title: Diffusive Dynamics of Contact Formation in Disordered Polypeptides.
abstract: Experiments measuring contact formation between probes in disordered chains provide information on the fundamental time scales relevant to protein folding. However, their interpretation usually relies on one-dimensional (1D) diffusion models, as do many experiments probing a single distance. Here, we use all-atom molecular simulations to capture both the time scales of contact formation, as well as the scaling with peptide length for tryptophan triplet quenching experiments, revealing the sensitivity of the experimental quenching times to the configurational space explored by the chain. We find a remarkable consistency between the results of the full calculation and from Szabo-Schulten-Schulten theory applied to a 1D diffusion model, supporting the validity of such models. The significant reduction in diffusion coefficient at the small probe separations which most influence quenching rate, suggests that contact formation and Förster resonance energy transfer correlation experiments provide complementary information on diffusivity.
authors.affiliation: Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA.
authors.forename: Gül H
authors.initials: GH
authors.lastname: Zerze
authors.affiliation: Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA.
authors.forename: Jeetain
authors.initials: J
authors.lastname: Mittal
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Best
mesh_terms: D003198:Computer Simulation; D004058:Diffusion; D031541:Fluorescence Resonance Energy Transfer; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D014364:Tryptophan / Q000737:chemistry
chemical_list: D010455:Peptides; D014364:Tryptophan