1kh0
From Proteopedia
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| - | [[Image:1kh0.jpg|left|200px]] | ||
| - | + | ==Accurate Computer Base Design of a New Backbone Conformation in the Second Turn of Protein L== | |
| - | + | <StructureSection load='1kh0' size='340' side='right'caption='[[1kh0]], [[Resolution|resolution]] 1.90Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <table><tr><td colspan='2'>[[1kh0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Finegoldia_magna_ATCC_29328 Finegoldia magna ATCC 29328]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KH0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KH0 FirstGlance]. <br> | |
| - | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> | |
| - | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kh0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kh0 OCA], [https://pdbe.org/1kh0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kh0 RCSB], [https://www.ebi.ac.uk/pdbsum/1kh0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kh0 ProSAT]</span></td></tr> | |
| - | + | </table> | |
| - | + | == Function == | |
| - | + | [https://www.uniprot.org/uniprot/Q51912_FINMA Q51912_FINMA] | |
| - | + | == Evolutionary Conservation == | |
| - | + | [[Image:Consurf_key_small.gif|200px|right]] | |
| - | + | Check<jmol> | |
| - | + | <jmolCheckbox> | |
| - | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kh/1kh0_consurf.spt"</scriptWhenChecked> | |
| - | == | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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=1kh0 ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
The rational design of loops and turns is a key step towards creating proteins with new functions. We used a computational design procedure to create new backbone conformations in the second turn of protein L. The Protein Data Bank was searched for alternative turn conformations, and sequences optimal for these turns in the context of protein L were identified using a Monte Carlo search procedure and an energy function that favors close packing. Two variants containing 12 and 14 mutations were found to be as stable as wild-type protein L. The crystal structure of one of the variants has been solved at a resolution of 1.9 A, and the backbone conformation in the second turn is remarkably close to that of the in silico model (1.1 A RMSD) while it differs significantly from that of wild-type protein L (the turn residues are displaced by an average of 7.2 A). The folding rates of the redesigned proteins are greater than that of the wild-type protein and in contrast to wild-type protein L the second beta-turn appears to be formed at the rate limiting step in folding. | The rational design of loops and turns is a key step towards creating proteins with new functions. We used a computational design procedure to create new backbone conformations in the second turn of protein L. The Protein Data Bank was searched for alternative turn conformations, and sequences optimal for these turns in the context of protein L were identified using a Monte Carlo search procedure and an energy function that favors close packing. Two variants containing 12 and 14 mutations were found to be as stable as wild-type protein L. The crystal structure of one of the variants has been solved at a resolution of 1.9 A, and the backbone conformation in the second turn is remarkably close to that of the in silico model (1.1 A RMSD) while it differs significantly from that of wild-type protein L (the turn residues are displaced by an average of 7.2 A). The folding rates of the redesigned proteins are greater than that of the wild-type protein and in contrast to wild-type protein L the second beta-turn appears to be formed at the rate limiting step in folding. | ||
| - | + | Accurate computer-based design of a new backbone conformation in the second turn of protein L.,Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D J Mol Biol. 2002 Jan 18;315(3):471-7. PMID:11786026<ref>PMID:11786026</ref> | |
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| - | Accurate computer-based design of a new backbone conformation in the second turn of protein L., Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D | + | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 1kh0" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Finegoldia magna ATCC 29328]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Baker D]] | ||
| + | [[Category: Kim DE]] | ||
| + | [[Category: Kuhlman B]] | ||
| + | [[Category: O'Neill JW]] | ||
| + | [[Category: Zhang KY]] | ||
Current revision
Accurate Computer Base Design of a New Backbone Conformation in the Second Turn of Protein L
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