Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins.
A long time ago, Kuhn predicted that long polymers should approach a limit where their global motion is controlled by solvent friction alone, with ruggedness of their energy landscapes having no consequences for their dynamics. In contrast, internal friction effects are important for polymers of modest length. Internal friction in proteins, in particular, affects how fast they fold or find their binding targets and, as such, has attracted much recent attention. Here we explore the molecular origins of internal friction in unfolded proteins using atomistic simulations, coarse-grained models and analytic theory. We show that the characteristic internal friction timescale is directly proportional to the timescale of hindered dihedral rotations within the polypeptide chain, with a proportionality coefficient b that is independent of the chain length. Such chain length independence of b provides experimentally testable evidence that internal friction arises from concerted, crankshaft-like dihedral rearrangements. In accord with phenomenological models of internal friction, we find the global reconfiguration timescale of a polypeptide to be the sum of solvent friction and internal friction timescales. At the same time, the time evolution of inter-monomer distances within polypeptides deviates both from the predictions of those models and from a simple, one-dimensional diffusion model.
Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, 78712, USA.|Leibniz Institute for Solid State and Materials Research (IFW Dresden), Helmholtzstraße 20, 01069, Dresden, Germany.
Stanislav M
SM
Avdoshenko
Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712, USA.
Atanu
A
Das
Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712, USA.
Rohit
R
Satija
Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
Garegin A
GA
Papoian
Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas, 78712, USA. makarov@cm.utexas.edu.|Department of Chemistry, University of Texas at Austin, Austin, Texas, 78712, USA. makarov@cm.utexas.edu.
Dmitrii E
DE
Makarov
D003198:Computer Simulation; D017276:Friction; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012997:Solvents / Q000378:metabolism
D011506:Proteins; D012997:Solvents