Coil-Library-Derived Amino-Acid-Specific Side-Chain χ1 Dihedral Angle Potentials for AMBER-Type Protein Force Field.

Abstract

The successful simulation of proteins by molecular dynamics (MD) critically depends on the accuracy of the applied force field. Here, we modify the AMBER-family ff99SBnmr2 force field through improvements to the side-chain χ₁ dihedral angle potentials in a residue-specific manner using conformational dihedral angle distributions from an experimental coil library as targets. Based on significant deviations observed for the parent force field with respect to the coil library, the χ₁ dihedral angle potentials of seven amino acids were modified, namely, Val, Ser, His, Asn, Trp, Tyr, and Phe. The new force field, named ff99SBnmr2Chi1, was benchmarked against NMR-derived χ₁ rotamer populations of denatured proteins, overall resulting in much better agreement and without any noticeable adverse consequences on the quality of the simulation of folded proteins. The new force field should allow more realistic modeling of protein side-chain properties by MD of both folded and unfolded protein systems, such as for the better in-silico characterization of protein-protein and protein-ligand interactions.