Studying Reactive Processes with Classical Dynamics: Rebinding Dynamics in MbNO

¹ University of Basel

^* To whom correspondence should be addressed. E-mail: m.meuwly{at}unibas.ch.

Submitted on July 27, 2005
Revised on August 23, 2005
Accepted on 7 November 2005

	Abstract

A surface crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented. The method is formulated for two intersecting, multidimensional potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one. The algorithm is extensively tested (almost 0.5 µs of total simulation time) for the rebinding of NO to myoglobin. The unbound surface (Fe···NO) is represented using a standard force field, whereas the bound surface (Fe--NO) is described by an ab initio potential energy surface. The rebinding is found to be non-exponential in time, in agreement with experimental studies, and can be described using two time constants. Depending on the asymptotic energy separation between the manifolds, the short rebinding time scale is between 1 and 9 ps while the longer time scale is about an order of magnitude larger. NO molecules which do not rebind within 1 ns are typically found in the Xenon-4 pocket, indicating the high affinity of NO to this region in the protein.

Key Words: nitrosyl-myoglobin, non-exponential kinetics, photodissociation, potential energy surface, reactive dynamics