1KD9

X-RAY STRUCTURE OF THE COILED COIL GCN4 ACID BASE HETERODIMER ACID-d12La16L BASE-d12La16L

Summary for 1KD9

• Entry DOI: 10.2210/pdb1kd9/pdb
• Related: 1KD8 1KDD
• Descriptor: GCN4 ACID BASE HETERODIMER ACID-d12La16L, GCN4 ACID BASE HETERODIMER BASE-d12La16L (3 entities in total)
• Functional Keywords: coiled coil heterodimer, de novo protein
• Total number of polymer chains: 6
• Total formula weight: 24940.92

Authors

Keating, A.E.,Malashkevich, V.N.,Tidor, B.,Kim, P.S. (deposition date: 2001-11-12, release date: 2001-11-28, Last modification date: 2024-10-30)

Primary citation

Keating, A.E.,Malashkevich, V.N.,Tidor, B.,Kim, P.S.
Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils.
Proc.Natl.Acad.Sci.USA, 98:14825-14830, 2001

PubMed Abstract: 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.

PubMed: 11752430
DOI: 10.1073/pnas.261563398

Experimental method

X-RAY DIFFRACTION (2.1 Å)