title: Folding Mechanism of Proteins Im7 and Im9: Insight from All-Atom Simulations in Implicit and Explicit Solvent.
abstract: Im7 and Im9 are evolutionary related proteins with almost identical native structures. In spite of their structural similarity, experiments show that Im7 folds through a long-lived on-pathway intermediate, while Im9 folds according to two-state kinetics. In this work, we use a recently developed enhanced path sampling method to generate many folding trajectories for these proteins, using realistic atomistic force fields, in both implicit and explicit solvent. Overall, our results are in good agreement with the experimental ϕ values and with the result of ϕ-value-restrained molecular dynamics (MD) simulations. However, our implicit solvent simulations fail to predict a qualitative difference in the folding pathways of Im7 and Im9. In contrast, our simulations in explicit solvent correctly reproduce the fact that only protein Im7 folds through a on-pathway intermediate. By analyzing our atomistic trajectories, we provide a physical picture which explains the observed difference in the folding kinetics of these chains.
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States.
authors.forename: F
authors.initials: F
authors.lastname: Wang
authors.affiliation: Physics Department, University of Trento , via Sommarive 14 Povo, Trento 38128, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Cazzolli
authors.affiliation: Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States.
authors.forename: P
authors.initials: P
authors.lastname: Wintrode
authors.affiliation: Physics Department, University of Trento , via Sommarive 14 Povo, Trento 38128, Italy.
authors.forename: P
authors.initials: P
authors.lastname: Faccioli
mesh_terms: D002352:Carrier Proteins / Q000737:chemistry*; D004926:Escherichia coli / Q000737:chemistry; D029968:Escherichia coli Proteins / Q000737:chemistry*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D017510:Protein Folding; D012997:Solvents / Q000737:chemistry
chemical_list: D002352:Carrier Proteins; C509253:E colicin-binding immunity protein Im7, E coli; C000626886:E colicin-binding immunity protein Im9, E coli; D029968:Escherichia coli Proteins; D012997:Solvents