first paper published were mainly attributed to turns in the structure and the orientation of the C terminus. The authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951553 G3p 2009-04-28T05:55:06Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. Differences from the first paper published were mainly attributed to turns in the structure and the orientation of the C terminus. The authors made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity but a “nearly identical fold”, question of sharing common origins or a gene duplication<ref name="lubkowski"/>.<br /> <br /> Used DALI to identify similar proteins with both domains, Lubkowski et al were unable to identify any evolutionarily related proteins<ref name="lubkowski"/>. When looking at individual domains, they found some similar proteins.<br /> <br /> ===D1===<br /> They reported a correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05)<ref name="lubkowski"/>. A comparison with a permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]] was made, but sequence homology did not exist<ref name="lubkowski"/>.<br /> ===D2=== <br /> Lubkowski et al identified the PDZ domain of Human discs large protein (1pdr) as a potentially related protein (Z score = 2.1). This protein is smaller than g3p, and consequently two beta strands in th core of domain share no identity with D2 <ref name="lubkowski"/>.(H and R, 9032075)<br /> <br /> PTB domain H and R, 9032075)<br /> <br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951552 G3p 2009-04-28T05:45:12Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]], but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951551 G3p 2009-04-28T05:44:13Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]], but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951550 G3p 2009-04-28T05:43:57Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <applet load='1g3p' size='200' frame='true' align='left' caption='D1 and D2 domains of g3p' /><br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]], but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' /><br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951549 G3p 2009-04-28T05:37:10Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> <applet load='1g3p' size='200' frame='true' align='right' caption='D1 and D2 domains of g3p' />They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> <applet load='1fgp' size='100' frame='true' align='right' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]], but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951548 G3p 2009-04-28T05:36:08Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> <applet load='1fgp' size='100' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]], but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951547 G3p 2009-04-28T05:35:22Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> <applet load='1fgp' size='100' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> <br /> ==Functional Implications==<br /> ===Infectivity===<br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]], but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951546 G3p 2009-04-28T05:32:11Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> <applet load='1fgp' size='100' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin [[http://dx.doi.org/10.2210/pdb1hxn/pdb (1hxn)]] Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain [[http://dx.doi.org/10.2210/pdb1tuc/pdb (1tuc)]], but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> PDB<br /> [[http://dx.doi.org/10.2210/pdb1fgp/pdb 1fgp]]<br /> [[http://dx.doi.org/10.2210/pdb1g3p/pdb 1g3p]]<br /> [[http://dx.doi.org/10.2210/pdb2g3p/pdb 2g3p]]<br /> [[http://dx.doi.org/10.2210/pdb1tol/pdb 1tol]]<br /> [[http://dx.doi.org/10.2210/pdb1s62/pdb 1s62]]<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951543 G3p 2009-04-28T05:15:01Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> <applet load='1fgp' size='100' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='D1 and D2 domains of g3p' /><br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951542 G3p 2009-04-28T05:13:18Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> <applet load='1fgp' size='100' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.<br /> <br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===D2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951541 G3p 2009-04-28T05:10:12Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> [[Image:F1_holliger_and_riechmann.jpg |frame|center|Figure Adapted from Holliger and Riechmann, 1997<ref name="holliger 97"> PMID:9032075 </ref>]] <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> <applet load='1fgp' size='150' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)<br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===N2 domain===<br /> This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951538 G3p 2009-04-28T04:45:04Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> <applet load='1fgp' size='150' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"> PMID:9032075 </ref>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <applet load='1g3p' size='300' frame='true' align='right' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)<br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951537 G3p 2009-04-28T04:41:22Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> <applet load='1fgp' size='150' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"> PMID:9032075 </ref>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)<applet load='1g3p' size='300' frame='true' align='right' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951536 G3p 2009-04-28T04:40:25Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> <applet load='1fgp' size='150' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"> PMID:9032075 </ref>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.