title: Dynamics of unfolded polypeptide chains in crowded environment studied by fluorescence correlation spectroscopy.
abstract: Proteins have evolved to fold and function within a cellular environment that is characterized by high macromolecular content. The earliest step of protein folding represents intrachain contact formation of amino acid residues within an unfolded polypeptide chain. It has been proposed that macromolecular crowding can have significant effects on rates and equilibria of biomolecular processes. However, the kinetic consequences on intrachain diffusion of polypeptides have not been tested experimentally, yet. Here, we demonstrate that selective fluorescence quenching of the oxazine fluorophore MR121 by the amino acid tryptophan (Trp) in combination with fast fluorescence correlation spectroscopy (FCS) can be used to monitor end-to-end contact formation rates of unfolded polypeptide chains. MR121 and Trp were incorporated at the terminal ends of polypeptides consisting of repetitive units of glycine (G) and serine (S) residues. End-to-end contact formation and dissociation result in "off" and "on" switching of MR121 fluorescence and underlying kinetics can be revealed in FCS experiments with nanosecond time resolution. We revisit previous experimental studies concerning the dependence of end-to-end contact formation rates on polypeptide chain length, showing that kinetics can be described by Gaussian chain theory. We further investigate effects of solvent viscosity and temperature on contact formation rates demonstrating that intrachain diffusion represents a purely diffusive, entropy-controlled process. Finally, we study the influence of macromolecular crowding on polypeptide chain dynamics. The data presented demonstrate that intrachain diffusion is fast in spite of hindered diffusion caused by repulsive interactions with macromolecules. Findings can be explained by effects of excluded volume reducing chain entropy and therefore accelerating the loop search process. Our results suggest that within a cellular environment the early formation of structural elements in unfolded proteins can still proceed quite efficiently in spite of hindered diffusion caused by high macromolecular content.
authors.affiliation: Applied Laser Physics and Laser Spectroscopy, University of Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany. neuweiler@physik.uni-bielefeld.de
authors.forename: Hannes
authors.initials: H
authors.lastname: Neuweiler
authors.forename: Marc
authors.initials: M
authors.lastname: Löllmann
authors.forename: Sören
authors.initials: S
authors.lastname: Doose
authors.forename: Markus
authors.initials: M
authors.lastname: Sauer
mesh_terms: D004058:Diffusion; D005453:Fluorescence; D046911:Macromolecular Substances / Q000378:metabolism*; D010078:Oxazines / Q000378:metabolism; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism*; D017510:Protein Folding; D012997:Solvents; D013050:Spectrometry, Fluorescence; D013696:Temperature; D014364:Tryptophan / Q000378:metabolism; D014783:Viscosity
chemical_list: C510593:MR121 oxazine fluorophore; D046911:Macromolecular Substances; D010078:Oxazines; D010455:Peptides; D012997:Solvents; D014364:Tryptophan