Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study.
Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations for 161.5 ns. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of nonamphipathic structures throughout the complete trajectory indicates that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure. Proteins 1999;36:383-399.
Chipot
C
C
Laboratoire de Chimie Théorique, Unité Mixte de Recherche CNRS No. 7565, Université Henri Poincaré-Nancy I, Vandoeuvre-lès-Nancy Cedex, France. chipot@lctn.u-nancy.fr
Maigret
B
B
Pohorille
A
A
D000465:Algorithms; D003198:Computer Simulation; D003201:Computers; D005973:Glutamine / Q000737:chemistry; D006586:Hexanes / Q000737:chemistry; D006860:Hydrogen Bonding; D007700:Kinetics; D007930:Leucine / Q000737:chemistry; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012996:Solutions; D013816:Thermodynamics; D013997:Time Factors; D014867:Water / Q000737:chemistry
D006586:Hexanes; D009842:Oligopeptides; D012996:Solutions; D014867:Water; D005973:Glutamine; D007930:Leucine