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Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

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  • Stefano Zamuner
  • Flavio Seno
  • Antonio Trovato

Abstract

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference state associated to the null interaction case. Despite their significant effectiveness, the physical interpretation of knowledge-based potentials has been repeatedly questioned, with no consensus on the choice of the reference state. Here we use the fact that the Flory theorem, originally derived for chains in a dense polymer melt, holds also for chain fragments within the core of globular proteins, if the average over buried fragments collected from different non-redundant native structures is considered. After verifying that the ensuing Gaussian statistics, a hallmark of effectively non-interacting polymer chains, holds for a wide range of fragment lengths, although with significant deviations at short spatial scales, we use it to define a ‘bona fide’ reference state. Notably, despite the latter does depend on fragment length, deviations from it do not. This allows to estimate an effective interaction potential which is not biased by the presence of correlations due to the connectivity of the protein chain. We show how different sequence-independent effective statistical potentials can be derived using this approach by coarse-graining the protein representation at varying levels. The possibility of defining sequence-dependent potentials is explored.

Suggested Citation

  • Stefano Zamuner & Flavio Seno & Antonio Trovato, 2022. "Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules," PLOS ONE, Public Library of Science, vol. 17(1), pages 1-20, January.
  • Handle: RePEc:plo:pone00:0254969
    DOI: 10.1371/journal.pone.0254969
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    References listed on IDEAS

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    1. Thomas Hamelryck & Mikael Borg & Martin Paluszewski & Jonas Paulsen & Jes Frellsen & Christian Andreetta & Wouter Boomsma & Sandro Bottaro & Jesper Ferkinghoff-Borg, 2010. "Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized," PLOS ONE, Public Library of Science, vol. 5(11), pages 1-11, November.
    2. David Baker, 2000. "A surprising simplicity to protein folding," Nature, Nature, vol. 405(6782), pages 39-42, May.
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