Computing free energies of protein conformations from explicit solvent simulations

• Published in: Methods (San Diego, Calif.) Calif.), 2010-09, Vol.52 (1), p.115-121
• Main Authors: Zhuravlev, Pavel I., Wu, Sangwook, Potoyan, Davit A., Rubinstein, Michael, Papoian, Garegin A.
• Format: Article
• Language: English
• Subjects: Computer Simulation; Entropy; Explicit solvent simulations; Models, Molecular; Native state ensemble; Path coordinate; Protein Conformation; Protein conformational free energy; Protein Unfolding; Solvents - chemistry; Thermodynamics
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1016/j.ymeth.2010.05.003

We report a fully general technique addressing a long standing challenge of calculating conformational free energy differences between various states of a polymer chain from simulations using explicit solvent force fields. The main feature of our method is a special mapping variable, a path coordinate, which continuously connects two conformations. The path variable has been designed to preserve locality in the phase space near the path endpoints. We avoid the problem of sampling the unfolded states by creating an artificial confinement “tube” in the phase space that prevents the molecule from unfolding without affecting the calculation of the desired free energy difference. We applied our technique to compute the free energy difference between two native-like conformations of the small protein Trp-cage using the CHARMM force field with explicit solvent. We verified this result by comparing it with an independent, significantly more expensive calculation. Overall, the present study suggests that the new method of computing free energy differences between polymer chain conformations is accurate and highly computationally efficient.