Unfolding simulations of the 85-102 beta-hairpin of barnase.
Molecular dynamics simulations are used to investigate the unfolding reaction of an isolated beta-hairpin formed by residues 85 to 102 of barnase, a ribonuclease from Bacillus amyloliquefaciens. This peptide was considered following evidence from experimental studies that it may act as an initiation site for barnase folding by adopting a native-like conformation early during the folding process. Three successive molecular dynamics simulations of about 300 ps each were carried out for an all-atom model of the hairpin in water at 300 K, 450 K, and 600 K, respectively. A detailed analysis of all three simulations is presented. In particular we investigate the behavior of the backbone hydrogen bonds, and of hydrophobic interactions between side-chains, where distinction is made between contributions from native and non-native contacts, respectively. Furthermore, we investigate peptide water interactions and monitor the presence and size of empty cavities. The behavior of the hairpin in the three simulations, when considered sequentially, describes a process whereby a native-like conformation evolves to an unfolded state. Unfolding starts at the beginning of the 450 K simulation with the loss of two hydrogen bonds at the free hairpin extremities. At about the same time, the centrally located H-bonds are weakened and exchange more frequently with water, but the turn tightens up as the beta-sheet extends into the turn region. All this is accompanied by a volume expansion and the formation of a large hydrophobic side-chain cluster promoted by both native and highly fluctuating non-native apolar contacts involving residues 87 to 90 and 95 to 99. This collapsed but more loosely packed state, essentially stabilized by hydrophobic interactions, is stable throughout the entire 450 K simulation and for about 150 ps at 600 K, after which point it proceeds rapidly to completely denatured conformations. This behavior presents clear analogies with known features of the unfolding reaction of complete proteins. It may indicate that this beta-hairpin has a well-defined conformation on its own, which would be in agreement with its role as an initiation site for folding.
Pugliese
L
L
Unité de Conformation des Macromolécules Biologiques Université Libre de Bruxelles, Belgium.
Prévost
M
M
Wodak
S J
SJ
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D001426:Bacterial Proteins; D003198:Computer Simulation; D006358:Hot Temperature; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012260:Ribonucleases / Q000737:chemistry* / Q000378:metabolism; D014867:Water / Q000378:metabolism
D000596:Amino Acids; D001426:Bacterial Proteins; D014867:Water; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease