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Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water
Author(s) -
Höfinger Siegfried,
Almeida Benjamin,
Hansmann Ulrich H. E.
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21268
Subject(s) - parallel tempering , molecular dynamics , folding (dsp implementation) , tempering , signal (programming language) , dynamics (music) , computer science , biological system , chemistry , computational chemistry , materials science , physics , acoustics , artificial intelligence , engineering , mechanical engineering , biology , programming language , bayesian probability , markov chain monte carlo , monte carlo molecular modeling , composite material
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.