DOI: 10.1002/prot.21565. Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein

Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein

10.1002/prot.21565

Crossref journal-article

Wiley

Proteins: Structure, Function, and Bioinformatics (311)

Abstract

AbstractThe effects of a single‐point mutation on folding thermodynamics and kinetics are usually interpreted by focusing on the native structure and the transition state. Here, the entire conformational spaces of a 20‐residue three‐stranded antiparallel β‐sheet peptide (double hairpin) and of its single‐point mutant W10V are sampled close to the melting temperature by equilibrium folding–unfolding molecular dynamics simulations for a total of 40 μs. The folded state as well as the most populated free energy basins in the denatured state are isolated by grouping conformations according to fast relaxation at equilibrium. Such kinetic analysis provides more detailed and useful information than a simple projection of the free energy. The W10V mutant has the same native structure as the wild type peptide, and similar folding rate and stability. In the denatured state, the N‐terminal hairpin is about 20% more structured in W10V than the wild type mainly because of van der Waals interactions. Notably, the W10V mutation influences also the van der Waals energy at the transition state ensemble causing a shift in the ratio of fluxes between two different transition state regions on parallel folding pathways corresponding to nucleation at either of the two β‐hairpins. Previous experimental studies have focused on the effects of denaturant‐dependent or temperature‐dependent changes in the structure of the denatured state. The atomistic simulations show that a single‐point mutation in the central strand of a β‐sheet peptide results in remarkable changes in the topography of the denatured state ensemble. These changes modulate the relative accessibility of parallel folding pathways because of kinetic partitioning of the denatured state. Therefore, the observed dependence of the folding process on the starting ensemble raises questions on the biological significance of in vitro folding studies under strongly denaturing conditions. Proteins 2008. © 2007 Wiley‐Liss, Inc.

Bibliography

Muff, S., & Caflisch, A. (2007). Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon singleâpoint mutation of a Î²âsheet miniprotein. Proteins: Structure, Function, and Bioinformatics, 70(4), 1185â1195. Portico.

Authors 2

Stefanie Muff (first)
Amedeo Caflisch (additional)

References 41 Referenced 81

10.1126/science.1749933
10.1038/nsb0197-10
10.1073/pnas.89.18.8721
10.1016/S0968-0004(00)01610-8
10.1038/nrm1126
10.1098/rsta.2004.1502
10.1021/bi047314
10.1021/cr040425u
10.1146/annurev.bi.60.070191.004051
10.1073/pnas.0406234101
10.1016/j.jmb.2004.06.063
10.1073/pnas.0605580103
10.1126/science.7618103
10.1016/j.jmb.2005.08.031
10.1016/S0022-2836(02)00888-4
10.1126/science.1060438
10.1038/nature02261
10.1016/j.jmb.2004.11.035
10.1110/ps.8.4.854 / Protein Sci / De novo design of a monomeric three‐stranded antiparallel β‐sheet by De Alba E (1999)
10.1073/pnas.190324897
10.1002/prot.10041
10.1073/pnas.0406754102
10.1002/prot.10001
10.1038/89638
10.1038/nsb947
10.1016/0022-2836(92)90561-W
10.1016/0263-7855(96)00009-4
10.1016/S0022-2836(02)00741-6
10.1073/pnas.0608099104
10.1021/ma60063a024
10.1016/j.jmb.2006.05.061
10.1016/j.jmb.2005.05.060
10.1063/1.475393
10.1063/1.1893753
10.1016/S0969-2126(02)00700-1
10.1016/j.jmb.2003.08.062
10.1016/j.sbi.2006.01.002
10.1002/jcc.540040211
10.1021/jp994157t
10.1146/annurev.biophys.29.1.327
{'journal-title': 'Bioinformatics', 'article-title': 'Wordom: a program for efficient analysis of molecular dynamics simulations', 'author': 'Seeber M', 'key': 'e_1_2_6_42_2'} / Bioinformatics / Wordom: a program for efficient analysis of molecular dynamics simulations by Seeber M

Dates

Type	When
Created	17 years, 11 months ago (Sept. 10, 2007, 5:16 p.m.)
Deposited	1 year, 10 months ago (Oct. 15, 2023, 5:51 p.m.)
Indexed	4 weeks, 1 day ago (July 30, 2025, 10:51 a.m.)
Issued	17 years, 11 months ago (Sept. 10, 2007)
Published	17 years, 11 months ago (Sept. 10, 2007)
Published Online	17 years, 11 months ago (Sept. 10, 2007)
Published Print	17 years, 5 months ago (March 1, 2008)

Funders 1

Swiss National Science Foundation 10.13039/501100001711 Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Region: Europe
pri (Trusts, charities, foundations (both public and private))
Labels10
1. Schweizerischer Nationalfonds
2. Swiss National Science Foundation
3. Fonds National Suisse de la Recherche Scientifique
4. Fondo Nazionale Svizzero per la Ricerca Scientifica
5. Fonds National Suisse
6. Fondo Nazionale Svizzero
7. Schweizerische Nationalfonds
8. SNF
9. SNSF
10. FNS

BibTeX

@article{Muff_2007, title={Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein}, volume={70}, ISSN={1097-0134}, url={http://dx.doi.org/10.1002/prot.21565}, DOI={10.1002/prot.21565}, number={4}, journal={Proteins: Structure, Function, and Bioinformatics}, publisher={Wiley}, author={Muff, Stefanie and Caflisch, Amedeo}, year={2007}, month=sep, pages={1185–1195} }

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