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Protein Structure and Its Folding Rate

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Mathematical Modelling of Biosystems

Part of the book series: Applied Optimization ((APOP,volume 102))

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Abstract

In the first part of this paper we overview protein structures, their spontaneous formation (“folding”) and thermodynamic and kinetic aspects of this phenomenon. It is stressed that universal features of folding are observed near the point of thermodynamic equilibrium between the native and denatured states of the protein. Here the “two-state” (“denatured state” ↔ “native state”) transition proceeds without accumulation of metastable intermediates, and only the transition state, i.e., the most unstable state in the folding pathway, is outlined by its essential influence on the folding/unfolding kinetics. In the second part of the paper, a theory of protein folding rates and related phenomena is presented. First, it is shown that the protein size determines the range of protein’s folding rates in the vicinity of the point of thermodynamic equilibrium between the native and denatured states of the protein. Then we present methods for calculating folding and unfolding rates of globular proteins from their sizes, stabilities and either 3D structures or amino acid sequences. And, at last, we show that the same theory outlines the location of the protein folding nucleus (i.e., the structured part of transition state) in a reasonable concordance with experimental data.

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Authors and Affiliations

  1. Laboratory of Protein Physics, Institute of Protein Research, Russian Academy of Sciences, 4 Institutskaya str., Pushchino, Moscow Region, 142290, Russian

    Alexei V. Finkelstein, Dmitry N. Ivankov, Sergiy O. Garbuzynskiy & Oxana V. Galzitskaya

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  1. Alexei V. Finkelstein
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  2. Dmitry N. Ivankov
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  3. Sergiy O. Garbuzynskiy
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  4. Oxana V. Galzitskaya
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Editors and Affiliations

  1. Federal University of Rio de Janeiro UFRJ-COPPE-Centre of Technology, 21.941-972-P.O. Box 68.511, Rio de Janeiro-RJ, Brazil

    Rubem P. Mondaini

  2. Center for Applied Optimization, University of Florida, 303 Weil Hall, P.O.Box 116595, Gainesville, FL, 32611-6595, USA

    Panos M. Pardalos

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Finkelstein, A.V., Ivankov, D.N., Garbuzynskiy, S.O., Galzitskaya, O.V. (2008). Protein Structure and Its Folding Rate. In: Mondaini, R.P., Pardalos, P.M. (eds) Mathematical Modelling of Biosystems. Applied Optimization, vol 102. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-76784-8_9

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