2009/06/01 by Osman Burak Okan, Okan, Osman Burak, Ali Rana Atılgan +5
Biochemistry, Genetics and Molecular Biology · Neuroscience · Physics and Astronomy · #Photoreceptor and optogenetics research #Protein Structure and Dynamics #Spectroscopy and Quantum Chemical Studies #cond-mat.soft #q-bio.QM
paper · pdf · doi:10.48550/arxiv.0906.0297
26 pages, 9 figures; suplementary materials added
arxiv created 2009/06/17 · arxiv updated 2009/12/01
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over from piecewise stationary to stationary processes that underlie the dynamics of protein motions. A two-time-scale function captures the non-exponential character of backbone structural relaxations. One is attributed to the collective segmental motions and the other to local relaxations. The former is well-defined by a single-exponential, nanosecond decay, operative at all temperatures. The latter is described by a set of processes that display a distribution of time-scales. Though their average remains on the picosecond time-scale, the distribution is markedly contracted at the onset of the transition. The collective motions are shown to impose bounds on time-scales spanned by local dynamical processes. The piecewise stationary character below the transition implicates the presence of a collection of sub-states whose interactions are restricted. At these temperatures, a wide distribution of local motion time-scales, extending beyond that of nanoseconds is observed. At physiological temperatures, local motions are confined to time-scales faster than nanoseconds. This relatively narrow window makes possible the appearance of multiple channels for the backbone dynamics to operate.