https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Amanda+ValdioseraProteopedia - User contributions [en]2026-09-27T20:01:42ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616342VRC01 gp120 complex2012-11-28T00:01:22Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. <br />
<Structure load='3SE9' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' scene='Insert optional scene name here' /><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref name="kwong">PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br/><br />
<br/><br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation<ref name="zhou">PMID: 20616231</ref>. [[Image: Target Site.jpg | thumb | alt=text | Picture 1]] In Picture 1B, the contact surface of VRC01 and CD4 are shown on gp120. The green represents VRC01's contact surface and yellow represents CD4's contact surface<ref name="kwong" />. Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and Arg71 of VRC01. Arg71 and Asp368 form a <scene name='VRC01_gp120_complex/Salt_bridge/1'>salt bridge</scene><ref name="zhou" />. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More <scene name='VRC01_gp120_complex/Hydrophobic_residues/2'>hydrophobic residues</scene> at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another <scene name='VRC01_gp120_complex/Conserved_residues/1'>conserved interaction</scene> is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref name="scheid">PMID: 21764753</ref>. <br />
<br />
Also, when 10 best antibody sequences were aligned, it was found that 68 heavy chain residues were conserved and 7 of these residues were involved in the contact between VRC01 and gp120. In comparison only 53 light chain residues were conserved and only 3 of these residues were involved in the contact between VRC01 and gp120. This is consistent with other research that has shown the light chain of VRC01 having a limited role in attachment to gp120 in comparison to the heavy chain<ref name="scheid" />. <br />
<br/><br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, <scene name='VRC01_gp120_complex/Tyr_28_and_ser_30/1'>Tyr28 and Ser30</scene>, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616335VRC01 gp120 complex2012-11-27T23:51:20Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. <br />
<Structure load='3SE9' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' scene='Insert optional scene name here' /><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br/><br />
<br/><br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image: Target Site.jpg | thumb | alt=text | Picture 1]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and Arg71 of VRC01. Arg71 and Asp368 form a <scene name='VRC01_gp120_complex/Salt_bridge/1'>salt bridge</scene><ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More <scene name='VRC01_gp120_complex/Hydrophobic_residues/2'>hydrophobic residues</scene> at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another <scene name='VRC01_gp120_complex/Conserved_residues/1'>conserved interaction</scene> is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref name="scheid">PMID: 21764753</ref>. <br />
<br />
Also, when 10 best antibody sequences were aligned, it was found that 68 heavy chain residues were conserved and 7 of these residues were involved in the contact between VRC01 and gp120. In comparison only 53 light chain residues were conserved and only 3 of these residues were involved in the contact between VRC01 and gp120. This is consistent with other research that has shown the light chain of VRC01 having a limited role in attachment to gp120 in comparison to the heavy chain<ref name="scheid" />. <br />
<br/><br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, <scene name='VRC01_gp120_complex/Tyr_28_and_ser_30/1'>Tyr28 and Ser30</scene>, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616315VRC01 gp120 complex2012-11-27T23:04:55Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. <br />
<Structure load='3SE9' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' scene='Insert optional scene name here' /><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image: Target Site.jpg | thumb | alt=text | Picture 1]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and Arg71 of VRC01. Arg71 and Asp368 form a <scene name='VRC01_gp120_complex/Salt_bridge/1'>salt bridge</scene><ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More <scene name='VRC01_gp120_complex/Hydrophobic_residues/2'>hydrophobic residues</scene> at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another <scene name='VRC01_gp120_complex/Conserved_residues/1'>conserved interaction</scene> is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref name="scheid">PMID: 21764753</ref>. <br />
<br />
Also, when 10 best antibody sequences were aligned, it was found that 68 heavy chain residues were conserved and 7 of these residues were involved in the contact between VRC01 and gp120. In comparison only 53 light chain residues were conserved and only 3 of these residues were involved in the contact between VRC01 and gp120. This is consistent with other research that has shown the light chain of VRC01 having a limited role in attachment to gp120 in comparison to the heavy chain<ref name="scheid" />. <br />
<br />
<br />
<br />
<br/><br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, <scene name='VRC01_gp120_complex/Tyr_28_and_ser_30/1'>Tyr28 and Ser30</scene>, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616304VRC01 gp120 complex2012-11-27T22:53:48Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. <br />
<Structure load='3SE9' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' scene='Insert optional scene name here' /><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image: Target Site.jpg | thumb | alt=text | Picture 1]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and Arg71 of VRC01. Arg71 and Asp368 form a <scene name='VRC01_gp120_complex/Salt_bridge/1'>salt bridge</scene><ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More <scene name='VRC01_gp120_complex/Hydrophobic_residues/2'>hydrophobic residues</scene> at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another <scene name='VRC01_gp120_complex/Conserved_residues/1'>conserved interaction</scene> is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref name="scheid">PMID: 21764753</ref>. <br />
<br />
Also, when 10 best antibody sequences were aligned, it was found that 68 heavy chain residues were conserved and 7 of these residues were involved in the contact between VRC01 and gp120. In comparison only 53 light chain residues were conserved and only 3 of these residues were involved in the contact between VRC01 and gp120. This is consistent with other research that has shown the light chain of VRC01 having a limited role in attachment to gp120 in comparison to the heavy chain<ref name="scheid" />. <br />
<br />
<br />
<br />
<br/><br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616300VRC01 gp120 complex2012-11-27T22:37:44Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. <br />
<Structure load='3SE9' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' scene='Insert optional scene name here' /><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image: Target Site.jpg | thumb | alt=text | Picture 1]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and Arg71 of VRC01. Arg71 and Asp368 form a <scene name='VRC01_gp120_complex/Salt_bridge/1'>salt bridge</scene><ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More <scene name='VRC01_gp120_complex/Hydrophobic_residues/2'>hydrophobic residues</scene> at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref name="scheid">PMID: 21764753</ref>. <br />
<br />
