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| | {{STRUCTURE_1kdd| PDB=1kdd | SCENE= }} | | {{STRUCTURE_1kdd| PDB=1kdd | SCENE= }} |
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| - | '''X-ray structure of the coiled coil GCN4 ACID BASE HETERODIMER ACID-d12La16I BASE-d12La16L'''
| + | ===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 <1 kcal/mol, and nonhydrogen atoms in the predicted structures superimpose onto the experimental structures with rms deviations <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.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_11752430}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 11752430 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_11752430}} |
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| | ==About this Structure== | | ==About this Structure== |
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| | [[Category: Tidor, B.]] | | [[Category: Tidor, B.]] |
| | [[Category: Coiled coil heterodimer]] | | [[Category: Coiled coil heterodimer]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 22:36:10 2008'' | + | |
| | + | ''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
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
