Quantum mechanics simulation of protein dynamics on long timescale.
Protein structure and dynamics are the keys to a wide range of problems in biology. In principle, both can be fully understood by using quantum mechanics as the ultimate tool to unveil the molecular interactions involved. Indeed, quantum mechanics of atoms and molecules have come to play a central role in chemistry and physics. In practice, however, direct application of quantum mechanics to protein systems has been prohibited by the large molecular size of proteins. As a consequence, there is no general quantum mechanical treatment that not only exceeds the accuracy of state-of-the-art empirical models for proteins but also maintains the efficiency needed for extensive sampling in the conformational space, a requirement mandated by the complexity of protein systems. Here we show that, given recent developments in methods, a general quantum mechanical-based treatment can be constructed. We report a molecular dynamics simulation of a protein, crambin, in solution for 350 ps in which we combine a semiempirical quantum-mechanical description of the entire protein with a description of the surrounding solvent, and solvent-protein interactions based on a molecular mechanics force field. Comparison with a recent very high-resolution crystal structure of crambin (Jelsch et al., Proc Natl Acad Sci USA 2000;102:2246-2251) shows that geometrical detail is better reproduced in this simulation than when several alternate molecular mechanics force fields are used to describe the entire system of protein and solvent, even though the structure is no less flexible. Individual atomic charges deviate in both directions from "canonical" values, and some charge transfer is found between the N and C-termini. The capability of simulating protein dynamics on and beyond the few hundred ps timescale with a demonstrably accurate quantum mechanical model will bring new opportunities to extend our understanding of a range of basic processes in biology such as molecular recognition and enzyme catalysis.
Liu
H
H
Department of Chemistry, Duke University, Durham, North Carolina, USA.
Elstner
M
M
Kaxiras
E
E
Frauenheim
T
T
Hermans
J
J
Yang
W
W
D000409:Alanine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D001696:Biomechanical Phenomena; D003198:Computer Simulation; D009842:Oligopeptides / Q000737:chemistry / Q000378:metabolism; D010940:Plant Proteins / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011789:Quantum Theory; D055672:Static Electricity; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry / Q000378:metabolism
D009842:Oligopeptides; D010940:Plant Proteins; D014867:Water; C024314:N-acetylalanyl-N-methylamide; C024934:crambin protein, Crambe abyssinica; D000409:Alanine