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2002 | 49 | 3 | 683-692
Article title

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

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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.
Physical description
  • Department of Chemistry, Warsaw University, L. Pasteura 1, 02-093 Warszawa, Poland
  • Department of Chemistry, Warsaw University, L. Pasteura 1, 02-093 Warszawa, Poland
  • Donald Danforth Plant Science Center, Bioinformatics and Computational Genomics, 893 North Warson Rd., St. Louis, MO 63141, U.S.A.
  • Aszodi A, Gradwell MJ, Taylor WR. (1995) Global fold determination from a small number of distance restraints. J Mol Biol.; 251: 308-26.
  • Creighton TE. (1993) Proteins structures and molecular properties. WH Freeman, Co, New York.
  • Gront D, Kolinski A, Skolnick J. (2000) Comparison of three Monte Carlo conformational search strategies for proteinlike homopolymer model: folding thermodynamics and identification of low-energy structures. J Chem Phys.; 113: 5065-71.
  • Hansmann UHE, Okamoto Y. (1999) New Monte Carlo algorithms for protein folding. Curr Opin Struct Biol.; 9: 177-83.
  • Hukushima K, Nemoto K. (1996) Exchange Monte Carlo method and application to spin glass simulations. J Phys Soc Jpn.; 65: 1604-8.
  • Ilkowski B, Skolnick J, Kolinski A. (2000) Helix-coil and beta sheet-coil transitions in a simplified, yet realistic protein model. Macromol Theory Simul.; 9: 523-33.
  • Kolinski A, Skolnick J. (1998) Assembly of protein structure from sparse experimental data, an efficient Monte Carlo model. Proteins Struct Funct Genet.; 32: 475-94.
  • Kolinski A, Jaroszewski L, Rotkiewicz P, Skolnick J. (1998) An efficient monte carlo model of protein chains modeling of short-range correlations between side group centers of mass. J Phys Chem B.; 102: 4628-37.
  • Kolinski A, Gront D, Pokarowski P, Skolnick J. (2002) Fast Monte Carlo technique for calculating the thermodynamic properties of model proteins. (submitted to J Chem Phys.)
  • Sikorski A. (2002) Properties of low-temperature structures of polymer chains the application of the replica exchange Monte Carlo method. Macromolecules.; 35: 7132-7.
  • Sikorski A, Kolinski A, Skolnick J. (2000) Computer simulations of the properties of the alpha2, alpha2C and alpha2D de novo designed helical proteins. Proteins Struct Funct Genet.; 38: 17-28.
  • Skolnick J, Kolinski A, Oritz AR. (1997) MONSSTER: A method for folding globular proteins with a small number of distance restraints. J Mol Biol.; 265: 217-41.
  • Smith-Brown MJ, Kominos D, Levy RM. (1993) Global folding of proteins using a limited number of distance restraints. Protein Eng.; 6: 605-14.
  • Sugita Y, Okamoto Y. (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett.; 314: 141-51.
  • Swendsen RH, Wang J-S. (1986) Replica Monte Carlo simulation of spin-glasses. Phys Rev Lett.; 57: 2607-9.
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