Exploration of compact protein conformations using the guided replication Monte Carlo method
| Autor: | Jerry E. Solomon, David Liney |
|---|---|
| Rok vydání: | 1995 |
| Předmět: |
Quantitative Biology::Biomolecules
Protein Folding Chemistry Protein Conformation Quantum Monte Carlo Organic Chemistry Monte Carlo method Biophysics Temperature Markov chain Monte Carlo General Medicine Biochemistry Protein Structure Secondary Biomaterials Hybrid Monte Carlo symbols.namesake Dynamic Monte Carlo method symbols Thermodynamics Monte Carlo method in statistical physics Kinetic Monte Carlo Statistical physics Monte Carlo Method Algorithms Monte Carlo molecular modeling |
| Zdroj: | Biopolymers. 36(5) |
| ISSN: | 0006-3525 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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