- Journal Home
- Volume 36 - 2024
- Volume 35 - 2024
- Volume 34 - 2023
- Volume 33 - 2023
- Volume 32 - 2022
- Volume 31 - 2022
- Volume 30 - 2021
- Volume 29 - 2021
- Volume 28 - 2020
- Volume 27 - 2020
- Volume 26 - 2019
- Volume 25 - 2019
- Volume 24 - 2018
- Volume 23 - 2018
- Volume 22 - 2017
- Volume 21 - 2017
- Volume 20 - 2016
- Volume 19 - 2016
- Volume 18 - 2015
- Volume 17 - 2015
- Volume 16 - 2014
- Volume 15 - 2014
- Volume 14 - 2013
- Volume 13 - 2013
- Volume 12 - 2012
- Volume 11 - 2012
- Volume 10 - 2011
- Volume 9 - 2011
- Volume 8 - 2010
- Volume 7 - 2010
- Volume 6 - 2009
- Volume 5 - 2009
- Volume 4 - 2008
- Volume 3 - 2008
- Volume 2 - 2007
- Volume 1 - 2006
Commun. Comput. Phys., 7 (2010), pp. 283-300.
Published online: 2010-02
Cited by
- BibTex
- RIS
- TXT
The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state, without populating metastable intermediate states. A central question is how to characterize the instable, partially folded conformations of two-state proteins, in particular the rate-limiting transition-state conformations between the denatured and the native state. These partially folded conformations are short-lived and cannot be observed directly in experiments. However, experimental data from detailed mutational analyses of the folding dynamics provide indirect access to transition states. The interpretation of these data, in particular the reconstruction of transition-state conformations, requires simulation and modeling. The traditional interpretation of the mutational data aims to reconstruct the degree of structure formation of individual residues in the transition state, while a novel interpretation aims at degrees of structure formation of cooperative substructures such as α-helices and β-hairpins. By splitting up mutation-induced free energies into secondary and tertiary structural components, the novel interpretation resolves some of the inconsistencies of the traditional interpretation.
}, issn = {1991-7120}, doi = {https://doi.org/10.4208/cicp.2009.08.202}, url = {http://global-sci.org/intro/article_detail/cicp/7629.html} }The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state, without populating metastable intermediate states. A central question is how to characterize the instable, partially folded conformations of two-state proteins, in particular the rate-limiting transition-state conformations between the denatured and the native state. These partially folded conformations are short-lived and cannot be observed directly in experiments. However, experimental data from detailed mutational analyses of the folding dynamics provide indirect access to transition states. The interpretation of these data, in particular the reconstruction of transition-state conformations, requires simulation and modeling. The traditional interpretation of the mutational data aims to reconstruct the degree of structure formation of individual residues in the transition state, while a novel interpretation aims at degrees of structure formation of cooperative substructures such as α-helices and β-hairpins. By splitting up mutation-induced free energies into secondary and tertiary structural components, the novel interpretation resolves some of the inconsistencies of the traditional interpretation.