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Predicting and Simulating Mutational Effects on Protein Folding Kinetics

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Protein Folding

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2376))

Abstract

Mutational perturbations of protein structures, i.e., phi-value analysis, are commonly employed to probe the extent of involvement of a particular residue in the rate-determining step(s) of folding. This generally involves the measurement of folding thermodynamic parameters and kinetic rate constants for the wild-type and mutant proteins. While computational approaches have been reasonably successful in understanding and predicting the effect of mutations on folding thermodynamics, it has been challenging to explore the same on kinetics due to confounding structural, energetic, and dynamic factors. Accordingly, the frequent observation of fractional phi-values (mean of ~0.3) has resisted a precise and consistent interpretation. Here, we describe how to construct, parameterize, and employ a simple one-dimensional free energy surface model that is grounded in the basic tenets of the energy landscape theory to predict and simulate the effect of mutations on folding kinetics. As a proof of principle, we simulate one-dimensional free energy profiles of 806 mutations from 24 different proteins employing just the experimental destabilization as input, reproduce the relative unfolding activation free energies with a correlation of 0.91, and show that the mean phi-value of 0.3 essentially corresponds to the extent of stabilization energy gained at the barrier top while folding.

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Authors and Affiliations

  1. Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India

    Athi N. Naganathan

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  1. Athi N. Naganathan
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Correspondence to Athi N. Naganathan .

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Editors and Affiliations

  1. Department of Bioengineering and Center for Cellular and Biomolecular Machines, University of California, Merced, Merced, CA, USA

    Victor Muñoz

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Naganathan, A.N. (2022). Predicting and Simulating Mutational Effects on Protein Folding Kinetics. In: Muñoz, V. (eds) Protein Folding. Methods in Molecular Biology, vol 2376. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1716-8_21

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  • DOI: https://doi.org/10.1007/978-1-0716-1716-8_21

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1715-1

  • Online ISBN: 978-1-0716-1716-8

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