<br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)<applet load='1g3p' size='300' frame='true' align='left' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951535 G3p 2009-04-28T04:38:06Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"> PMID:9032075 </ref>. They used NMR spectroscopy to create a structure of the first domains of g3p. Observations of secondary structure are below.<applet load='1fgp' size='200' frame='true' align='left' caption='Insert caption here' /><br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)<applet load='1g3p' size='300' frame='true' align='left' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>. <br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951534 G3p 2009-04-28T04:16:55Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"> PMID:9032075 </ref>. They used NMR spectroscopy to create a structure of the first two domains of g3p, which they called D1 and D2. Observations of secondary structure are below.<br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)<applet load='1g3p' size='300' frame='true' align='left' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted an <scene name='G3p/N_terminal_alpha_helix/1'>initial alpha helix at N terminal domain</scene> <ref name="lubkowski"/> in their respective analyses<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/><br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/><br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951533 G3p 2009-04-28T04:10:28Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Five major papers will be discussed outlining the evolution of structure analysis of g3p.<br /> <br /> ===Initial Observations===<br /> The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"> PMID:9032075 </ref>. They used NMR spectroscopy to create a structure of the first two domains of g3p, which they called D1 and D2. Observations of secondary structure are below.<br /> <br /> In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations: <br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/><br /> (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)<applet load='1g3p' size='400' frame='true' align='left' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> ===D1 domain===<br /> The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted an <scene name='G3p/N_terminal_alpha_helix/1'>initial alpha helix at N terminal domain</scene> <ref name="lubkowski"/> in their respective analyses<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/><br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/><br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951532 G3p 2009-04-28T04:00:54Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Lubkowski et al<ref name="lubkowski"/> crystallized N1 and N2 together using <br /> His tag<br /> Redox shuffle to form disulfide bonds<br /> Immobilized metal ion affinity chromatography (IMAC)<br /> Anion exchange chromatography<br /> Gel filtration<br /> Selenomethionine labeling to determine phases (???) in crystallography <br /> <br /> ===Initial Observations===<br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/><br /> (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)<applet load='1g3p' size='400' frame='true' align='left' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> <br /> ===D1 domain===<br /> The<br /> <scene name='G3p/N_terminal_alpha_helix/1'>Initial alpha helix at N terminal domain</scene> <ref name="lubkowski"/><br /> Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/><br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/><br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951531 G3p 2009-04-28T03:50:59Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Lubkowski et al<ref name="lubkowski"/> crystallized N1 and N2 together using <br /> His tag<br /> Redox shuffle to form disulfide bonds<br /> Immobilized metal ion affinity chromatography (IMAC)<br /> Anion exchange chromatography<br /> Gel filtration<br /> Selenomethionine labeling to determine phases (???) in crystallography <br /> <br /> ===Initial Observations===<br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/><br /> (2)<scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)<applet load='1g3p' size='400' frame='true' align='left' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> <br /> ===N1 domain===<br /> Initial alpha helix at N terminal domain <ref name="lubkowski"/><br /> Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/><br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/><br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951530 