Multiscale complex network of protein conformational fluctuations in single-molecule time series.
Conformational dynamics of proteins can be interpreted as itinerant motions as the protein traverses from one state to another on a complex network in conformational space or, more generally, in state space. Here we present a scheme to extract a multiscale state space network (SSN) from a single-molecule time series. Analysis by this method enables us to lift degeneracy--different physical states having the same value for a measured observable--as much as possible. A state or node in the network is defined not by the value of the observable at each time but by a set of subsequences of the observable over time. The length of the subsequence can tell us the extent to which the memory of the system is able to predict the next state. As an illustration, we investigate the conformational fluctuation dynamics probed by single-molecule electron transfer (ET), detected on a photon-by-photon basis. We show that the topographical features of the SSNs depend on the time scale of observation; the longer the time scale, the simpler the underlying SSN becomes, leading to a transition of the dynamics from anomalous diffusion to normal Brownian diffusion.
Li
Chun-Biu
CB
Nonlinear Sciences Laboratory, Department of Earth and Planetary Sciences, Faculty of Science, Kobe University, Nada, Kobe 657-8501, Japan.
Yang
Haw
H
Komatsuzaki
Tamiki
T
D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D004058:Diffusion; D004583:Electrons; D031541:Fluorescence Resonance Energy Transfer; D008390:Markov Chains; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D017785:Photons; D011487:Protein Conformation; D017510:Protein Folding; D013053:Spectrophotometry / Q000379:methods; D013995:Time; D013997:Time Factors