A Coupled Two-Dimensional Main Chain Torsional Potential for Protein Dynamics

Abstract

A new AMBER compatible force field is proposed for balanced representation of secondary structures. In this modified AMBER force field (AMBER2D), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the potential energy surface generated by quantum mechanical calculations of small peptides in solution at M06 2X/aug-cc-pvtz//HF/6-31G∗∗ level. Solvation model based on solute electron density (SMD) developed in Truhlar's group was considered. The benchmark systems used in the validation of this force field include capped dipeptides (Ace-X-NME, XP), tripeptides (XXX, XA, G, V}; GYG, Y {A, V, F, L, S, E, K, M}), alanine tetrapeptide, Ac-(AAQAA)3 -NH2, and ubiquitin. Besides, we also investigate the folding of two representative proteins (PDB ID 2I9M and 1LE1). The results demonstrated that this 2D main chain torsion is effective in delineating the energy variation associated with main chain torsions. Furthermore, the electrostatic polarization effect is very important for long peptides or proteins. This work also serves as an implication for the necessity of more accurate functional forms for main chain torsions in the future development of force field.