Intrinsic Mean Square Displacements in Proteins

Orateur : Henry R. GLYDE (Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA)

We propose a method for obtaining the intrinsic, long time mean square displacement (MSD) of atoms and molecules in proteins from -finite time simulations. Typical data from simulations are limited to times of 1 to 10 ns and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fi-tting a model to simulated values of the incoherent intermediate scattering function, I_inc(Q,t), for fi-nite times. The I_inc(Q,t) and its Fourier transform, S(Q,w), are observed in neutron scattering measurements. The fi-nite time MSD, , appears as a parameter in the model and is determined by -fits of the model to the fi-nite time I_inc(Q,t). Specifi-cally, the is defi-ned in the usual way in terms of the Debye-Waller factor as I(Q,t=inf) = exp(-Q^2/3). The method is illustrated by obtaining the intrinsic MSD of hydrated lysozyme powder (h = 0.4 g water/g protein) over a wide temperature range. The intrinsic obtained from data out to 1 ns and to 10 ns is found to be the same. The intrinsic is approximately twice the value of the MSD that is reached in simulations after times of 1 ns which correspond to those observed using neutron instruments that have an energy resolution width of 1 µeV.

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