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Exploring the Levinthal limit in protein folding

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Abstract

According to the thermodynamic hypothesis, the native state of proteins is uniquely defined by their amino acid sequence. On the other hand, according to Levinthal, the native state is just a local minimum of the free energy and a given amino acid sequence, in the same thermodynamic conditions, can assume many, very different structures that are as thermodynamically stable as the native state. This is the Levinthal limit explored in this work. Using computer simulations, we compare the interactions that stabilize the native state of four different proteins with those that stabilize three non-native states of each protein and find that the nature of the interactions is very similar for all such 16 conformers. Furthermore, an enhancement of the degree of fluctuation of the non-native conformers can be explained by an insufficient relaxation to their local free energy minimum. These results favor Levinthal’s hypothesis that protein folding is a kinetic non-equilibrium process.

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Acknowledgments

LC received national funds from FCT - Foundation for Science and Technology, Portugal, through the project UID/Multi/04326/2013. LD thanks the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP), and to the Conselho Nacional de Desenvolvimento Cientía co e Tecnológico (CNPq) for financial support.

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Authors and Affiliations

  1. CCMAR and FCT, Universidade do Algarve, Campus de Gambelas, Faro, 8005-139, Portugal

    Leonor Cruzeiro

  2. Grupo de Simulação Molecular, Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14040-901, Ribeirão Preto, São Paulo, Brazil

    Léo Degrève

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  1. Leonor Cruzeiro
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  2. Léo Degrève
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Correspondence to Leonor Cruzeiro.

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Cruzeiro, L., Degrève, L. Exploring the Levinthal limit in protein folding. J Biol Phys 43, 15–30 (2017). https://doi.org/10.1007/s10867-016-9431-6

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  • DOI: https://doi.org/10.1007/s10867-016-9431-6

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