Paper Citing NAMD - Abstract
Sieradzan, Adam K.; Scheraga, Harold A.; Liwo, Adam
Determination of Effective Potentials for the Stretching of C-alpha center dot center dot center dot C-alpha Virtual Bonds in Polypeptide Chains for Coarse-Grained Simulations of Proteins from ab Initio Energy Surfaces of N-Methylacetamide and N-Acetylpyrrolidine
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1334-1343, APR 2012
The potentials of mean force (PMFs) for the deformation of the C-alpha center dot center dot center dot C-alpha virtual bonds in polypeptide chains were determined from the diabatic energy surfaces of N-methylacetamide (modeling regular peptide groups) and N-acetylpyrrolidine (modeling the peptide groups preceding proline), calculated at the Moller-Plesset (MP2) ab initio level of theory with the 6-31G(d,p) basis set. The energy surfaces were expressed in the C-alpha ... C-alpha virtual-bond length (d) and the H-N-C-alpha center dot center dot center dot C' improper dihedral angle (alpha) that describes the pyramidicity of the amide nitrogen, or in the C-alpha-C'(O)-N-C-alpha dihedral angle (omega) and the angle alpha. For each grid point, the potential energy was minimized with respect to all remaining degrees of freedom. The PMFs obtained from the (d,alpha) energy surfaces produced realistic free-energy barriers to the trans-cis transition (10 and 13 kcal/mol for the regular and proline peptide groups, respectively, compared to 12.6-13.9 kcal/mol and 17.3-19.6 kcal/mol determined experimentally for glycylglycine and N-acylprolines, respectively), while those obtained from the (omega,alpha) energy maps produced either low-quality PMF curves when direct Boltzmann summation was implemented to compute the PMFs or too-flat curves with too-low free-energy barriers to the trans-cis transition if harmonic extrapolation was used to estimate the contributions to the partition function. An analytical bimodal logarithmic-Gaussian expression was fitted to the PMFs, and the potentials were implemented in the UNRES force field. Test Langevin-dynamics simulations were carried out for the Gly-Gly and Gly-Pro dipeptides, which showed a 10(6)-fold increase of the simulated rate of the trans-cis isomerization with respect to that measured experimentally; effectively the same result was obtained with the analytical Kramers theory of reaction rate applied to the UNRES representation of the peptide groups. Application of Kramers' theory to the computation of the rate constants from the all-atom ab initio energy surfaces of the model compounds studied resulted in isomerization rates close to the experimental values, which demonstrates that the increase of the isomerization rate in UNRES simulations results solely from averaging out the secondary degrees of freedom.
