1kd8: Difference between revisions
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New page: left|200px<br /><applet load="1kd8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kd8, resolution 1.90Å" /> '''X-RAY STRUCTURE OF T... |
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[[Image:1kd8.jpg|left|200px]]<br /><applet load="1kd8" size=" | [[Image:1kd8.jpg|left|200px]]<br /><applet load="1kd8" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1kd8, resolution 1.90Å" /> | caption="1kd8, resolution 1.90Å" /> | ||
'''X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L'''<br /> | '''X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12Ia16V BASE-d12La16L'''<br /> | ||
==Overview== | ==Overview== | ||
An important goal in biology is to predict from sequence data the | 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. | ||
==About this Structure== | ==About this Structure== | ||
1KD8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with ACE as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | 1KD8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=ACE:'>ACE</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KD8 OCA]. | ||
==Reference== | ==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11752430 11752430] | 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11752430 11752430] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Keating, A | [[Category: Keating, A E.]] | ||
[[Category: Kim, P | [[Category: Kim, P S.]] | ||
[[Category: Malashkevich, V | [[Category: Malashkevich, V N.]] | ||
[[Category: Tidor, B.]] | [[Category: Tidor, B.]] | ||
[[Category: ACE]] | [[Category: ACE]] | ||
[[Category: coiled coil heterodimer]] | [[Category: coiled coil heterodimer]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:32:46 2008'' | ||
