Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.
A new hierarchical method for the simulation of the protein folding process and the de novo prediction of protein three-dimensional structure is proposed. The reduced representation of the protein alpha-carbon backbone employs lattice discretizations of increasing geometrical resolution and a single ball representation of side chain rotamers. In particular, coarser and finer lattice backbone descriptions are used. The coarser (finer) lattice represents C alpha traces of native proteins with an accuracy of 1.0 (0.7) A rms. Folding is simulated by means of very fast Monte Carlo lattice dynamics. The potential of mean force, predominantly of statistical origin, contains several novel terms that facilitate the cooperative assembly of secondary structure elements and the cooperative packing of the side chains. Particular contributions to the interaction scheme are discussed in detail. In the accompanying paper (Kolinski, A., Skolnick, J. Monte Carlo simulation of protein folding. II. Application to protein A, ROP, and crambin. Proteins 18:353-366, 1994), the method is applied to three small globular proteins.
Kolinski
A
A
Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037.
Skolnick
J
J
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D017510:Protein Folding; D017434:Protein Structure, Tertiary
D000596:Amino Acids