Abstract
The paper describes preliminary results of a molecular dynamics simulation study on the influence of non-denaturing hydrostatic pressure on the structure and the relaxation dynamics of lysozyme. The overall compression and the structural changes are in agreement with results from recent nuclear magnetic resonance experiments. We find that moderate hydrostatic pressure reduces essentially the amplitudes of the atomic motions, but does not change the characteristics of the slow internal dynamics. The latter is well described by a fractional Ornstein–Uhlenbeck process, concerning both single particle and collective motions.
Highlights
Different experimental techniques, like quasielastic neutron scattering, fluorescence correlation spectroscopy (FCS), and kinetic studies of ligand rebinding show that protein dynamics is characterized by a vast spectrum of relaxation rates, ranging from picoseconds to hours [1,2,3]
The typical time scales observed by quasielastic neutron scattering are in the picosecond to nano-second range (10À12–10À9 s), FCS probes protein dynamics in the millisecond to second range, and studying ligand rebinding after flash photolysis explores time scales in the millisecond to hour range
It has been shown that fractional Brownian Dynamics is seen on the pico- to nano-second time scale, which is explored by quasielastic neutron scattering and molecular dynamics (MD) computer simulations [6,7]
Summary
Like quasielastic neutron scattering, fluorescence correlation spectroscopy (FCS), and kinetic studies of ligand rebinding show that protein dynamics is characterized by a vast spectrum of relaxation rates, ranging from picoseconds to hours [1,2,3]. It has been shown that fractional Brownian Dynamics is seen on the pico- to nano-second time scale, which is explored by quasielastic neutron scattering and molecular dynamics (MD) computer simulations [6,7]. Using techniques known from signal processing, one can in particular compute memory functions of time correlation functions from the simulated trajectories [8]. The latter yield a rigourous description of relaxation processes on a microscopic basis [9]. The paper is concluded by a short discussion of the results
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