Also, when 10 best antibody sequences were aligned, it was found that 68 heavy chain residues were conserved and 7 of these residues were involved in the contact between VRC01 and gp120. In comparison only 53 light chain residues were conserved and only 3 of these residues were involved in the contact between VRC01 and gp120. This is consistent with other research that has shown the light chain of VRC01 having a limited role in attachment to gp120 in comparison to the heavy chain<ref name="scheid" />. <br />
<br />
<br />
<br />
<br/><br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616297VRC01 gp120 complex2012-11-27T22:16:05Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. <br />
<Structure load='3SE9' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' scene='Insert optional scene name here' /><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image: Target Site.jpg | thumb | alt=text | Picture 1]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and Arg71 of VRC01. Arg71 and Asp368 form a <scene name='VRC01_gp120_complex/Salt_bridge/1'>salt bridge</scene><ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref name="scheid">PMID: 21764753</ref>. <br />
<br />
Also, when 10 best antibody sequences were aligned, it was found that 68 heavy chain residues were conserved and 7 of these residues were involved in the contact between VRC01 and gp120. In comparison only 53 light chain residues were conserved and only 3 of these residues were involved in the contact between VRC01 and gp120. This is consistent with other research that has shown the light chain of VRC01 having a limited role in attachment to gp120 in comparison to the heavy chain<ref name="scheid" />. <br />
<br />
<br />
<br />
<br/><br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616287VRC01 gp120 complex2012-11-27T21:24:46Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. <br />
<Structure load='3SE9' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' scene='Insert optional scene name here' /><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and Arg71 of VRC01<ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref name="scheid">PMID: 21764753</ref>. <br />
<br />
Also, when 10 best antibody sequences were aligned, it was found that 68 heavy chain residues were conserved and 7 of these residues were involved in the contact between VRC01 and gp120. In comparison only 53 light chain residues were conserved and only 3 of these residues were involved in the contact between VRC01 and gp120. This is consistent with other research that has shown the light chain of VRC01 having a limited role in attachment to gp120 in comparison to the heavy chain<ref name="scheid" />. <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616286VRC01 gp120 complex2012-11-27T21:23:46Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. <br />
<Structure load='3SE9' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' scene='Insert optional scene name here' /><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01<ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref name="scheid">PMID: 21764753</ref>. <br />
<br />
Also, when 10 best antibody sequences were aligned, it was found that 68 heavy chain residues were conserved and 7 of these residues were involved in the contact between VRC01 and gp120. In comparison only 53 light chain residues were conserved and only 3 of these residues were involved in the contact between VRC01 and gp120. This is consistent with other research that has shown the light chain of VRC01 having a limited role in attachment to gp120 in comparison to the heavy chain<ref name="scheid" />. <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616250VRC01 gp120 complex2012-11-27T20:31:48Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01<ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref name="scheid">PMID: 21764753</ref>. <br />
<br />
Also, when 10 best antibody sequences were aligned, it was found that 68 heavy chain residues were conserved and 7 of these residues were involved in the contact between VRC01 and gp120. In comparison only 53 light chain residues were conserved and only 3 of these residues were involved in the contact between VRC01 and gp120. This is consistent with other research that has shown the light chain of VRC01 having a limited role in attachment to gp120 in comparison to the heavy chain<ref name="scheid" />. <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616241VRC01 gp120 complex2012-11-27T20:10:41Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4<ref>PMID: 21715490</ref>. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01<ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref>PMID: 21764753</ref>. <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616236VRC01 gp120 complex2012-11-27T20:05:10Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01<ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions<ref>PMID: 21764753</ref>. <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616234VRC01 gp120 complex2012-11-27T20:03:01Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01<ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain<ref>PMID: 22033520</ref>. Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions. (Scheid) <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616233VRC01 gp120 complex2012-11-27T20:01:05Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01<ref name="zhou">PMID: 20616231</ref>. <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain. (Diskin) Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions. (Scheid) <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding<ref name="zhou" />.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616232VRC01 gp120 complex2012-11-27T19:57:44Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01. (Zhou) <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain. (Diskin) Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions. (Scheid) <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding. (Zhou)<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV<ref>PMID: 22832125</ref>.<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616231VRC01 gp120 complex2012-11-27T19:55:50Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01. (Zhou) <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain. (Diskin) Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions. (Scheid) <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding. (Zhou)<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours<ref>PMID: 12579198</ref>. These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616230VRC01 gp120 complex2012-11-27T19:53:46Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120<ref name="wu">PMID: 21835983</ref>. VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell<ref>PMID: 22807678</ref>. VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01. (Zhou) <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain. (Diskin) Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions. (Scheid) <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding. (Zhou)<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616229VRC01 gp120 complex2012-11-27T19:50:19Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. <ref name="wu">PMID: 21835983</ref> VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120<ref>PMID: 22789610</ref>. Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01. (Zhou) <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain. (Diskin) Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions. (Scheid) <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding. (Zhou)<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616226VRC01 gp120 complex2012-11-27T19:47:26Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. <ref name="wu">PMID: 21835983</ref> VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120<ref name="wu" />. This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell<ref name="wu" />.<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01. (Zhou) <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57<ref name="wu" />. More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain. (Diskin) Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions. (Scheid) <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding. (Zhou)<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==<br />
