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Entropy 2018, 20(8), 580; https://doi.org/10.3390/e20080580

Entropic Stabilization of Cas4 Protein SSO0001 Predicted with Popcoen

1
Department of Condensed Matter Physics, University of Barcelona, Carrer Martí i Franquès 1, 08028 Barcelona, Spain
2
Department of Inorganic and Organic Chemistry, University of Barcelona, Carrer Martí i Franquès 1, 08028 Barcelona, Spain
3
Molecular Biology Institute of Barcelona (IBMB-CSIC, Maria de Maeztu Unit of Excellence), Carrer Baldiri Reixac 4-8, 08028 Barcelona, Spain
*
Author to whom correspondence should be addressed.
Received: 28 June 2018 / Revised: 27 July 2018 / Accepted: 28 July 2018 / Published: 7 August 2018
(This article belongs to the Special Issue Entropy: From Physics to Information Sciences and Geometry)
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Abstract

Popcoen is a method for configurational entropy estimation of proteins based on machine-learning. Entropy is predicted with an artificial neural network which was trained on simulation trajectories of a large set of representative proteins. Popcoen is extremely fast compared to other approaches based on the sampling of a multitude of microstates. Consequently, Popcoen can be incorporated into a large class of protein software which currently neglects configurational entropy for performance reasons. Here, we apply Popcoen to various conformations of the Cas4 protein SSO0001 of Sulfolobus solfataricus, a protein that assembles to a decamer of known toroidal shape. We provide numerical evidence that the native state (NAT) of a SSO0001 monomer has a similar structure to the protomers of the oligomer, where NAT of the monomer is stabilized mainly entropically. Due to its large amount of configurational entropy, NAT has lower free energy than alternative conformations of very low enthalpy and solvation free-energy. Hence, SSO0001 serves as an example case where neglecting configurational entropy leads to incorrect conclusion. Our results imply that no refolding of the subunits is required during oligomerization which suggests that configurational entropy is employed by nature to largely enhance the rate of assembly. View Full-Text
Keywords: configurational entropy; entropy estimation; protein conformations; entropic stabilization; CRISPR/Cas system; oligomerization configurational entropy; entropy estimation; protein conformations; entropic stabilization; CRISPR/Cas system; oligomerization
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Goethe, M.; Fita, I.; Rubi, J.M. Entropic Stabilization of Cas4 Protein SSO0001 Predicted with Popcoen. Entropy 2018, 20, 580.

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