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1kdd

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{{STRUCTURE_1kdd| PDB=1kdd | SCENE= }}
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'''X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L'''
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===X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L===
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==Overview==
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An important goal in biology is to predict from sequence data the high-resolution structures of proteins and the interactions that occur between them. In this paper, we describe a computational approach that can make these types of predictions for a series of coiled-coil dimers. Our method comprises a dual strategy that augments extensive conformational sampling with molecular mechanics minimization. To test the performance of the method, we designed six heterodimeric coiled coils with a range of stabilities and solved x-ray crystal structures for three of them. The stabilities and structures predicted by the calculations agree very well with experimental data: the average error in unfolding free energies is &lt;1 kcal/mol, and nonhydrogen atoms in the predicted structures superimpose onto the experimental structures with rms deviations &lt;0.7 A. We have also tested the method on a series of homodimers derived from vitellogenin-binding protein. The predicted relative stabilities of the homodimers show excellent agreement with previously published experimental measurements. A critical step in our procedure is to use energy minimization to relax side-chain geometries initially selected from a rotamer library. Our results show that computational methods can predict interaction specificities that are in good agreement with experimental data.
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(as it appears on PubMed at http://www.pubmed.gov), where 11752430 is the PubMed ID number.
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{{ABSTRACT_PUBMED_11752430}}
==About this Structure==
==About this Structure==
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[[Category: Tidor, B.]]
[[Category: Tidor, B.]]
[[Category: Coiled coil heterodimer]]
[[Category: Coiled coil heterodimer]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 22:36:10 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 10:10:01 2008''

Revision as of 07:10, 2 July 2008

Image:1kdd.png

Template:STRUCTURE 1kdd

X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L

Template:ABSTRACT PUBMED 11752430

About this Structure

Full crystallographic information is available from OCA.

Reference

Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils., Keating AE, Malashkevich VN, Tidor B, Kim PS, Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):14825-30. PMID:11752430

Page seeded by OCA on Wed Jul 2 10:10:01 2008

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