Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests.
We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.
Kaminski
George A
GA
Department of Chemistry, Columbia University, New York, New York 10027, USA.
Stern
Harry A
HA
Berne
B J
BJ
Friesner
Richard A
RA
Cao
Yixiang X
YX
Murphy
Robert B
RB
Zhou
Ruhong
R
Halgren
Thomas A
TA
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004563:Electrochemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory; D012997:Solvents
D000596:Amino Acids; D010455:Peptides; D011506:Proteins; D012997:Solvents