Spatiotemporal correlations in denatured proteins: The dependence of fluorescence resonance energy transfer (FRET)-derived protein reconfiguration times on the location of the FRET probes

摘要

There has been considerable effort to understand the inherent time scale for conformational reconfiguration of denatured proteins. Even a simple homopolymer, however, exhibits a spectrum of fluctuation time scales rather than a unique characteristic time. Consequently, different time scales may be probed by different measurements. Motivated by recent single-molecule fluorescence resonance energy transfer experiments, here I have studied theoretically how the characteristic time scale exhibited by fluctuations of the distance between two residues within an unfolded polypeptide depends on the choice of the residue pair. This time scale was generally found to become shorter as the sequence separation between the residues is reduced. The maximum reconfiguration time, however, corresponds not to the residues being located at the ends of the chain but rather to each residue residing a short length apart from the ends. Comparison of these findings with recent single-molecule measurements suggests that the latter may bear signatures of transient residual structure. © 2010 American Institute of Physics Article Outline INTRODUCTION MONOMER-DEPENDENT RECONFIGURATION TIME FOR A ROUSE CHAIN Definition of reconfiguration time Reconfiguration time decreases as the sequence separation between monomers is decreased Reconfiguration time increases with increasing tail length A MORE REALISTIC MODEL: FRET DYNAMICS IN AN UNFOLDED POLYPEPTIDE DISCUSSION Effects introduced by bulky dyes Internal friction effects Effect of residual order