<references /></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616225VRC01 gp120 complex2012-11-27T19:31:55Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. [[Image:ts.jpeg]] Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01. (Zhou) <br />
<br/><br />
<br/><br />
<br />
<u>Similarities to other antibodies in complex with gp120</u>. Although only about 50% of the amino acids in the variable region of the heavy chains of different CD4 binding site antibodies were conserved, the structures of each of their complex with gp120 was similar. Comparison between other CD4 binding site antibodies show that the Arg71 and Asp368 interaction is also conserved. From sequence analysis of 10 antibodies of the same IGHV1-2*02 germline, 70-90 nucleotide changes are made. Only two residues changes from this germline mature into the same amino acids. These changes occur in a hydrophobic contact of the heavy chain second complementary-determining region. The two amino acid changes are Gly56 into Ala56 and Thr57 into Val57. (Wu) More hydrophobic residues at this position led to an increased potency and breadth by increasing contacts with gp120’s bridging domain. (Diskin) Another conserved interaction is the interaction of Tyr91 and Glu96 of VRC01 with loop D of gp120. These residues engage loop D by polar interactions. (Scheid) <br />
<br />
<br/> [[Image:ts.jpeg|center|300px|thumb|]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding. (Zhou)<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616221VRC01 gp120 complex2012-11-27T18:28:42Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. However, VRC01’s binding site extends outside that of CD4, making it vulnerable to resistance of VRC01 neutralization by antigenic variation. Insert figure Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01. (Zhou) <br />
<br/><br />
<br/><br />
<u>Similarities to other antibodies in complex with gp120</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding. (Zhou)<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616050VRC01 gp120 complex2012-11-27T07:52:59Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. Insert figure Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and <scene name='VRC01_gp120_complex/Arg_71/2'>Arg71</scene> of VRC01. (Zhou) <br />
<br/><br />
<br/><br />
<u>Similarities to other antibodies in complex with gp120</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding. (Zhou)<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616038VRC01 gp120 complex2012-11-27T07:23:00Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. Analysis of VRC01 in complex with gp120 shows that this complex covers 98% of the CD4 binding site. Insert figure Both the heavy chain and light chain of VRC01 contribute to the contact surfaces of the VRC01 gp120 complex. The focus of the binding is on the heavy chain second complementary-determining region. Over 50% of the surface contact involves the heavy chain second complementary-determining region; this is similar to CD4’s interaction with gp120. Two dominant residues, Phe43 and Arg59, are involved in CD4’s binding to gp120. Of these two residues, only the arginine interaction is mimicked by VRC01. This dominant interaction is between Asp368 of gp120 and Arg59 of the CD4 receptor and between Asp368 of gp120 and Arg71 of VRC01. (Zhou) <br />
<br/><br />
<br/><br />
<u>Similarities to other antibodies in complex with gp120</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Other features</u>. VRC01 light chain residues, Tyr28 and Ser30, make contacts with the protein-proximal N-acetyl-glucosamine from the N-linked glycan residue 276 of gp120. While other structures are blocked from binding because glycan shielding, VRC01 takes advantage of the glycan for binding. (Zhou)<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1616034VRC01 gp120 complex2012-11-27T07:13:48Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC01 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>Similarities to CD4 in complex with gp120</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Similarities to other antibodies in complex with gp120</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Other features</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
<br />
bcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615939VRC01 gp120 complex2012-11-27T02:44:59Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<Structure load='3NGB' size='500' frame='true' align='left' caption='Trimeric gp120 in complex with VRC01 antibodies' scene='Insert optional scene name here' /><br />
<br />
<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='left' caption='VRC-PG04 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
<br />
bcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615764VRC01 gp120 complex2012-11-26T07:36:57Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<Structure load='3NGB' size='500' frame='true' align='right' caption='Trimeric gp120 in complex with VRC01 antibodies' scene='Insert optional scene name here' /><br />
<br />
<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615763VRC01 gp120 complex2012-11-26T07:32:25Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<Structure load='3NGB' size='500' frame='true' align='right' caption='Trimeric gp120 in complex with VRC01 antibodies' scene='Insert optional scene name here' /><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='right' caption='VRC-PG04 in complex with gp120' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615762VRC01 gp120 complex2012-11-26T07:25:54Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='right' caption='Trimeric gp120 in Complex with VRC01 antibodies, [[3NGB]]' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615761VRC01 gp120 complex2012-11-26T07:23:12Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='right' caption='Trimeric gp120 in Complex with VRC01 antibodies, [[3NGB]]' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
==Further Study==<br />
Conclusive results about what activates ToxT itself has not yet been found. The varying activity of ToxT dependent on the presence of <i>cis</i>-palmitoleate or other unsaturated fatty acids represents a detailed method of effective pathogenicity in humans, but may not be a reasonable target for drug treatment. By restricting transcription (and thus translation and protein production) of virulence genes until the bacterium is determined to be in a favorable location for infection, <i>Vibrio cholerae</i> avoids wasting energy producing virulence factors that will just be cleared by the intestine. This is a specific mechanism to ensure that the bacterium also injects CT and TCP where they will do the most damage, perpetuating the infection. <ref>Kenneth Todar [http://www.textbookofbacteriology.net/cholera.html] ''Vibrio cholerae'' and Asiatic Cholera, Todar's Online Textbook of Bacteriology. Date of access: 2011-11-28.</ref> Despite the lack of information about what activates ToxT itself, it is understood that the transcription of ctxA and tcpA by vibrio cholerae is sharply reduced in the presence of oleic, linoleic acid, and arachidonic acid, all of which are components of bile. Therefore, one may hypothesize that it may be possible to use the structure of a UFA or SFA to design a small molecule inhibitor of ToxT which may be used to treat or prevent cholera.<br />
<br />
