Multiscale complex network of protein conformational fluctuations in single-molecule time series

Chun Biu Li, Haw Yang, Tamiki Komatsuzaki

Research output: Contribution to journalArticle

116 Scopus citations

Abstract

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 fluctutation 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.

Original languageEnglish (US)
Pages (from-to)536-541
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume105
Issue number2
DOIs
StatePublished - Jan 15 2008
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General

Keywords

  • Anomalous diffusion
  • Single-molecule experiment
  • Time series analysis

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