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Combining Neutron Scattering with MD Simulation to Understand Protein Motion


by Liang Hong

The incoherent neutron scattering is a powerful experimental tool to characterize atomic motions in biological materials as it probes directly the fluctuation in nuclear position, and the wavelength of the incoming neutron is comparable to the length scale of thermal motion in biological materials. However, biological systems, such as proteins, usually possess complex dynamics, i.e., several relaxation processes occur on similar time and length scales. Thus microscopic details of different relaxation process are hard to be appreciated by analyzing ensemble-averaged neutron scattering data. Combining MD simulation with neutron scattering can yield the desired description.

In the present work, the neutron scattering spectra, presented as dynamic susceptibility, of hydrated lysozyme powder derived from MD simulation is shown to quantitatively agree with experiment (Fig. 1). The experimental data is acquired by combining three instruments (HFBS, BASIS, disc-chopper TOF) together, while a single MD simulation is sufficient to obtain such spectrum. Further analysis of MD trajectory reveals that the protein motions on the ps to ns time scales can be decomposed into three components: localized diffusion, methyl group rotations and non-methyl-rotation jumps. The contribution of these three components to the over neutron scattering spectrum is derived (Fig. 2). The methyl group rotation is a major component, presenting a noticeable peak around 10GHz. The localized diffusion exhibits a rather flat feature in the 1 to 100 GHz frequency range. The non-methyl rotation jumps exist mostly below 10GHz.


Fig1
Fig. 1 neutron scattering spectra of hydrated lysozyme powder measured by experiment and simulation. The hydration level is 0.3 g water / g protein, and temperature is 295K. The experiments were performed on hydrogenated lysozyme hydrated in D2O, and the simulation-derived spectrum only takes the non-exchangeable hydrogen into account.


Fig2
Fig. 2 Decomposition of neutron scattering spectrum of protein into different atomic motions: the localized diffusion (χ″ld), the methyl group rotations (χ″me), and the non- methyl-rotation jumps (χ″nmj).

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