Computer simulations of protein folding with a small number of distance restraints.

• Authors: Andrzej Sikorski , Andrzej Kolinski , Jeffrey Skolnick
• Languages of publication: EN

Abstracts

EN

A high coordination lattice model was used to represent the protein chain. Lattice points correspond to amino-acid side groups. A complicated force field was designed in order to reproduce a protein-like behavior of the chain. Long-distance tertiary restraints were also introduced into the model. The Replica Exchange Monte Carlo method was applied to find the lowest energy states of the folded chain and to solve the problem of multiple minima. In this method, a set of replicas of the model chain was simulated independently in different temperatures with the exchanges of replicas allowed. The model chains, which consisted of up to 100 residues, were folded to structures whose root-mean-square deviation (RMSD) from their native state was between 2.5 and 5 Å. Introduction of restrain based on the positions of the backbone hydrogen atoms led to an improvement in the number of successful simulation runs. A small improvement (about 0.5 Å) was also achieved in the RMSD of the folds. The proposed method can be used for the refinement of structures determined experimentally from NMR data.

Keywords

EN

lattice models; NMR structure refinement; Monte Carlo method; reduced protein models; protein folding

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2002
• Volume: 49
• Issue: 3
• Pages: 683-692

Dates

published

2002

received

2002-04-16

revised

2002-06-26

accepted

2002-09-01

Contributors

author

Andrzej Sikorski

• Department of Chemistry, Warsaw University, L. Pasteura 1, 02-093 Warszawa, Poland

author

Andrzej Kolinski

• Department of Chemistry, Warsaw University, L. Pasteura 1, 02-093 Warszawa, Poland

author

Jeffrey Skolnick

• Donald Danforth Plant Science Center, Bioinformatics and Computational Genomics, 893 North Warson Rd., St. Louis, MO 63141, U.S.A.

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