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Topological Quantities Determining the Folding/Unfolding Rate of Two-state Folding Proteins

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Abstract

We investigate various topological and energy parameters from the protein native structure and find combinations of some parameters that are well correlated with the rate of folding/unfolding. For folding, the topological quantity that combines the clustering coefficient and the long-range order (or total contact distance/contact order) has a high correlation with the folding rate, expressed as ln k F , obtained from standard experimental conditions. For unfolding, a combination of the impact of edge removal, obtained from the protein structure, and the stability of the native protein structure, as expressed by the free energy change ΔG, gives a good correlation with unfolding rate, ln k U .

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Authors and Affiliations

  1. Graduate School of System Informatics, Kobe University, Nada-ku, Kobe, 657-8501, Japan

    Jaewoon Jung

  2. Department of Chemistry, Korea Advanced Institute of Science and Technology, Yusong-gu, Daejeon, 351-701, Korea

    Alan J. Buglass & Eok-Kyun Lee

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  1. Jaewoon Jung
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  2. Alan J. Buglass
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  3. Eok-Kyun Lee
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Correspondence to Jaewoon Jung.

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Jung, J., Buglass, A.J. & Lee, EK. Topological Quantities Determining the Folding/Unfolding Rate of Two-state Folding Proteins. J Solution Chem 39, 943–958 (2010). https://doi.org/10.1007/s10953-010-9556-3

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  • DOI: https://doi.org/10.1007/s10953-010-9556-3

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