<br />
==Evolution== <br />
Vibrio cholerae is a highly diverse species in which some strains are completely harmless, whereas other strains have the capacity to cause global cholera pandemics. It has been discovered that in each epidemic and pandemic strain, there is a chromosomal pathogenicity island (PAI) that is not present in the nonpathogenic strains. The region containing two ToxR-regulated genes (aldA and tagA) is composed of 13kb of previously unidentified DNA. <ref>Bailey, Camella "A Vibrio cholerae pathogenicity island associated with epidemic and pademic strains" (1997).</ref>This region is part of a PAI that contains ToxT and a gene cluster a critical colonization factor and TCP. The PAI is 39.5 kb long, contains putative integrase and transposase genes, and inserts near a 10Sa RNA gene. One may infer that the PAI could have originated from a bacteriophage. This PAI was also found in two non-O1/non-O139 (which are both pandemic) sero type strains. Therefore, one may hypothesize that the PAI could be transferred within other strains of Vibrio cholerae.<br />
<br />
[[Image:centroid.png|center|300px|thumb| Centroid RNA [[1xtc]]]]<br />
<br />
==HIV Prevention Research==<br />
In 2003, Veazey and fellow researchers found that early broadly neutralizing antibodies had microbicide potential by using a monkey cell as the model. The microbicide used on these monkeys consisted of b12, a broadly neutralizing antibody. These monkeys were challenged with SHIV, simian-human immunodeficiency virus, through the vagina. Only three of the twelve monkeys became infected. It was also found that the protection against HIV lasts for up to two hours. (Veazy)These results show that microbicides containing antibodies are effective at preventing HIV in monkeys.<br />
<br />
A similar experiment was done in 2012; it used humanized mouse models called RAG-hu mice, which contained human target cells. Results show that seven out of nine mice that were administered the VRC01 antibody and all mice that were given a cocktail containing four broadly neutralizing antibodies as a topical gel were protected against HIV-1. These results showed that broadly neutralizing antibodies could be used as a topical microbicide to prevent vaginal transmission of HIV and that a combination of antibodies can provide better protection against HIV. When the VRC01 antibody and the broadly neutralizing antibody cocktail were administered to the humanized mice via the intravenous route, none of the mice were infected with SHIV. (Veselinovic)<br />
<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615755VRC01 gp120 complex2012-11-26T06:10:15Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='right' caption='Trimeric gp120 in Complex with VRC01 antibodies, [[3NGB]]' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
==Further Study==<br />
Conclusive results about what activates ToxT itself has not yet been found. The varying activity of ToxT dependent on the presence of <i>cis</i>-palmitoleate or other unsaturated fatty acids represents a detailed method of effective pathogenicity in humans, but may not be a reasonable target for drug treatment. By restricting transcription (and thus translation and protein production) of virulence genes until the bacterium is determined to be in a favorable location for infection, <i>Vibrio cholerae</i> avoids wasting energy producing virulence factors that will just be cleared by the intestine. This is a specific mechanism to ensure that the bacterium also injects CT and TCP where they will do the most damage, perpetuating the infection. <ref>Kenneth Todar [http://www.textbookofbacteriology.net/cholera.html] ''Vibrio cholerae'' and Asiatic Cholera, Todar's Online Textbook of Bacteriology. Date of access: 2011-11-28.</ref> Despite the lack of information about what activates ToxT itself, it is understood that the transcription of ctxA and tcpA by vibrio cholerae is sharply reduced in the presence of oleic, linoleic acid, and arachidonic acid, all of which are components of bile. Therefore, one may hypothesize that it may be possible to use the structure of a UFA or SFA to design a small molecule inhibitor of ToxT which may be used to treat or prevent cholera.<br />
<br />
<br />
==Evolution== <br />
Vibrio cholerae is a highly diverse species in which some strains are completely harmless, whereas other strains have the capacity to cause global cholera pandemics. It has been discovered that in each epidemic and pandemic strain, there is a chromosomal pathogenicity island (PAI) that is not present in the nonpathogenic strains. The region containing two ToxR-regulated genes (aldA and tagA) is composed of 13kb of previously unidentified DNA. <ref>Bailey, Camella "A Vibrio cholerae pathogenicity island associated with epidemic and pademic strains" (1997).</ref>This region is part of a PAI that contains ToxT and a gene cluster a critical colonization factor and TCP. The PAI is 39.5 kb long, contains putative integrase and transposase genes, and inserts near a 10Sa RNA gene. One may infer that the PAI could have originated from a bacteriophage. This PAI was also found in two non-O1/non-O139 (which are both pandemic) sero type strains. Therefore, one may hypothesize that the PAI could be transferred within other strains of Vibrio cholerae.<br />
<br />
[[Image:centroid.png|center|300px|thumb| Centroid RNA [[1xtc]]]]<br />
<br />
==RNA Structure==<br />
Here we have the centroid structure of the mRNA of ToxT. This mRNA is shown in its most stable conformation, with the less stable, higher energy regions in red. The lighter colored regions are more stable and lower in energy.<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615748VRC01 gp120 complex2012-11-26T05:30:08Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01 and VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3NGB' color='structure' size='500' frame='true' align='right' caption='VRC01 in complex with viral gp120, [[3NGB]]' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
==Further Study==<br />
Conclusive results about what activates ToxT itself has not yet been found. The varying activity of ToxT dependent on the presence of <i>cis</i>-palmitoleate or other unsaturated fatty acids represents a detailed method of effective pathogenicity in humans, but may not be a reasonable target for drug treatment. By restricting transcription (and thus translation and protein production) of virulence genes until the bacterium is determined to be in a favorable location for infection, <i>Vibrio cholerae</i> avoids wasting energy producing virulence factors that will just be cleared by the intestine. This is a specific mechanism to ensure that the bacterium also injects CT and TCP where they will do the most damage, perpetuating the infection. <ref>Kenneth Todar [http://www.textbookofbacteriology.net/cholera.html] ''Vibrio cholerae'' and Asiatic Cholera, Todar's Online Textbook of Bacteriology. Date of access: 2011-11-28.</ref> Despite the lack of information about what activates ToxT itself, it is understood that the transcription of ctxA and tcpA by vibrio cholerae is sharply reduced in the presence of oleic, linoleic acid, and arachidonic acid, all of which are components of bile. Therefore, one may hypothesize that it may be possible to use the structure of a UFA or SFA to design a small molecule inhibitor of ToxT which may be used to treat or prevent cholera.<br />
<br />
<br />
==Evolution== <br />
