Folding dynamics of 10-residue beta-hairpin peptide chignolin.
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.
Suenaga
Atsushi
A
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
Narumi
Tetsu
T
Futatsugi
Noriyuki
N
Yanai
Ryoko
R
Ohno
Yousuke
Y
Okimoto
Noriaki
N
Taiji
Makoto
M
D006860:Hydrogen Bonding; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding
D009842:Oligopeptides; C506175:chignolin