G3p 2009-04-28T03:47:41Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Lubkowski et al<ref name="lubkowski"/> crystallized N1 and N2 together using <br /> His tag<br /> Redox shuffle to form disulfide bonds<br /> Immobilized metal ion affinity chromatography (IMAC)<br /> Anion exchange chromatography<br /> Gel filtration<br /> Selenomethionine labeling to determine phases (???) in crystallography <br /> <br /> ===Initial Observations===<br /> (1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near c terminal end</scene> <ref name="lubkowski"/><br /> Oxidation of tryptophan <ref name="lubkowski"/> not found in other structures (Holliger et al)<applet load='1g3p' size='400' frame='true' align='left' caption='Important characteristics of the N-terminal domains of g3p' /><br /> <br /> <br /> ===N1 domain===<br /> Initial alpha helix at N terminal domain <ref name="lubkowski"/><br /> Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/><br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/><br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951529 G3p 2009-04-28T03:45:19Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Lubkowski et al<ref name="lubkowski"/> crystallized N1 and N2 together using <br /> His tag<br /> Redox shuffle to form disulfide bonds<br /> Immobilized metal ion affinity chromatography (IMAC)<br /> Anion exchange chromatography<br /> Gel filtration<br /> Selenomethionine labeling to determine phases (???) in crystallography <br /> <br /> ===Initial Observations===<br /> <applet load='1g3p' size='400' frame='true' align='left' caption='Important characteristics of the N-terminal domains of g3p' /><scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near c terminal end</scene> <ref name="lubkowski"/><br /> Oxidation of tryptophan <ref name="lubkowski"/> not found in other structures (Holliger et al)<br /> <br /> ===N1 domain===<br /> Initial alpha helix at N terminal domain <ref name="lubkowski"/><br /> Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/><br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/><br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951528 G3p 2009-04-28T03:20:57Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Lubkowski et al<ref name="lubkowski"/> crystallized N1 and N2 together using <br /> His tag<br /> Redox shuffle to form disulfide bonds<br /> Immobilized metal ion affinity chromatography (IMAC)<br /> Anion exchange chromatography<br /> Gel filtration<br /> Selenomethionine labeling to determine phases (???) in crystallography <br /> <br /> Important characteristics:<br /> <applet load='1g3p' size='400' frame='true' align='left' caption='Important characteristics of the N-terminal domains of g3p' />Cis proline near c terminal end <ref name="lubkowski"/><br /> Oxidation of tryptophan <ref name="lubkowski"/> not found in other structures (Holliger et al)<br /> <br /> ===N1 domain===<br /> Initial alpha helix at N terminal domain <ref name="lubkowski"/><br /> Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/><br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/><br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951527 G3p 2009-04-28T03:16:23Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ==Structural Analysis==<br /> Lubkowski et al<ref name="lubkowski"/> crystallized N1 and N2 together using <br /> His tag<br /> Redox shuffle to form disulfide bonds<br /> Immobilized metal ion affinity chromatography (IMAC)<br /> Anion exchange chromatography<br /> Gel filtration<br /> Selenomethionine labeling to determine phases (???) in crystallography <br /> <br /> Important characteristics:<br /> Cis proline near c terminal end <ref name="lubkowski"/><br /> Oxidation of tryptophan <ref name="lubkowski"/> not found in other structures (Holliger et al)<br /> <br /> ===N1 domain===<br /> Initial alpha helix at N terminal domain <ref name="lubkowski"/><br /> Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/><br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/><br /> <br /> ===N2 domain===<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ==Functional Implications==<br /> ===Infectivity===<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ===Phage Display=== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ==Evolutionarily Related Proteins==<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ===N2=== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ===N1===<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ==Links to Available Structures==<br /> <br /> ==References==<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951526 G3p 2009-04-28T03:12:16Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ===Structural Analysis===<br /> Lubkowski et al<ref name="lubkowski"/> crystallized N1 and N2 together using <br /> His tag<br /> Redox shuffle to form disulfide bonds<br /> Immobilized metal ion affinity chromatography (IMAC)<br /> Anion exchange chromatography<br /> Gel filtration<br /> Selenomethionine labeling to determine phases (???) in crystallography <br /> <br /> Important characteristics:<br /> Cis proline near c terminal end <ref name="lubkowski"/><br /> Oxidation of tryptophan <ref name="lubkowski"/> not found in other structures (Holliger et al)<br /> <br /> ====N1 domain====<br /> Initial alpha helix at N terminal domain <ref name="lubkowski"/><br /> Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/><br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/><br /> <br /> ====N2 domain====<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet <ref name="lubkowski"/><br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions <ref name="lubkowski"/><br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) <ref name="lubkowski"/><br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions <ref name="lubkowski"/><br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ===Functional Implications===<br /> ====Infectivity====<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity <ref name="lubkowski"/>.<br /> N1 interacts with TolA protein anchoring it to bacterial cell. <ref name="lubkowski"/>( and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center <ref name="lubkowski"/>, this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe <ref name="lubkowski"/>.<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ====Phage Display==== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ===Evolutionarily Related Proteins===<br /> N1 and N2 have 15% identity <ref name="lubkowski"/> but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains <ref name="lubkowski"/>  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> ====N2==== <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 <ref name="lubkowski"/>(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> ====N1====<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) <ref name="lubkowski"/><br /> Compared with permuted SH3 domain (1tuc), but no sequence homology <ref name="lubkowski"/><br /> ===Links to Available Structures===<br /> <br /> ===References===<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951524 G3p 2009-04-28T03:08:39Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ===Structural Analysis===<br /> (Lubkowski et al) crystallized N1 and N2 together using <br /> His tag<br /> Redox shuffle to form disulfide bonds<br /> Immobilized metal ion affinity chromatography (IMAC)<br /> Anion exchange chromatography<br /> Gel filtration<br /> Selenomethionine labeling to determine phases (???) in crystallography <br /> <br /> Important characteristics:<br /> Cis proline near c terminal end (Lubkowski et al)<br /> Oxidation of tryptophan (Lubkowski et al)  not found in other structures (Holliger et al)<br /> N1 domain<br /> Initial alpha helix at N terminal domain (Lubkowski et al)<br /> Five beta strands arranged as a barrel-like motif, participate with two other strands from second domain to make an antiparallel sheet (Lubkowski et al)<br /> Disulfide between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) (Lubkowski et al)<br /> N2 domain<br /> - 8 beta strands, 6 in a mixed beta sheet, 2 interacting with N2 antiparallel sheet (Lubkowski et al)<br /> Strand between B6 and B7 doesn’t have a specific motif but contributes via stabilizing hydrophobic interactions (Lubkowski et al)<br /> 3 hairpins between 8 and 9, 9 and 10, and 10 and 11 (cis proline in the last hairpin) (Lubkowski et al)<br /> One alpha helix that interacts with rest of N2 domain by hydrophobic interactions (Lubkowski et al)<br /> Cation pi interaction between His 191 and Phe 199<br /> C terminus of N2 has seven peptides, 3 of which are proline, 1 of which is in the cis conformation<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ===Functional Implications===<br /> ====Infectivity====<br /> The linkers don’t have a specific purpose but appear to give the protein better flexibility providing optimal infectivity (Lubkowski et al).<br /> N1 interacts with TolA protein anchoring it to bacterial cell. (Lubkowski et al and Cabilly)  see Riechmann and Holliger. The C terminal domain of TolA is the coreceptor for filamentous phage infection of E coli. Cell 90, 351-360 (1997)<br /> N1 and N2 have 15% identity (Lubkowski et al) but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> D2 domain binds to F pilus (Chatellier et al)<br /> D3 domain “anchors” to F pilus (Chatellier et al) and is necessary for phage packaging (Holliger et al)<br /> Infection with filamentous phage does not cause host cell lysis or death (Gailus and Rasched)<br /> Without N2 domain, infectivity is very low but initial contact is via N1 domain (Lubkowski et al).<br /> The complex formed by D1 and D2 may prevent destruction of the protein from bacterial proteases, Upon binding the protein opens up and D3 can then reach the inner membrane of the bacteria. (Chatellier). <br /> Horseshoe shaped molecule with polar molecules facing toward the center (Lubkowski et al), this central area is thought to interact with pilus…however pilus is almost completely hydrophobic?? <br /> Peptides can be fused to CT domain or to the N1 domain, neither areas are near the central area of the horseshoe (Lubkowski et al).<br /> Amino terminus domain is necessary for infection, but full protein does not need to exist for all five particles on the surface (Cabilly).