Vibrio cholerae is a highly diverse species in which some strains are completely harmless, whereas other strains have the capacity to cause global cholera pandemics. It has been discovered that in each epidemic and pandemic strain, there is a chromosomal pathogenicity island (PAI) that is not present in the nonpathogenic strains. The region containing two ToxR-regulated genes (aldA and tagA) is composed of 13kb of previously unidentified DNA. <ref>Bailey, Camella "A Vibrio cholerae pathogenicity island associated with epidemic and pademic strains" (1997).</ref>This region is part of a PAI that contains ToxT and a gene cluster a critical colonization factor and TCP. The PAI is 39.5 kb long, contains putative integrase and transposase genes, and inserts near a 10Sa RNA gene. One may infer that the PAI could have originated from a bacteriophage. This PAI was also found in two non-O1/non-O139 (which are both pandemic) sero type strains. Therefore, one may hypothesize that the PAI could be transferred within other strains of Vibrio cholerae.<br />
<br />
[[Image:centroid.png|center|300px|thumb| Centroid RNA [[1xtc]]]]<br />
<br />
==RNA Structure==<br />
Here we have the centroid structure of the mRNA of ToxT. This mRNA is shown in its most stable conformation, with the less stable, higher energy regions in red. The lighter colored regions are more stable and lower in energy.<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615746VRC01 gp120 complex2012-11-26T03:49:49Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of a binding site for the co-receptor, usually CCR5 OR CXCR4. (Li) The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='right' caption='VRC-PG04 in complex with viral gp120, [[3SE9]]' ><br />
<br />
<br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
==Further Study==<br />
Conclusive results about what activates ToxT itself has not yet been found. The varying activity of ToxT dependent on the presence of <i>cis</i>-palmitoleate or other unsaturated fatty acids represents a detailed method of effective pathogenicity in humans, but may not be a reasonable target for drug treatment. By restricting transcription (and thus translation and protein production) of virulence genes until the bacterium is determined to be in a favorable location for infection, <i>Vibrio cholerae</i> avoids wasting energy producing virulence factors that will just be cleared by the intestine. This is a specific mechanism to ensure that the bacterium also injects CT and TCP where they will do the most damage, perpetuating the infection. <ref>Kenneth Todar [http://www.textbookofbacteriology.net/cholera.html] ''Vibrio cholerae'' and Asiatic Cholera, Todar's Online Textbook of Bacteriology. Date of access: 2011-11-28.</ref> Despite the lack of information about what activates ToxT itself, it is understood that the transcription of ctxA and tcpA by vibrio cholerae is sharply reduced in the presence of oleic, linoleic acid, and arachidonic acid, all of which are components of bile. Therefore, one may hypothesize that it may be possible to use the structure of a UFA or SFA to design a small molecule inhibitor of ToxT which may be used to treat or prevent cholera.<br />
<br />
<br />
==Evolution== <br />
Vibrio cholerae is a highly diverse species in which some strains are completely harmless, whereas other strains have the capacity to cause global cholera pandemics. It has been discovered that in each epidemic and pandemic strain, there is a chromosomal pathogenicity island (PAI) that is not present in the nonpathogenic strains. The region containing two ToxR-regulated genes (aldA and tagA) is composed of 13kb of previously unidentified DNA. <ref>Bailey, Camella "A Vibrio cholerae pathogenicity island associated with epidemic and pademic strains" (1997).</ref>This region is part of a PAI that contains ToxT and a gene cluster a critical colonization factor and TCP. The PAI is 39.5 kb long, contains putative integrase and transposase genes, and inserts near a 10Sa RNA gene. One may infer that the PAI could have originated from a bacteriophage. This PAI was also found in two non-O1/non-O139 (which are both pandemic) sero type strains. Therefore, one may hypothesize that the PAI could be transferred within other strains of Vibrio cholerae.<br />
<br />
[[Image:centroid.png|center|300px|thumb| Centroid RNA [[1xtc]]]]<br />
<br />
==RNA Structure==<br />
Here we have the centroid structure of the mRNA of ToxT. This mRNA is shown in its most stable conformation, with the less stable, higher energy regions in red. The lighter colored regions are more stable and lower in energy.<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615744VRC01 gp120 complex2012-11-26T03:21:29Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of VRC01-like antibodies are studied to define with characteristics are important in neutralizing HIV-1. (cite!)<br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of epitopes that can be bound by co-receptors, usually chemokine receptors. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='right' caption='VRC-PG04 in complex with viral gp120, [[3SE9]]' ><br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
==Further Study==<br />
Conclusive results about what activates ToxT itself has not yet been found. The varying activity of ToxT dependent on the presence of <i>cis</i>-palmitoleate or other unsaturated fatty acids represents a detailed method of effective pathogenicity in humans, but may not be a reasonable target for drug treatment. By restricting transcription (and thus translation and protein production) of virulence genes until the bacterium is determined to be in a favorable location for infection, <i>Vibrio cholerae</i> avoids wasting energy producing virulence factors that will just be cleared by the intestine. This is a specific mechanism to ensure that the bacterium also injects CT and TCP where they will do the most damage, perpetuating the infection. <ref>Kenneth Todar [http://www.textbookofbacteriology.net/cholera.html] ''Vibrio cholerae'' and Asiatic Cholera, Todar's Online Textbook of Bacteriology. Date of access: 2011-11-28.</ref> Despite the lack of information about what activates ToxT itself, it is understood that the transcription of ctxA and tcpA by vibrio cholerae is sharply reduced in the presence of oleic, linoleic acid, and arachidonic acid, all of which are components of bile. Therefore, one may hypothesize that it may be possible to use the structure of a UFA or SFA to design a small molecule inhibitor of ToxT which may be used to treat or prevent cholera.<br />
<br />
<br />
==Evolution== <br />
Vibrio cholerae is a highly diverse species in which some strains are completely harmless, whereas other strains have the capacity to cause global cholera pandemics. It has been discovered that in each epidemic and pandemic strain, there is a chromosomal pathogenicity island (PAI) that is not present in the nonpathogenic strains. The region containing two ToxR-regulated genes (aldA and tagA) is composed of 13kb of previously unidentified DNA. <ref>Bailey, Camella "A Vibrio cholerae pathogenicity island associated with epidemic and pademic strains" (1997).</ref>This region is part of a PAI that contains ToxT and a gene cluster a critical colonization factor and TCP. The PAI is 39.5 kb long, contains putative integrase and transposase genes, and inserts near a 10Sa RNA gene. One may infer that the PAI could have originated from a bacteriophage. This PAI was also found in two non-O1/non-O139 (which are both pandemic) sero type strains. Therefore, one may hypothesize that the PAI could be transferred within other strains of Vibrio cholerae.<br />
<br />
[[Image:centroid.png|center|300px|thumb| Centroid RNA [[1xtc]]]]<br />
<br />
==RNA Structure==<br />
Here we have the centroid structure of the mRNA of ToxT. This mRNA is shown in its most stable conformation, with the less stable, higher energy regions in red. The lighter colored regions are more stable and lower in energy.<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615737VRC01 gp120 complex2012-11-26T03:15:18Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of ToxT is resolved in monomeric form, after isolation from <i>Vibrio cholerae</i> strain O395.<ref name="structure">PMID: 20133655</ref><br />
