title: Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water.
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.
authors.affiliation: Department of Physics, Michigan Technological University, Houghton, Michigan 49331-1295, USA. shoefing@mtu.edu
authors.forename: Siegfried
authors.initials: S
authors.lastname: Höfinger
authors.forename: Benjamin
authors.initials: B
authors.lastname: Almeida
authors.forename: Ulrich H E
authors.initials: UH
authors.lastname: Hansmann
mesh_terms: D000444:Aldehyde Dehydrogenase / Q000737:chemistry; D000818:Animals; D008099:Liver / Q000201:enzymology; D019906:Nuclear Magnetic Resonance, Biomolecular; D017510:Protein Folding; D021382:Protein Sorting Signals; D051381:Rats; D014867:Water / Q000737:chemistry*
chemical_list: D021382:Protein Sorting Signals; D014867:Water; D000444:Aldehyde Dehydrogenase