Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations

Colombo, G., Roccatano, D. and Mark, A. E. (2002) Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations. Proteins-structure Function And Genetics, 46 4: 380-392. doi:10.1002/prot.1175


Author Colombo, G.
Roccatano, D.
Mark, A. E.
Title Folding and stability of the three-stranded beta-sheet peptide betanova: Insights from molecular dynamics simulations
Journal name Proteins-structure Function And Genetics   Check publisher's open access policy
ISSN 0887-3585
Publication date 2002-01-01
Sub-type Article (original research)
DOI 10.1002/prot.1175
Volume 46
Issue 4
Start page 380
End page 392
Total pages 13
Place of publication New York
Publisher Wiley-liss
Language eng
Abstract The dynamics of the three-stranded beta-sheet peptide Betanova has been studied at four different temperatures (280, 300, 350, and 450 K by molecular dynamics simulation techniques, in explicit water. Two 20-ns simulations at 280 K indicate that the peptide remains very flexible under "folding" conditions sampling a range of conformations that together satisfy the nuclear magnetic resonance (NMR)-derived experimental constraints. Two simulations at 300 K (above the experimental folding, temperature) of 20 ns each show partial formation of "native"-like structure, which also satisfies most of the NOE constraints at 280 K. At higher temperature, the presence of compact states, in which a series of hydrophobic contacts remain present, are observed. This is consistent with experimental observations regarding the role of hydrophobic contacts in determining the peptide's stability and in initiating the formation of turns and loops. A set of different structures is shown to satisfy NMR-derived distance restraints and a possible mechanism for the folding of the peptide into the NMR-determined structure is proposed. (C) 2002 Wiley-Liss Inc.
Keyword Biochemistry & Molecular Biology
Biophysics
protein folding
molecular dynamics
beta-sheet
peptide conformation in water
Betanova
De-novo Design
Protein-g
Hairpin Formation
Aqueous-solution
Linear Peptide
Alpha-helices
Side-chain
Thermodynamics
Conformation
Transition
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Created: Thu, 20 Sep 2007, 02:13:35 EST