<br />
==Introduction==<br />
HIV-1 has a high level of antigenic and genetic diversity. HIV-1 has also evolved mechanisms to evade the humoral immune response. These aspects of HIV-1 have made it difficult to develop a vaccine. After several years of infection, 10 to 25% of HIV-1 infected individuals develop neutralizing antibodies. Some antibodies target the transmembrane gp41 molecules of the HIV-1 viral spike, however most target the surface protein gp120. (Wu) VRC01 and VRC01-like antibodies bind to gp120 and are able to neutralize about 90% of HIV-1 isolates. Structural analysis has shown which characteristics of antibodies are essential to its binding with gp120. (Kwong) Discovery of the structure of these antibodies can help develop an effective HIV-1 vaccine.<br />
<br />
==HIV-1 Neutralization==<br />
HIV-1 enters its host by binding viral gp120, a surface glycoprotein of HIV, to the host cell’s CD4 receptor. This interaction induces conformational changes in gp120. (Wu) This conformational change results in the exposure of epitopes that can be bound by co-receptors, usually chemokine receptors. The conformational changes also result in the formation of a pre-hairpin intermediate conformation in which gp41, a transmembrane glycoprotein of HIV, rearranges its molecules so that its N-terminal peptides form a trimer of helices that present a fusion peptide to the target cell. Once fusion occurs between the fusion peptide and the target cell membrane, HIV is able to enter and infect the target cell. (Tran) VRC01 binds to CD4’s binding site on gp120, preventing the CD4 receptor from binding to HIV and infecting the cell. (Wu).<br />
<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='right' caption='ToxT complex with palmitoleic acid, 1.9 Angstrom resolution crystal structure, [[3gbg]]' ><br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
==Further Study==<br />
Conclusive results about what activates ToxT itself has not yet been found. The varying activity of ToxT dependent on the presence of <i>cis</i>-palmitoleate or other unsaturated fatty acids represents a detailed method of effective pathogenicity in humans, but may not be a reasonable target for drug treatment. By restricting transcription (and thus translation and protein production) of virulence genes until the bacterium is determined to be in a favorable location for infection, <i>Vibrio cholerae</i> avoids wasting energy producing virulence factors that will just be cleared by the intestine. This is a specific mechanism to ensure that the bacterium also injects CT and TCP where they will do the most damage, perpetuating the infection. <ref>Kenneth Todar [http://www.textbookofbacteriology.net/cholera.html] ''Vibrio cholerae'' and Asiatic Cholera, Todar's Online Textbook of Bacteriology. Date of access: 2011-11-28.</ref> Despite the lack of information about what activates ToxT itself, it is understood that the transcription of ctxA and tcpA by vibrio cholerae is sharply reduced in the presence of oleic, linoleic acid, and arachidonic acid, all of which are components of bile. Therefore, one may hypothesize that it may be possible to use the structure of a UFA or SFA to design a small molecule inhibitor of ToxT which may be used to treat or prevent cholera.<br />
<br />
<br />
==Evolution== <br />
Vibrio cholerae is a highly diverse species in which some strains are completely harmless, whereas other strains have the capacity to cause global cholera pandemics. It has been discovered that in each epidemic and pandemic strain, there is a chromosomal pathogenicity island (PAI) that is not present in the nonpathogenic strains. The region containing two ToxR-regulated genes (aldA and tagA) is composed of 13kb of previously unidentified DNA. <ref>Bailey, Camella "A Vibrio cholerae pathogenicity island associated with epidemic and pademic strains" (1997).</ref>This region is part of a PAI that contains ToxT and a gene cluster a critical colonization factor and TCP. The PAI is 39.5 kb long, contains putative integrase and transposase genes, and inserts near a 10Sa RNA gene. One may infer that the PAI could have originated from a bacteriophage. This PAI was also found in two non-O1/non-O139 (which are both pandemic) sero type strains. Therefore, one may hypothesize that the PAI could be transferred within other strains of Vibrio cholerae.<br />
<br />
[[Image:centroid.png|center|300px|thumb| Centroid RNA [[1xtc]]]]<br />
<br />
==RNA Structure==<br />
Here we have the centroid structure of the mRNA of ToxT. This mRNA is shown in its most stable conformation, with the less stable, higher energy regions in red. The lighter colored regions are more stable and lower in energy.<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615724VRC01 gp120 complex2012-11-26T01:43:30Z<p>Amanda Valdiosera: </p>
<hr />
<div>The crystal structure of ToxT is resolved in monomeric form, after isolation from <i>Vibrio cholerae</i> strain O395.<ref name="structure">PMID: 20133655</ref><br />
==Introduction==<br />
<b>ToxT</b> is a molecule at the end of a transcriptional cascade that autoregulates the transcription of the primary virulence factors of <i>Vibrio cholerae</i>[http://en.wikipedia.org/wiki/Vibrio_cholerae] and itself. ToxT is a cytoplasmic protein that is activated in turn by ToxR, which is itself activated by ToxS in response to environmental stimuli.<ref>Kenneth Todar [http://www.textbookofbacteriology.net/cholera.html] ''Vibrio cholerae'' and Asiatic Cholera, Todar's Online Textbook of Bacteriology. Date of access: 2011-11-28.</ref> These two factors, cholera toxin (CT)[http://en.wikipedia.org/wiki/Cholera_toxin] and the toxin co-regulated pilus (TCP), are instrumental in causing the disease <b>cholera</b>[http://en.wikipedia.org/wiki/Cholera]. This is an intestinal infection resulting in massive water loss in the affected individual, causing extreme dehydration.[http://en.wikipedia.org/wiki/Cholera] Rehydration is sufficient as treatment.<br />
<StructureSection load='3SE9' color='structure' size='500' frame='true' align='right' caption='ToxT complex with palmitoleic acid, 1.9 Angstrom resolution crystal structure, [[3gbg]]' ><br />
<br />
<br />
==Structural Features==<br />
<u>DNA-binding</u>. ToxT belongs to a family of transcriptional regulators headed by and known as AraC.<ref name="structure">PMID: 20133655</ref> The AraC family is characterized by a 100 amino acid region of sequence similarity that forms a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Two_hth_domains/1'>DNA-binding domain</scene> with two helix-turn-helix motifs (one on either side of the black linker). <ref name="arac">PMID: 11282467</ref> This DNA binding domain is composed of seven alpha helices. HTH1 is composed of alpha helices five and six, while HTH2 is composed of alpha helices eight and nine. The two HTH regions are linked by the very polar alpha helix seven(shown in black). The overall domain is located at the C-terminus.<ref name="structure">PMID: 20133655</ref> Assuming ToxT is similar in mechanism to other AraC proteins, helix six from HTH1 and helix nine from HTH2 become aligned with the help of helix seven. Helix seven is positioned to attach to the N terminal binding pocket(the polar linking region) to allow binding to major consecutive grooves of target DNA (specific promoters for virulence genes).<ref name="structure">PMID: 20133655</ref>[http://www.pnas.org/content/107/7/2860/F3.large.jpg]. The conformation of helix seven is dependent on the ligand bound.<br />
<br/><br />
<br/><br />
