This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1vjq

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1vjq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1vjq, resolution 2.098&Aring;" /> '''Designed protein ba...)
Current revision (00:04, 28 December 2023) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1vjq.gif|left|200px]]<br /><applet load="1vjq" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1vjq, resolution 2.098&Aring;" />
 
-
'''Designed protein based on backbone conformation of procarboxypeptidase-A (1AYE) with sidechains chosen for maximal predicted stability.'''<br />
 
-
==Overview==
+
==Designed protein based on backbone conformation of procarboxypeptidase-A (1AYE) with sidechains chosen for maximal predicted stability.==
-
A previously developed computer program for protein design, RosettaDesign, was used to predict low free energy sequences for nine naturally occurring, protein backbones. RosettaDesign had no knowledge of the naturally, occurring sequences and on average 65% of the residues in the designed, sequences differ from wild-type. Synthetic genes for ten completely, redesigned proteins were generated, and the proteins were expressed, purified, and then characterized using circular dichroism, chemical and, temperature denaturation and NMR experiments. Although high-resolution, structures have not yet been determined, eight of these proteins appear to, be folded and their circular dichroism spectra are similar to those of, their wild-type counterparts. Six of the proteins have stabilities equal, to or up to 7kcal/mol greater than their wild-type counterparts, and four, of the proteins have NMR spectra consistent with a well-packed, rigid, structure. These encouraging results indicate that the computational, protein design methods can, with significant reliability, identify amino, acid sequences compatible with a target protein backbone.
+
<StructureSection load='1vjq' size='340' side='right'caption='[[1vjq]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1vjq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VJQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VJQ FirstGlance]. <br>
-
1VJQ is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VJQ OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.098&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vjq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vjq OCA], [https://pdbe.org/1vjq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vjq RCSB], [https://www.ebi.ac.uk/pdbsum/1vjq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vjq ProSAT]</span></td></tr>
-
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins., Dantas G, Kuhlman B, Callender D, Wong M, Baker D, J Mol Biol. 2003 Sep 12;332(2):449-60. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12948494 12948494]
+
</table>
-
[[Category: ]]
+
== Evolutionary Conservation ==
-
[[Category: Protein complex]]
+
[[Image:Consurf_key_small.gif|200px|right]]
-
[[Category: Baker, D.]]
+
Check<jmol>
-
[[Category: Merritt, E.A.]]
+
<jmolCheckbox>
-
[[Category: SGPP, Structural.Genomics.of.Pathogenic.Protozoa.Consortium.]]
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vj/1vjq_consurf.spt"</scriptWhenChecked>
-
[[Category: engineered protein]]
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
[[Category: protein structure initiative]]
+
<text>to colour the structure by Evolutionary Conservation</text>
-
[[Category: psi]]
+
</jmolCheckbox>
-
[[Category: sgpp]]
+
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vjq ConSurf].
-
[[Category: structural genomics]]
+
<div style="clear:both"></div>
-
[[Category: structural genomics of pathogenic protozoa consortium]]
+
__TOC__
-
 
+
</StructureSection>
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:36:11 2007''
+
[[Category: Large Structures]]
 +
[[Category: Baker D]]
 +
[[Category: Merritt EA]]

Current revision

Designed protein based on backbone conformation of procarboxypeptidase-A (1AYE) with sidechains chosen for maximal predicted stability.

PDB ID 1vjq

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1vjq"
Personal tools