Reoptimization of the AMBER force field parameters for peptide bond (Omega) torsions using accelerated molecular dynamics.
Improving the accuracy of molecular mechanics force field parameters for atomistic simulations of proteins and nucleic acids has been an ongoing effort. The availability of computer power and improved methodologies for conformational sampling has allowed the assessment of these parameters by comparing the free energies calculated from molecular dynamic (MD) simulations and those measured from thermodynamic experiments. Here, we focus on testing and optimizing the AMBER force field parameters for the omega dihedral, which represents rotation around the peptide bond of proteins. Due to the very slow isomerization rate of the peptide bond, it is not possible to sample the phase space with standard MD simulations. We therefore employed an accelerated MD method in explicit water in which the original Hamiltonian is modified to speed up conformational sampling and the correct canonical distribution is recaptured. Using well-studied model systems for the peptide and peptidyl prolyl bonds, we discovered that the AMBER omega dihedral parameters underestimated experimentally measured activation free energy barriers for cis/trans conversion as well as failed to reproduce the free energy difference between the two isomers. We reoptimized the original AMBER omega dihedral parameters and further validated their transferability on several experimentally studied dipeptides. The revised set of parameters successfully reproduced the cis/trans equilibria and free energy barriers within experimental and simulation errors. We also investigated the structures of the transition state and cis/trans isomers of prolyl peptide bonds in terms of pyramidality, a measure of the puckering of the prolyl ring. We observed, as expected from quantum mechanical studies, significant bidirectional, out-of-plane motions of prolyl nitrogen in the transition state.
Doshi
Urmi
U
Department of Chemistry and The Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-4098, USA.
Hamelberg
Donald
D
D000081:Acetamides / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry*; D007536:Isomerism; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics
D000081:Acetamides; D004151:Dipeptides; C018595:N-methylacetamide