Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A

摘要: We developed a software package for improved free energy calculation, in which spherical solvent boundary potential, cell multipole method, and Nose-Hoover equation are employed. The performance of the is demonstrated case valine to alanine mutation 57th residue chymotrypsin inhibitor 2. By using this package, we obtained results quantitatively comparable experimental results. component analysis, it shown that leucine 51, arginine 65, 67, phenylalanine 69 residues contribute significantly total shift, ΔΔG. Among them, contribution from hydrophilic 67 residue, close contact with site, largest. Structure around site largely changed by mutation. structure change caused mainly two effects, hydrophobic interaction short-range along sequence. Effects algorithm Kirkwood reaction field also discussed. Proteins 30:388–400, 1998. © 1998 Wiley-Liss, Inc.