Harmonicity in slow protein dynamics

摘要: The slow dynamics of proteins around its native folded state is usually described by diffusion in a strongly anharmonic potential. In this paper, we try to understand the form and origin anharmonicities, with principal aim gaining better understanding motion types, but also order develop more efficient numerical methods for simulating neutron scattering spectra large proteins. First, decompose molecular (MD) trajectory 1.5 ns C-phycocyanin dimer surrounded layer water into three contributions that expect be independent: global residues, rigid-body sidechains relative backbone, internal deformations sidechains. We show they are indeed almost independent verifying factorization incoherent intermediate function. Then, residue motions, which include all large-scale backbone can reproduced simple harmonic model contains two contributions: short-time vibrational term, standard normal mode calculation local minimum, long-time diffusive Brownian an effective potential friction constants were fitted MD data. major contribution function comes from This used calculate functions scales very efficiently, thus provides useful complement simulations, best suited detailed studies on smaller systems or shorter time scales.