1kd9
From Proteopedia
(New page: 200px<br /><applet load="1kd9" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kd9, resolution 2.1Å" /> '''X-RAY STRUCTURE OF TH...) |
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| - | [[Image:1kd9.jpg|left|200px]]<br /><applet load="1kd9" size=" | + | [[Image:1kd9.jpg|left|200px]]<br /><applet load="1kd9" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1kd9, resolution 2.1Å" /> | caption="1kd9, resolution 2.1Å" /> | ||
'''X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L'''<br /> | '''X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L 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== | ||
| - | 1KD9 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:// | + | 1KD9 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=1KD9 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 13:32:47 2008'' |
Revision as of 11:32, 21 February 2008
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X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L
Overview
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
1KD9 is a Protein complex structure of sequences from [1] with as ligand. 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
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