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 pres...

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Bibliographic Details
Published in:Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 1999-09, Vol.36 (4), p.383-399
Main Authors: Chipot, Christophe, Maigret, Bernard, Pohorille, Andrew
Format: Article
Language:English
Subjects:
Algorithms
amphipathic peptides
aqueous interfaces
Computer Simulation
Computers
Exobiology
free energy calculations
Glutamine - chemistry
Hexanes - chemistry
Hydrogen Bonding
Kinetics
Leucine - chemistry
molecular dynamics simulations
Oligopeptides - chemistry
peptide folding
Protein Conformation
Protein Folding
Protein Structure, Secondary
Solutions
Space life sciences
Thermodynamics
Time Factors
Water - chemistry
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Summary: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. Copyright 1999 Wiley-Liss, Inc.
ISSN:0887-3585
1097-0134
DOI:10.1002/(SICI)1097-0134(19990901)36:4<383::AID-PROT2>3.0.CO;2-P