3b83: Difference between revisions

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{{Seed}}
[[Image:3b83.png|left|200px]]


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==Computer-Based Redesign of a beta Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo beta Sheet Design.==
The line below this paragraph, containing "STRUCTURE_3b83", creates the "Structure Box" on the page.
<StructureSection load='3b83' size='340' side='right'caption='[[3b83]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3b83]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B83 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B83 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b83 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b83 OCA], [https://pdbe.org/3b83 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b83 RCSB], [https://www.ebi.ac.uk/pdbsum/3b83 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b83 ProSAT]</span></td></tr>
{{STRUCTURE_3b83|  PDB=3b83  |  SCENE=  }}
</table>
== 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/b8/3b83_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=3b83 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The de novo design of globular beta sheet proteins remains largely an unsolved problem. It is unclear whether most designs are failing because the designed sequences do not have favorable energies in the target conformations or whether more emphasis should be placed on negative design, that is, explicitly identifying sequences that have poor energies when adopting undesired conformations. We tested whether we could redesign the sequence of a naturally occurring beta sheet protein, tenascin, with a design algorithm that does not include explicit negative design. Denaturation experiments indicate that the designs are significantly more stable than the wild-type protein and the crystal structure of one design closely matches the design model. These results suggest that extensive negative design is not required to create well-folded beta sandwich proteins. However, it is important to note that negative design elements may be encoded in the conformation of the protein backbone which was preserved from the wild-type protein.


===Tba===
Computer-based redesign of a beta sandwich protein suggests that extensive negative design is not required for de novo beta sheet design.,Hu X, Wang H, Ke H, Kuhlman B Structure. 2008 Dec 10;16(12):1799-805. PMID:19081056<ref>PMID:19081056</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
3B83 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B83 OCA].
<div class="pdbe-citations 3b83" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Hu, X.]]
[[Category: Hu X]]
[[Category: Ke, H.]]
[[Category: Ke H]]
[[Category: Kuhlman, B.]]
[[Category: Kuhlman B]]
[[Category: Alternative splicing]]
[[Category: Beta sheet]]
[[Category: Cell adhesion]]
[[Category: Coiled coil]]
[[Category: Computational redesigned protein]]
[[Category: Egf-like domain]]
[[Category: Extracellular matrix]]
[[Category: Glycoprotein]]
[[Category: Phosphorylation]]
[[Category: Polymorphism]]
[[Category: Secreted]]
[[Category: Unknown function]]
 
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Retrieved from "https://proteopedia.org/3b83"