title: Complex pathways in folding of protein G explored by simulation and experiment.
abstract: The B1 domain of protein G has been a classic model system of folding for decades, the subject of numerous experimental and computational studies. Most of the experimental work has focused on whether the protein folds via an intermediate, but the evidence is mostly limited to relatively slow kinetic observations with a few structural probes. In this work we observe folding on the submillisecond timescale with microfluidic mixers using a variety of probes including tryptophan fluorescence, circular dichroism, and photochemical oxidation. We find that each probe yields different kinetics and compare these observations with a Markov State Model constructed from large-scale molecular dynamics simulations and find a complex network of states that yield different kinetics for different observables. We conclude that there are many folding pathways before the final folding step and that these paths do not have large free energy barriers.
authors.affiliation: Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan. Electronic address: lapidus@msu.edu.
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Lapidus
authors.affiliation: Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan.
authors.forename: Srabasti
authors.initials: S
authors.lastname: Acharya
authors.affiliation: Department of Chemistry, Stanford University, Stanford, California.
authors.forename: Christian R
authors.initials: CR
authors.lastname: Schwantes
authors.affiliation: Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan.
authors.forename: Ling
authors.initials: L
authors.lastname: Wu
authors.affiliation: Department of Chemistry, Stanford University, Stanford, California; Simbios Program, Stanford University, Stanford, California.
authors.forename: Diwakar
authors.initials: D
authors.lastname: Shukla
authors.affiliation: Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan.
authors.forename: Michael
authors.initials: M
authors.lastname: King
authors.affiliation: Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: DeCamp
authors.affiliation: Department of Chemistry, Stanford University, Stanford, California; Simbios Program, Stanford University, Stanford, California; Department of Structural Biology, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Department of Computer Science, Stanford University, Stanford, California.
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D002942:Circular Dichroism; D004926:Escherichia coli; D005453:Fluorescence; D019204:GTP-Binding Proteins / Q000737:chemistry*; D007700:Kinetics; D008390:Markov Chains; D046210:Microfluidic Analytical Techniques; D056004:Molecular Dynamics Simulation; D010083:Oxidants, Photochemical / Q000737:chemistry; D055668:Photochemical Processes; D017510:Protein Folding; D013997:Time Factors; D014364:Tryptophan / Q000737:chemistry
chemical_list: D010083:Oxidants, Photochemical; D014364:Tryptophan; D019204:GTP-Binding Proteins