Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds

de Groot, B. L., Daura, X., Mark, A. E. and Grubmuller, H. (2001) Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. Journal of Molecular Biology, 309 1: 299-313. doi:10.1006/jmbi.2001.4655


Author de Groot, B. L.
Daura, X.
Mark, A. E.
Grubmuller, H.
Title Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds
Journal name Journal of Molecular Biology   Check publisher's open access policy
ISSN 0022-2836
Publication date 2001-01-01
Sub-type Article (original research)
DOI 10.1006/jmbi.2001.4655
Volume 309
Issue 1
Start page 299
End page 313
Total pages 15
Place of publication London
Publisher Academic Press Ltd
Language eng
Abstract A principal component analysis has been applied on equilibrium simulations of a beta -heptapeptide that shows reversible folding in a methanol solution. The analysis shows that the configurational space contains only three dense sub-states. These states of relatively low free energy correspond to the "native" left-handed helix, a partly helical intermediate, and a hairpin-like structure. The collection of unfolded conformations form a relatively diffuse cloud with little substructure, Internal hydrogen-bonding energies were found to correlate well with the degree of folding. The native helical structure folds from the N terminus; the transition from the major folding intermediate to the native helical structure involves the formation of the two most C-terminal backbone hydrogen bonds. A four-state Markov model was found to describe transition frequencies between the conformational states within error limits, indicating that memory-effects are negligible beyond the nanosecond time-scale. The dominant native state fluctuations were found to be very similar to unfolding motions, suggesting that unfolding pathways can be inferred from fluctuations in the native state. The low-dimensional essential subspace, describing 69% of the collective atomic fluctuations, was found to converge at time-scales of the order of one nanosecond at all temperatures investigated, whereas folding/unfolding takes place at significantly longer time-scales, even above the melting temperature. (C) 2001 Academic Press.
Keyword Biochemistry & Molecular Biology
conformational molecular dynamics
Markov model
peptide folding
principal component analysis
structure prediction
Principal Component Analysis
Molecular-dynamics
Protein Dynamics
Beta-heptapeptide
Simulations
Motions
Stability
Molscript
Hairpin
Program
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
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 95 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 103 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Thu, 20 Sep 2007, 02:29:11 EST