<u>Ligand-binding</u>. <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Barrel/1'>A nine-stranded beta sheet sandwich</scene> or "jelly-roll" with three other alpha helices (overall making up the <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/N-terminus/1'>N-terminus</scene>) contain a <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/1'>binding pocket</scene>. This is made from several residues from the N-terminus (Y12, Y20, F22, L25, I27, K31, F33, L61, F69, L71, V81, and V83), and a few from the C-terminus (I226, K230, M259, V261, Y266, and M269). This pocket contains a sixteen-carbon fatty acid positioned in a conformation such that its negatively charged carboxylate group forms salt bridges between K31 of the N-terminal domain, and K230 from the C-terminal domain. The pocket is highly hydrophobic, and has a known volume of 780.9 Angstroms.<ref name="structure">PMID: 20133655</ref> This pocket contains a ligand: <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Binding_pocket/2'>cis-palmitoleate</scene> <ref name="structure">PMID: 20133655</ref> which appears to have a negative effect on virulence when present in vitro. The <i>cis</i>-palmitoleate forms <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Salt_bridges_pam/1'>salt bridges</scene> with residues K31 and K230 (for detail, see Figure 1B of: [http://www.pnas.org/content/107/7/2860/F1.large.jpg]). This unsaturated fatty acid, like other UFAs,[http://en.wikipedia.org/wiki/Fatty_acid#Unsaturated_fatty_acids] tend to inhibit genes under the control of ToxT.<br />
Specifically, the <i>cis</i>-palmitoleate (PAM) appears to change ToxT's conformation, and thus lower its ability to bind DNA and form dimers.<ref name="structure">PMID: 20133655</ref> The presence of UFAs is associated with being in the lumen of the intestine during the bacterial infection. PAM brings K31 and K230 together from either end of the protein, and essentially closes off ToxT. K230 is at the end of helix seven, and binding to K31 causes helix six to be pulled into an unfavorable conformation that deters DNA binding. In lower concentration of fatty acids, ie: after penetrating the intestine's mucus, PAM is in lower concentration. At this point, charge-charge repulsion between K31 and K230 leads to a destabilization of the closed conformation of ToxT. This repulsion prompts the opening of the N and C terminal domains. The freedom of helices six and seven to find a favorable configuration allows DNA binding to occur.<ref name="structure">PMID: 20133655</ref><br />
<br/> [[Image:MSA.png|center|300px|thumb| MSA [[1xtc]]]]<br />
<br/><br />
<u>Dimerization</u>. Though the structure shown is a monomer with two overall domains (N-terminal and C-terminal), ToxT tends to form a dimer.<ref name="dimerization">PMID: 21415495<br />
</ref> The preferred state of ToxT varies between promoters, but binding to the <i>ctx</i> promoter to generate cholera toxin appears to be possible only in the dimer form.<ref name="virstatin">PMID:17283330</ref>ToxT binds to thirteen base pair sequences (can be single, direct, or inverted repeats) called toxboxes in order to activate their respective promoters.[http://www.sigwiki.info/wiki/Signature:ToxBox]<br />
==Ligand==<br />
In this resolved structure, <scene name='ToxT_Transcriptional_Regulator_in_Vibrio_cholerae/Pam/2'>cis-palmitoleate</scene>[http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=3gbg&template=ligands.html&l=1.1] is shown, which can be bound in the beta sheet barrel (as discussed above). This unsaturated fatty acid reduces virulence expression in <i>Vibrio cholerae</i>.<br />
</StructureSection><br />
<br />
<br />
==Further Study==<br />
Conclusive results about what activates ToxT itself has not yet been found. The varying activity of ToxT dependent on the presence of <i>cis</i>-palmitoleate or other unsaturated fatty acids represents a detailed method of effective pathogenicity in humans, but may not be a reasonable target for drug treatment. By restricting transcription (and thus translation and protein production) of virulence genes until the bacterium is determined to be in a favorable location for infection, <i>Vibrio cholerae</i> avoids wasting energy producing virulence factors that will just be cleared by the intestine. This is a specific mechanism to ensure that the bacterium also injects CT and TCP where they will do the most damage, perpetuating the infection. <ref>Kenneth Todar [http://www.textbookofbacteriology.net/cholera.html] ''Vibrio cholerae'' and Asiatic Cholera, Todar's Online Textbook of Bacteriology. Date of access: 2011-11-28.</ref> Despite the lack of information about what activates ToxT itself, it is understood that the transcription of ctxA and tcpA by vibrio cholerae is sharply reduced in the presence of oleic, linoleic acid, and arachidonic acid, all of which are components of bile. Therefore, one may hypothesize that it may be possible to use the structure of a UFA or SFA to design a small molecule inhibitor of ToxT which may be used to treat or prevent cholera.<br />
<br />
<br />
==Evolution== <br />
Vibrio cholerae is a highly diverse species in which some strains are completely harmless, whereas other strains have the capacity to cause global cholera pandemics. It has been discovered that in each epidemic and pandemic strain, there is a chromosomal pathogenicity island (PAI) that is not present in the nonpathogenic strains. The region containing two ToxR-regulated genes (aldA and tagA) is composed of 13kb of previously unidentified DNA. <ref>Bailey, Camella "A Vibrio cholerae pathogenicity island associated with epidemic and pademic strains" (1997).</ref>This region is part of a PAI that contains ToxT and a gene cluster a critical colonization factor and TCP. The PAI is 39.5 kb long, contains putative integrase and transposase genes, and inserts near a 10Sa RNA gene. One may infer that the PAI could have originated from a bacteriophage. This PAI was also found in two non-O1/non-O139 (which are both pandemic) sero type strains. Therefore, one may hypothesize that the PAI could be transferred within other strains of Vibrio cholerae.<br />
<br />
[[Image:centroid.png|center|300px|thumb| Centroid RNA [[1xtc]]]]<br />
<br />
==RNA Structure==<br />
Here we have the centroid structure of the mRNA of ToxT. This mRNA is shown in its most stable conformation, with the less stable, higher energy regions in red. The lighter colored regions are more stable and lower in energy.<br />
<br />
==References==</div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615691VRC01 gp120 complex2012-11-25T22:24:45Z<p>Amanda Valdiosera: </p>
<hr />
<div><StructureSection load='3SE9' size='500' frame='true' align='right' caption='VRC01-like antibody in complex with HIV-1 gp120 [[3SE9]]' scene=''><br />
<br />
==Introduction==<br />
<br />
Caspases (cysteine-aspartic proteases) are proteolytic enzymes that play essential roles in [http://en.wikipedia.org/wiki/Apoptosis apoptosis], development, inflammation, and the immune system. As the name suggests, caspases cleave proteins on the C-side of aspartic acid residues. As of now, around 15 caspases have been identified in two categories, inflammatory (in which caspase-1 is classified) and apoptotic. Apoptotic caspases are further divided into initiator (apical) caspases and effector (executioner) caspases. Initiator caspases cleave and activate effector caspases, which in turn start apoptosis by cleaving other proteins in a cascade reaction. Faulty or premature apoptosis is a main component of autoimmune diseases, leading to research into caspase inhibitors to treat diseases like Alzheimer's. Inflammatory caspases on the other hand usually work by proteolytically activating cytokines, leading to a different kind of cell mediated death called [http://en.wikipedia.org/wiki/Pyroptosis pyroptosis].<br />
[[image:Caspase-1_Zymogen.jpg|thumb|left|200px|'''Human Caspase-1 Zymogen''']]<br />
