Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water

Authors

Siegfried Höfinger, Michigan Technological UniversityFollow
Benjamin Almeida, Novartis Institutes for BioMedical Research
Ulrich H.E Hansmann, Michigan Technological UniversityFollow

Document Type

Article

Publication Date

8-15-2007

Department

Department of Physics

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.

Publisher's Statement

© 2007 Wiley-Liss, Inc. Publisher’s version of record: https://doi.org/10.1002/prot.21268

Publication Title

Proteins: Structure, Function and Genetics

Recommended Citation

Höfinger, S., Almeida, B., & Hansmann, U. H. (2007). Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water. Proteins: Structure, Function and Genetics, 68(3), 662-669. http://doi.org/10.1002/prot.21268
Retrieved from: https://digitalcommons.mtu.edu/michigantech-p/3858