<br /> Fusions to N terminus (no affect on infectivity), between D12 and D3 (100 fold reduction for peptide insertion, and a 1000 to 100,000 fold for noncovalently interacting peptides)(Chatellier et al)<br /> ====Phage Display==== <br /> N terminus can be truncated and the peptide of choice can be inserted (Cabilly)<br /> Insertions can also be done between D2 and D3 (H and R, 9032075)<br /> <br /> ===Evolutionarily Related Proteins===<br /> N1 and N2 have 15% identity (Lubkowski et al) but a “nearly identical fold”, question of sharing common origins?? Possible gene duplication<br /> <br /> Used DALI to identify similar proteins with both domains (Lubkowski et al)  did not identify any<br /> When looking at each domain, they found some similar proteins<br /> N2 <br /> PDZ domain of Human discs large protein (1pdr) Z score = 2.1) while smaller, 2 beta strands in core of domain share no identity with N2 (Lubkowski et al)(H and R, 9032075)<br /> PTB domain H and R, 9032075)<br /> <br /> N1<br /> Reported correlation with homopexin (1hxn) Z score 1.1 (p>0.05) (Lubkowski et al)<br /> Compared with permuted SH3 domain (1tuc), but no sequence homology (Lubkowski et al)<br /> ===Links to Available Structures===<br /> <br /> ===References===<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951521 G3p 2009-04-28T01:53:08Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> [[Image:wt_and_pIII.jpg |frame|right|Figure Adapted from Hill and Stockley et al, 1996 <ref name="hill"> PMID:8793867 </ref>]] <br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties. <br /> <br /> <br /> <br /> <br /> ===Structural Analysis===<br /> Information regarding structure of g3p goes here. <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> ===Functional Implications===<br /> The relationship between domains and infectivity goes here. <br /> <br /> ===Evolutionarily Related Proteins===<br /> <br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> "Show Preview" at the bottom of this page to see how it goes.<br /> ===References===<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951513 G3p 2009-04-28T01:36:27Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> Gene 3 protein (g3p pr pIII) is a minor coat protein found on the surface of filamentous bacteriophage <ref name="lubkowski"> PMID:9461080 </ref>. The protein consists of 406 amino acids divided into three domains interspaced with glycine linkers <ref name="lubkowski"/> <ref name="cabilly"> PMID:10596371 </ref>. Peptides or proteins can be fused to g3p and evaluated for binding or other properties <br /> <br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> <br /> ===Structural Analysis===<br /> Information regarding structure of g3p goes here. <br /> <br /> ===Functional Implications===<br /> The relationship between domains and infectivity goes here. <br /> <br /> ===Evolutionarily Related Proteins===<br /> <br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> "Show Preview" at the bottom of this page to see how it goes.<br /> ===References===<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951505 G3p 2009-04-28T01:21:16Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> g3p is a minor coat protein found on the surface of filamentous bacteriophage.{{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> <br /> ===Structural Analysis===<br /> Information regarding structure of g3p goes here. <br /> <br /> ===Functional Implications===<br /> The relationship between domains and infectivity goes here. <br /> <br /> ===Evolutionarily Related Proteins===<br /> <br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> "Show Preview" at the bottom of this page to see how it goes.<br /> ===References===<br /> <references/></div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951489 G3p 2009-04-27T23:00:41Z

<p>Leah Novinger: </p> <hr /> <div>==Overview==<br /> g3p is a minor coat protein found on the surface of filamentous bacteriophage.{{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}<br /> <br /> ===Structural Analysis===<br /> Information regarding structure of g3p goes here. <br /> <br /> ===Functional Implications===<br /> The relationship between domains and infectivity goes here. <br /> <br /> ===Evolutionarily Related Proteins===<br /> <br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> "Show Preview" at the bottom of this page to see how it goes.</div>

Leah Novinger https://proteopedia.org/index.php?title=G3p&diff=951488 G3p 2009-04-27T22:55:55Z

<p>Leah Novinger: New page: ==Overview== g3p is a minor coat protein found on the surface of filamentous bacteriophage. This is a placeholder text to help you get started in placing a Jmol applet on your page. At a...</p> <hr /> <div>==Overview==<br /> g3p is a minor coat protein found on the surface of filamentous bacteriophage.<br /> <br /> This is a placeholder text to help you get started in <br /> placing a Jmol applet on your page. At any time, click<br /> "Show Preview" at the bottom of this page to see how it goes.<br /> <br /> Replace the PDB id (use lowercase!) after the STRUCTURE_ and after PDB= to load <br /> and display another structure.<br /> <br /> {{STRUCTURE_2g3p | PDB=2g3p | SCENE= }}</div>

Leah Novinger