Quantum-dynamical picture of a multistep enzymatic process: reaction catalyzed by phospholipase A(2).
A quantum-classical molecular dynamics model (QCMD), applying explicit integration of the time-dependent Schrödinger equation (QD) and Newtonian equations of motion (MD), is presented. The model is capable of describing quantum dynamical processes in complex biomolecular systems. It has been applied in simulations of a multistep catalytic process carried out by phospholipase A(2) in its active site. The process includes quantum-dynamical proton transfer from a water molecule to histidine localized in the active site, followed by a nucleophilic attack of the resulting OH(-) group on a carbonyl carbon atom of a phospholipid substrate, leading to cleavage of an adjacent ester bond. The process has been simulated using a parallel version of the QCMD code. The potential energy function for the active site is computed using an approximate valence bond (AVB) method. The dynamics of the key proton is described either by QD or classical MD. The coupling between the quantum proton and the classical atoms is accomplished via Hellmann-Feynman forces, as well as the time dependence of the potential energy function in the Schrödinger equation (QCMD/AVB model). Analysis of the simulation results with an Advanced Visualization System revealed a correlated rather than a stepwise picture of the enzymatic process. It is shown that an sp(2)--> sp(3) configurational change at the substrate carbonyl carbon is mostly responsible for triggering the activation process.
Bała
P
P
Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, 02-106 Warsaw, Poland.
Grochowski
P
P
Nowiński
K
K
Lesyng
B
B
McCammon
J A
JA
D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D007700:Kinetics; D008958:Models, Molecular; D008962:Models, Theoretical; D010741:Phospholipases A / Q000737:chemistry* / Q000378:metabolism*; D017433:Protein Structure, Secondary; D011789:Quantum Theory
D010741:Phospholipases A