title: Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models.
abstract: Recent experiments showed that the reconfiguration dynamics of unfolded proteins are often adequately described by simple polymer models. In particular, the Rouse model with internal friction (RIF) captures internal friction effects as observed in single-molecule fluorescence correlation spectroscopy (FCS) studies of a number of proteins. Here we use RIF, and its non-free draining analog, Zimm model with internal friction, to explore the effect of internal friction on the rate with which intramolecular contacts can be formed within the unfolded chain. Unlike the reconfiguration times inferred from FCS experiments, which depend linearly on the solvent viscosity, the first passage times to form intramolecular contacts are shown to display a more complex viscosity dependence. We further describe scaling relationships obeyed by contact formation times in the limits of high and low internal friction. Our findings provide experimentally testable predictions that can serve as a framework for the analysis of future studies of contact formation in proteins.
authors: Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA.
authors: Ryan R
authors: RR
authors: Cheng
authors: Alexander T
authors: AT
authors: Hawk
authors: Dmitrii E
authors: DE
authors: Makarov
mesh_terms: D017276:Friction; D008958:Models, Molecular; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry*; D014783:Viscosity
chemical_list: D011506:Proteins