Summary
I illustrate the use of the replica exchange molecular dynamics (REMD) algorithm to study the folding of a small (57 amino acids) protein that folds into a three-helix bundle, protein A. The REMD is a trivially parallel method that uses multiple copies of the system of interest to study the canonical ensemble equilibrium properties. Each replica represents a different thermodynamic state, usually at different temperatures. This method enhances the configurational sampling of proteins and allows us to study folding in simulations that are much shorter than the folding timescale for the system at ambient temperature. I show that using REMD and the Amber force field, I can obtain stable configurations of protein A whose backbone root mean square distance (RMSD) is within 0.17 nm of the nuclear magnetic resonance (NMR)-determined structure without biasing the system toward the folded structure. The simulations are done in explicit solvent and starting from nearly extended configurations. This calculation shows that currently available force fields and enhanced sampling methods perform reasonably well in describing the folded structure of small proteins.
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Acknowledgments
The author gratefully acknowledges support by the National Science Foundation MCB-0543769. The author thanks D. Paschek, H. Herce, and R.~Day for valuable discussions.
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Garcia, A.E. (2008). Molecular Dynamics Simulations of Protein Folding. In: Zaki, M.J., Bystroff, C. (eds) Protein Structure Prediction. Methods in Molecular Biology™, vol 413. Humana Press. https://doi.org/10.1007/978-1-59745-574-9_12
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