title: The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure.
abstract: The 36 residue villin headpiece helical subdomain (HP36) is one of the fastest cooperatively folding proteins, folding on the microsecond timescale. HP36's simple three helix topology, fast folding and small size have made it an attractive model system for computational and experimental studies of protein folding. Recent experimental studies have explored the denatured state of HP36 using fragment analysis coupled with relatively low-resolution spectroscopic techniques. These studies have shown that there is apparently only a small tendency to form locally stabilized secondary structure. Here, we complement the experimental studies by using replica exchange molecular dynamics with explicit solvent to investigate the structural features of these peptide models of unfolded HP36. To ensure convergence, two sets of simulations for each fragment were performed with different initial structures, and simulations were continued until these generated very similar final ensembles. These simulations reveal low populations of native-like structure and early folding events that cannot be resolved by experiment. For each fragment, calculated J-coupling constants and helical propensities are in good agreement with experimental trends. HP-1, corresponding to residues 41 to 53 and including the first alpha-helix, contains the highest helical population. HP-3, corresponding to residues 62 through 75 and including the third alpha-helix, contains a small population of helical turn residing at the N terminus while HP-2, corresponding to residues 52 through 61 and including the second alpha-helix, formed little to no structure in isolation. Overall, HP-1 was the only fragment to adopt a native-like conformation, but the low population suggests that formation of significant structure only occurs after formation of specific tertiary interactions.
authors.affiliation: Biochemistry and Structural Biology Program, State University of New York at Stony Brook, Stony Brook, NY 11794, USA.
authors.forename: Lauren
authors.initials: L
authors.lastname: Wickstrom
authors.forename: Asim
authors.initials: A
authors.lastname: Okur
authors.forename: Kun
authors.initials: K
authors.lastname: Song
authors.forename: Viktor
authors.initials: V
authors.lastname: Hornak
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Raleigh
authors.forename: Carlos L
authors.initials: CL
authors.lastname: Simmerling
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D016000:Cluster Analysis; D003198:Computer Simulation; D006801:Humans; D008840:Microfilament Proteins / Q000737:chemistry*; D008958:Models, Molecular; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012996:Solutions
chemical_list: D000596:Amino Acids; D008840:Microfilament Proteins; D012996:Solutions; C026615:villin