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| {{STRUCTURE_1kd9| PDB=1kd9 | SCENE= }} | | {{STRUCTURE_1kd9| PDB=1kd9 | SCENE= }} |
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| '''X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L'''
| | ===X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L 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 22:36:00 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 2 10:09:35 2008'' |