G3p: Difference between revisions

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===Initial Observations===

<applet load='1fgp' size='~~150~~' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.

<applet load='1fgp' size='100' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>. They used NMR spectroscopy to create a structure of the first domains of g3p. Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.

In 1998, Lubkowski et al crystallized the first two domains of g3p. They made two overall observations:

(1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures ~~(Holliger et al)~~

(1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>. The cis proline identified will later turn out to be important for function of the protein. The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.

===D1 domain===

The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>. This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>.

===N2 domain===

===D2 domain===

This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>. The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.

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@@ Line 8: / Line 8: @@
 ===Initial Observations===
-<applet load='1fgp' size='150' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.  They used NMR spectroscopy to create a structure of the first domains of g3p.  Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.
+<applet load='1fgp' size='100' frame='true' align='left' caption='Initial structure of D1' />The first structure of g3p entered into the PDB was by Holliger and Riechmann in late 1996-early 1997<ref name="holliger 97"/>.  They used NMR spectroscopy to create a structure of the first domains of g3p.  Shown is a combination of the 15 most energetically favorable states. Observations of secondary structure are below.
 <applet load='1g3p' size='300' frame='true' align='right' caption='Important characteristics of the N-terminal domains of g3p' />
 In 1998, Lubkowski et al crystallized the first two domains of g3p.  They made two overall observations:
-(1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/> not found in other structures (Holliger et al)
+(1) <scene name='G3p/Pro_213_in_cis_conformation/1'>Cis proline near C terminal end</scene> <ref name="lubkowski"/> and (2) <scene name='G3p/Oxidized_tryptophan/1'>An oxidized tryptophan</scene> <ref name="lubkowski"/>.  The cis proline identified will later turn out to be important for function of the protein.  The oxidized tryptophan, however, was not found in other structures <ref name="holliger 99"> PMID:10329170 </ref>.
 ===D1 domain===
 The D1 domain consists of mostly beta sheets. Both Holliger and Riechmann as well as Lubowski et al noted a <scene name='G3p/N_terminal_alpha_helix/1'>N terminal alpha helix</scene> <ref name="lubkowski"/> in their respective publications<ref name="holliger 97"/><ref name="lubkowski"/>.  This aside, five <scene name='G3p/Beta_strands/1'>beta strands</scene> arranged as a barrel-like motif, which participates with two other strands from second domain to make an antiparallel sheet <ref name="lubkowski"/>. Disulfide bonds exist between Cys 7 and Cys 36 (left handed helix) and Cys 46 and Cys 53 (right handed hook) <ref name="lubkowski"/>.
-===N2 domain===
+===D2 domain===
 This domain contains eight beta strands: six in a mixed beta sheet and two interacting with D1 antiparallel sheet (β6 and β13 <ref name="lubkowski"/>. The amino acids between β6 and β7 doesn’t have a specific motif but has stabilizing hydrophobic interactions with other parts of the domain <ref name="lubkowski"/>. Three hairpins exist in this domain: between β8 and β9, β9 and β10, and β10 and β11 (cis proline in the last hairpin) <ref name="lubkowski"/>.  The final secondary structural element is an alpha helix that interacts with rest of the domain via hydrophobic interactions <ref name="lubkowski"/>. Of note, there is a cation-π interaction between His 191 and Phe 199. The C terminus of D2 has seven peptides, 3 of which are proline, 1 of which is <scene name='G3p/Pro_213_in_cis_conformation/1'>in the cis conformation</scene> <ref name="lubkowski"/>.