title: How the diffusivity profile reduces the arbitrariness of protein folding free energies.
abstract: The concept of a protein diffusing in its free-energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We analyze extensive simulation data of an alpha-helix in explicit water solvent as it stochastically folds and unfolds. The free-energy profiles for different RCs exhibit significant variations, some having an activation barrier, while others not. We show that this variation has little effect on the predicted folding kinetics if the diffusivity profiles are properly taken into account. This kinetic quasi-universality is rationalized by an RC rescaling, which, due to the reparameterization invariance of the Fokker-Planck equation, allows the combination of free-energy and diffusivity effects into a single function, the rescaled free-energy profile. This rescaled free energy indeed shows less variation among different RCs than the bare free energy and diffusivity profiles separately do, if we properly distinguish between RCs that contain knowledge of the native state and those that are purely geometric in nature. Our method for extracting diffusivity profiles is easily applied to experimental single molecule time series data and might help to reconcile conflicts that arise when comparing results from different experimental probes for the same protein.
authors.affiliation: Department of Physics, Technical University of Munich, 85748 Garching, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Hinczewski
authors.forename: Y
authors.initials: Y
authors.lastname: von Hansen
authors.forename: J
authors.initials: J
authors.lastname: Dzubiella
authors.forename: R R
authors.initials: RR
authors.lastname: Netz
mesh_terms: D004058:Diffusion; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D009842:Oligopeptides; D011506:Proteins; D014867:Water