1097-0134/asset/PROT_centre.gif?v=1&s=77b56b1f2cdaba74cb3bb149bd9b029cd8803cdb)
Research Article
Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water
Article first published online: 17 MAY 2007
DOI: 10.1002/prot.21268
Copyright © 2007 Wiley-Liss, Inc.
Issue
1097-0134/asset/cover.gif?v=1&s=d817e79b67ba6cacf8bdcce1a819c04de300a7e3 "Proteins: Structure, Function, and Bioinformatics")
Proteins: Structure, Function, and Bioinformatics
Volume 68, Issue 3, pages 662–669, 15 August 2007
Additional Information
How to Cite
Höfinger, S., Almeida, B. and Hansmann, U. H. E. (2007), Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water. Proteins: Structure, Function, and Bioinformatics, 68: 662–669. doi: 10.1002/prot.21268
Publication History
- Issue published online: 27 JUN 2007
- Article first published online: 17 MAY 2007
- Manuscript Accepted: 21 SEP 2006
- Manuscript Revised: 23 AUG 2006
- Manuscript Received: 11 MAY 2006
Funded by
- National Institutes of Health. Grant Number: GM62838
Keywords:
- enhanced sampling;
- aldehyde dehydrogenase;
- structure determination;
- structure prediction;
- solvation
Abstract
Parallel temperature molecular dynamics simulations are used to explore the folding of a signal peptide, a short but functionally independent domain at the N-terminus of proteins. The peptide has been analyzed previously by NMR, and thus a solid reference state is provided with the experimental structure. Particular attention is paid to the role of water considered in full atomic detail. Different partial aspects in the folding process are quantified. The major group of obtained structures matches the NMR structure very closely. An important biological consequence is that in vivo folding of signal peptides seems to be possible within aqueous environments. Proteins 2007. © 2007 Wiley-Liss, Inc.