Refining the description of peptide backbone conformations improves protein simulations using the GROMOS 53A6 force field.
The GROMOS 53A6 parameter sets have been shown to reproduce an extensive range of thermodynamics data in condensed phase (Oostenbrink et al., J Comput Chem 2004, 25, 1656), mainly due to the reoptimized nonbonded interactions. Here, we derive refinements for the descriptions of peptide backbone conformations for this parameter set. A two-dimensional adaptive umbrella sampling procedure was employed to determine the free energy surfaces of model alanine and glycine dipeptides in solution to high accuracy, with sampling errors below 0.8 kJ mol(-1) for relative free energies between major minima. Comparisons of these surfaces with quantum mechanical ones and conformation distributions in protein crystal structures indicated that refined treatments of backbone torsional angle terms are necessary. The high accuracy of the computed free energy surfaces allowed us to consider two types of corrections, one numerically and exactly reproducing the quantum mechanical results, and the other using small analytical terms to correct major deficiencies for the dipeptide systems. In addition, aiming at improving the directionality of backbone-backbone hydrogen bonds, we optimized and tested an off-center charge model for the peptide backbone carbonyl oxygen. Extensive molecular dynamics simulations of five proteins and two peptides in solution indicate that refined treatments of backbone dihedral angles lead to substantial improvements of the simulations. Being much simpler, the analytical terms perform as good as or even slightly better than the exact numerical corrections. Although using off-center charges brought some improvements, the directionality of hydrogen bonds have not been significantly improved.
Cao
Zanxia
Z
Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Lin
Zhixiong
Z
Wang
Jun
J
Liu
Haiyan
H
D003198:Computer Simulation; D006860:Hydrogen Bonding; D008722:Methods; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins