title: Integrated view of internal friction in unfolded proteins from single-molecule FRET, contact quenching, theory, and simulations.
abstract: Internal friction is an important contribution to protein dynamics at all stages along the folding reaction. Even in unfolded and intrinsically disordered proteins, internal friction has a large influence, as demonstrated with several experimental techniques and in simulations. However, these methods probe different facets of internal friction and have been applied to disparate molecular systems, raising questions regarding the compatibility of the results. To obtain an integrated view, we apply here the combination of two complementary experimental techniques, simulations, and theory to the same system: unfolded protein L. We use single-molecule Förster resonance energy transfer (FRET) to measure the global reconfiguration dynamics of the chain, and photoinduced electron transfer (PET), a contact-based method, to quantify the rate of loop formation between two residues. This combination enables us to probe unfolded-state dynamics on different length scales, corresponding to different parts of the intramolecular distance distribution. Both FRET and PET measurements show that internal friction dominates unfolded-state dynamics at low denaturant concentration, and the results are in remarkable agreement with recent large-scale molecular dynamics simulations using a new water model. The simulations indicate that intrachain interactions and dihedral angle rotation correlate with the presence of internal friction, and theoretical models of polymer dynamics provide a framework for interrelating the contribution of internal friction observed in the two types of experiments and in the simulations. The combined results thus provide a coherent and quantitative picture of internal friction in unfolded proteins that could not be attained from the individual techniques.
authors.affiliation: Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland; schuler@bioc.uzh.ch soranno@wustl.edu.
authors.forename: Andrea
authors.initials: A
authors.lastname: Soranno
authors.affiliation: Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Andrea
authors.initials: A
authors.lastname: Holla
authors.affiliation: Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Fabian
authors.initials: F
authors.lastname: Dingfelder
authors.affiliation: Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Nettels
authors.affiliation: Department of Chemistry, University of Texas at Austin, Austin, TX 78712.|Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, TX 78712.
authors.forename: Dmitrii E
authors.initials: DE
authors.lastname: Makarov
authors.affiliation: Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland; schuler@bioc.uzh.ch soranno@wustl.edu.|Department of Physics, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Schuler
mesh_terms: D004579:Electron Transport; D031541:Fluorescence Resonance Energy Transfer; D064267:Intrinsically Disordered Proteins / Q000737:chemistry*; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation; D011108:Polymers / Q000737:chemistry; D017510:Protein Folding; D000072760:Single Molecule Imaging; D014867:Water / Q000737:chemistry
chemical_list: D064267:Intrinsically Disordered Proteins; D011108:Polymers; D014867:Water
keywords: PET quenching; Rouse model with internal friction; intrinsically disordered proteins; nanosecond FCS; single-molecule FRET