Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations

Burgi, R., Daura, X., Mark, A. E., Bellanda, M., Mammi, S., Peggion, E. and van Gunsteren, W. (2001) Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations. Journal of Peptide Research, 57 2: 107-118. doi:10.1034/j.1399-3011.2001.00793.x


Author Burgi, R.
Daura, X.
Mark, A. E.
Bellanda, M.
Mammi, S.
Peggion, E.
van Gunsteren, W.
Title Folding study of an Aib-rich peptide in DMSO by molecular dynamics simulations
Journal name Journal of Peptide Research   Check publisher's open access policy
ISSN 1397-002X
Publication date 2001-02-01
Sub-type Article (original research)
DOI 10.1034/j.1399-3011.2001.00793.x
Volume 57
Issue 2
Start page 107
End page 118
Total pages 12
Place of publication Copenhagen
Publisher Munksgaard Int Publ Ltd
Language eng
Subject 03 Chemical Sciences
Abstract To evaluate the ability of molecular dynamics (MD) simulations using atomic force-fields to correctly predict stable folded conformations of a peptide in solution, we show results from MD simulations of the reversible folding of an octapeptide rich in alpha -aminoisobutyric acid (2-amino-2-methyl-propanoic acid, Aib) solvated in di-methyl-sulfoxide (DMSO). This solvent generally prevents the formation of secondary structure, whereas Aib-rich peptides show a high propensity to form secondary structural elements, in particular 3(10)- and alpha -helical structures. Aib is, moreover, achiral, so that Aib-rich peptides can form left- or right-handed helices depending on the overall composition of the peptide, the temperature, and the solvation conditions. This makes the system an interesting case to study the ensembles of peptide conformations as a function of temperature by MD simulation. Simulations involving the folding and unfolding of the peptide were performed starting from two initial structures, a right-handed alpha -helical structure and an extended structure, at three temperatures, 298 K, 340 K, and 380 K, and the results are compared with experimental nuclear magnetic resonance (NMR) data measured at 298 K and 340 K. The simulations generally reproduce the available experimental nuclear Overhauser effect (NOE) data, even when a wide range of conformations is sampled at each temperature. The importance of adequate statistical sampling in order to reliably interpret the experimental data is discussed.
Keyword Biochemical Research Methods
Biochemistry & Molecular Biology
Aib
DMSO
GROMOS
3(10) helix
molecular dynamics
peptide folding
Beta-heptapeptide
Thermodynamics
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Chemistry and Molecular Biosciences
 
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Created: Thu, 20 Sep 2007, 02:38:17 EST