title: Folding dynamics of 10-residue beta-hairpin peptide chignolin.
abstract: Short peptides that fold into beta-hairpins are ideal model systems for investigating the mechanism of protein folding because their folding process shows dynamics typical of proteins. We performed folding, unfolding, and refolding molecular dynamics simulations (total of 2.7 micros) of the 10-residue beta-hairpin peptide chignolin, which is the smallest beta-hairpin structure known to be stable in solution. Our results revealed the folding mechanism of chignolin, which comprises three steps. First, the folding begins with hydrophobic assembly. It brings the main chain together; subsequently, a nascent turn structure is formed. The second step is the conversion of the nascent turn into a tight turn structure along with interconversion of the hydrophobic packing and interstrand hydrogen bonds. Finally, the formation of the hydrogen-bond network and the complete hydrophobic core as well as the arrangement of side-chain-side-chain interactions occur at approximately the same time. This three-step mechanism appropriately interprets the folding process as involving a combination of previous inconsistent explanations of the folding mechanism of the beta-hairpin, that the first event of the folding is formation of hydrogen bonds and the second is that of the hydrophobic core, or vice versa.
authors.affiliation: High-Performance Molecular Simulation Team, Computational and Experimental System Biology Group, RIKEN Genomic Sciences Center, 61-1 Ono-cho, Tsurumi, Yokohama, Kanagawa 230-0046, Japan. suenaga@gsc.riken.jp
authors.forename: Atsushi
authors.initials: A
authors.lastname: Suenaga
authors.forename: Tetsu
authors.initials: T
authors.lastname: Narumi
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Futatsugi
authors.forename: Ryoko
authors.initials: R
authors.lastname: Yanai
authors.forename: Yousuke
authors.initials: Y
authors.lastname: Ohno
authors.forename: Noriaki
authors.initials: N
authors.lastname: Okimoto
authors.forename: Makoto
authors.initials: M
authors.lastname: Taiji
mesh_terms: D006860:Hydrogen Bonding; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding
chemical_list: D009842:Oligopeptides; C506175:chignolin