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The reconstruction of side-chain conformations from protein Cα coordinates

✍ Scribed by Kaiwan Gan; James M. Coxon; A. John McKinnon; Gillian H. Worth

Publisher
Wiley (John Wiley & Sons)
Year
1997
Tongue
English
Weight
216 KB
Volume
41
Category
Article
ISSN
0006-3525

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✦ Synopsis

A model of nine proteins including side-chain atoms have been built from the known C a coordinates and amino acid sequences using a Monte Carlo Protein Building Annealing method. The Cartesian coordinates for the side-chain atoms were established with bond lengths and angles selected randomly from within previously determined ranges. A simulated annealing technique is used to generate some 300 structures with differing side-chain conformations. The atomic coordinates of the backbone atoms are fixed during the simulated annealing process. The coordinates of the side-chain atoms of 300 low energy conformations are averaged to obtain a mean structure that is minimized with the C a atoms constrained to their position in the x-ray structure using the OPLS/AMBER force field with the GB/SA water model. The rms deviation of the main-chain atoms (without C b ) compared with the corresponding crystal structures is in the range 0.20-0.64 A ˚. The rms deviation of the side-chain atoms is between 1.72 and 2.71 A ˚and for all atoms is between 1.19 and 1.99 A ˚. The method is insensitive to random errors in the C a positions and the computational requirement is modest. ᭧ 1997 John Wiley & Sons, Inc.

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