<br />
==Activation and Regulation==<br />
<br />
<scene name='Human_Caspase-1/Caspase-1/1'>Caspase-1</scene> begins as a [http://en.wikipedia.org/wiki/Zymogen zymogen], with its two subunits and a CARD prodomain all in one peptide sequence. Activation is thought to be initiated by removal of the [http://en.wikipedia.org/wiki/CARD_domain CARD domain] and dimerization. Bonds between subunits can be cleaved, leading to the maturation of the enzyme, but this does not necessarily convey greater activity. ASC and Ipaf have been identified as possible regulators of caspase-1 in a structure called the inflammasome. ASC leads to ATP-driven activation of caspase-1, while Ipaf connects signals triggered by intracellular pathogens.<ref name=Mariathasan>PMID:15190255</ref> Both of these activators are essential for caspase-1 driven cell death, showing a link between inflammation and apoptosis. Adaptors in the inflammasome react to extracellular and endogenous danger signals, usually flaggelin, to activate caspase-1 and begin the inflammatory response.<ref name=Franchi>PMID:19221555</ref><br />
<br />
==Structure==<br />
<br />
Caspase-1 consists of four subunits, two <scene name='Human_Caspase-1/Alpha_subunit/1'>20kDa (alpha)</scene> and two <scene name='Human_Caspase-1/Beta_subunit/1'>10kDa (beta)</scene> pieces, joining to make a homodimer. It has two active sites, which can be linked as is the case with caspase-1. The large alpha subunit contains the proteolytic dyad residues <scene name='Human_Caspase-1/Cys285_and_his_237/1'>Cys285 and His237</scene>, while the smaller subunit contains residues that form a groove for ligand binding. A '<scene name='Human_Caspase-1/Asp_socket/2'>socket</scene>' composed of Arg179, Gln283, and Arg341 holds the carboxylate side chain of the Asp residue tightly in place.<br />
<br />
==Function==<br />
<br />
Caspase-1, also known as ICE (interleukin-1beta converting enzyme) recognizes four residue sequences, requiring an aspartic acid in the P1 position of it's substrates, while P2 - P4 can be ambiguous. It's primary function is to activate the inflammatory cytokines IL1-beta and IL18 by cleaving their precursors. <br />
<br />
Caspase-1 also displays cooperative binding through active states, an on-state when ligand is bound and an off state when the active site is vacant or when synthetic ligands are bound at the allosteric site. The allosteric site exists at the dimer interface and is connected to the active sites by a system of 21 hydrogen bonds from 9 residues. Of these 9 residues, only two have a major effect on enzyme activity- <scene name='Human_Caspase-1/Allosteric_salt_bridge/1'>Arg286 and Glu390</scene>, which form a salt bridge. Although only some of the residues are necessary for activity, the continuous string of interactions connecting the active site to the allosteric site to the second active site make up a kind of circuit leading to cooperative binding. <ref name=Datta>PMID:18590738</ref><br />
<br />
==3D structures of caspase==<br />
<br />
[[Caspase]]<br />
<br />
</StructureSection></div>Amanda Valdioserahttps://proteopedia.org/index.php?title=VRC01_gp120_complex&diff=1615690VRC01 gp120 complex2012-11-25T22:14:03Z<p>Amanda Valdiosera: New page: <StructureSection load='2h4w' size='500' frame='true' align='right' caption='Caspase-1 complex with allosteric ligand 2h4w' scene=''> ==Introduction== Caspases (cysteine-aspartic pro...</p>
<hr />
<div><StructureSection load='2h4w' size='500' frame='true' align='right' caption='Caspase-1 complex with allosteric ligand [[2h4w]]' scene=''><br />
<br />
==Introduction==<br />
<br />
Caspases (cysteine-aspartic proteases) are proteolytic enzymes that play essential roles in [http://en.wikipedia.org/wiki/Apoptosis apoptosis], development, inflammation, and the immune system. As the name suggests, caspases cleave proteins on the C-side of aspartic acid residues. As of now, around 15 caspases have been identified in two categories, inflammatory (in which caspase-1 is classified) and apoptotic. Apoptotic caspases are further divided into initiator (apical) caspases and effector (executioner) caspases. Initiator caspases cleave and activate effector caspases, which in turn start apoptosis by cleaving other proteins in a cascade reaction. Faulty or premature apoptosis is a main component of autoimmune diseases, leading to research into caspase inhibitors to treat diseases like Alzheimer's. Inflammatory caspases on the other hand usually work by proteolytically activating cytokines, leading to a different kind of cell mediated death called [http://en.wikipedia.org/wiki/Pyroptosis pyroptosis].<br />
[[image:Caspase-1_Zymogen.jpg|thumb|left|200px|'''Human Caspase-1 Zymogen''']]<br />
<br />
==Activation and Regulation==<br />
<br />
<scene name='Human_Caspase-1/Caspase-1/1'>Caspase-1</scene> begins as a [http://en.wikipedia.org/wiki/Zymogen zymogen], with its two subunits and a CARD prodomain all in one peptide sequence. Activation is thought to be initiated by removal of the [http://en.wikipedia.org/wiki/CARD_domain CARD domain] and dimerization. Bonds between subunits can be cleaved, leading to the maturation of the enzyme, but this does not necessarily convey greater activity. ASC and Ipaf have been identified as possible regulators of caspase-1 in a structure called the inflammasome. ASC leads to ATP-driven activation of caspase-1, while Ipaf connects signals triggered by intracellular pathogens.<ref name=Mariathasan>PMID:15190255</ref> Both of these activators are essential for caspase-1 driven cell death, showing a link between inflammation and apoptosis. Adaptors in the inflammasome react to extracellular and endogenous danger signals, usually flaggelin, to activate caspase-1 and begin the inflammatory response.<ref name=Franchi>PMID:19221555</ref><br />
<br />
==Structure==<br />
<br />
Caspase-1 consists of four subunits, two <scene name='Human_Caspase-1/Alpha_subunit/1'>20kDa (alpha)</scene> and two <scene name='Human_Caspase-1/Beta_subunit/1'>10kDa (beta)</scene> pieces, joining to make a homodimer. It has two active sites, which can be linked as is the case with caspase-1. The large alpha subunit contains the proteolytic dyad residues <scene name='Human_Caspase-1/Cys285_and_his_237/1'>Cys285 and His237</scene>, while the smaller subunit contains residues that form a groove for ligand binding. A '<scene name='Human_Caspase-1/Asp_socket/2'>socket</scene>' composed of Arg179, Gln283, and Arg341 holds the carboxylate side chain of the Asp residue tightly in place.<br />
<br />
==Function==<br />
<br />
Caspase-1, also known as ICE (interleukin-1beta converting enzyme) recognizes four residue sequences, requiring an aspartic acid in the P1 position of it's substrates, while P2 - P4 can be ambiguous. It's primary function is to activate the inflammatory cytokines IL1-beta and IL18 by cleaving their precursors. <br />
<br />
Caspase-1 also displays cooperative binding through active states, an on-state when ligand is bound and an off state when the active site is vacant or when synthetic ligands are bound at the allosteric site. The allosteric site exists at the dimer interface and is connected to the active sites by a system of 21 hydrogen bonds from 9 residues. Of these 9 residues, only two have a major effect on enzyme activity- <scene name='Human_Caspase-1/Allosteric_salt_bridge/1'>Arg286 and Glu390</scene>, which form a salt bridge. Although only some of the residues are necessary for activity, the continuous string of interactions connecting the active site to the allosteric site to the second active site make up a kind of circuit leading to cooperative binding. <ref name=Datta>PMID:18590738</ref><br />
<br />
==3D structures of caspase==<br />
<br />
[[Caspase]]<br />
<br />
</StructureSection></div>Amanda Valdiosera