ISSN:
0006-3525
Keywords:
Chemistry
;
Polymer and Materials Science
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
Notes:
We have studied the use of a new Monte Carlo (MC) chain generation algorithm, introduced by T. Garel and H. Orland[(1990) Journal of Physics A, Vol. 23, pp. L621-L626], for examining the thermodynamics of protein folding transitions and for generating candidate Cαbackbone structures as starting points for a de now protein structure paradigm. This algorithm, termed the guided replication Monte Carlo method, allows a rational approach to the introduction of known “native” folded characteristics as constraints in the chain generation process. We have shown this algorithm to be computationally very efficient in generating large ensembles of candidate Cαchains on the face centered cubic lattice, and illustrate its use by calculating a number of thermodynamic quantities related to protein folding characteristics. In particular, we have used this static MC algorithm to compute such temperature-dependent quantities as the ensemble mean energy, ensemble mean free energy, the heat capacity, and the mean-square radius of gyration. We also demonstrate the use of several simple “guide fields” for introducing protein-specific constraints into the ensemble generation process. Several extensions to our current model are suggested, and applications of the method to other folding related problems are discussed. © 1995 John Wiley & Sons, Inc.
Additional Material:
11 Ill.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/bip.360360504
