title: Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments.
abstract: As the fastest folding protein, the villin headpiece (HP35) serves as an important bridge between simulation and experimental studies of protein folding. Despite the simplicity of this system, experiments continue to reveal a number of surprises, including structure in the unfolded state and complex equilibrium dynamics near the native state. Using 2.5 ms of molecular dynamics and Markov state models, we connect to current experimental results in three ways. First, we present and validate a novel method for the quantitative prediction of triplet-triplet energy transfer experiments. Second, we construct a many-state model for HP35 that is consistent with previous experiments. Finally, we predict contact-formation time traces for all 1,225 possible triplet-triplet energy transfer experiments on HP35.
authors.affiliation: Biochemistry, Physics, and Chemistry Departments, Stanford University, Stanford, CA 94305, USA.
authors.forename: Kyle A
authors.initials: KA
authors.lastname: Beauchamp
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Ensign
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D004579:Electron Transport; D004735:Energy Transfer; D007700:Kinetics; D008840:Microfilament Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008956:Models, Chemical; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D008840:Microfilament Proteins; C026615:villin