doi: 10.1063/1.3000009.
Free energy landscapes of a highly structured beta-hairpin peptide and its single mutant
Affiliations
- PMID: 19045319
- DOI: 10.1063/1.3000009
Item in Clipboard
Free energy landscapes of a highly structured beta-hairpin peptide and its single mutant
J Chem Phys.
.
Abstract
We investigated the free energy landscapes of a highly structured beta-hairpin peptide (MBH12) and a less structured peptide with a single mutation of Tyr6 to Asp6 (MBH10). For the free energy mapping, starting from an extended conformation, the replica exchange molecular dynamic simulations for two beta-hairpins were performed using a modified version of an all-atom force field employing an implicit solvation (param99MOD5/GBSA). With the present simulation approach, we demonstrated that detailed stability changes associated with the sequence modification from MBH12 to MBH10 are quantitatively well predicted at the all-atom level.
Similar articles
-
Direct folding simulation of alpha-helices and beta-hairpins based on a single all-atom force field with an implicit solvation model.Proteins. 2007 Jan 1;66(1):53-60. doi: 10.1002/prot.21173. Proteins. 2007. PMID: 17063490
-
Free energy landscape of protein folding in water: explicit vs. implicit solvent.Proteins. 2003 Nov 1;53(2):148-61. doi: 10.1002/prot.10483. Proteins. 2003. PMID: 14517967
-
Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model.Proteins. 2004 Aug 1;56(2):310-21. doi: 10.1002/prot.20104. Proteins. 2004. PMID: 15211514
-
Application of the accelerated molecular dynamics simulations to the folding of a small protein.J Chem Phys. 2007 Mar 28;126(12):125102. doi: 10.1063/1.2709639. J Chem Phys. 2007. PMID: 17411164 Review.
-
De novo design of monomeric beta-hairpin and beta-sheet peptides.Methods Mol Biol. 2006;340:27-51. doi: 10.1385/1-59745-116-9:27. Methods Mol Biol. 2006. PMID: 16957331 Review.
Cited by
-
Peptide and Protein Structure Prediction with a Simplified Continuum Solvent Model.J Phys Chem B. 2018 Dec 13;122(49):11355-11362. doi: 10.1021/acs.jpcb.8b07264. Epub 2018 Oct 5. J Phys Chem B. 2018. PMID: 30230838 Free PMC article.
-
Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation.J Mol Graph Model. 2010 Aug 24;29(1):2-12. doi: 10.1016/j.jmgm.2010.03.011. Epub 2010 Apr 4. J Mol Graph Model. 2010. PMID: 20466569 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
