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Entropy 2016, 18(3), 67; doi:10.3390/e18030067

Role of Disulfide Bonds in Stabilizing the Conformation of Selected Enzymes—An Approach Based on Divergence Entropy Applied to the Structure of Hydrophobic Core in Proteins

1
Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland
2
Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, 30-059 Krakow, Poland
3
Department of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland
*
Author to whom correspondence should be addressed.
Academic Editor: Raúl Alcaraz Martínez
Received: 23 December 2015 / Revised: 14 February 2016 / Accepted: 18 February 2016 / Published: 25 February 2016
(This article belongs to the Section Information Theory)
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Abstract

One of the factors responsible for tertiary structural stabilization in proteins is the presence of the hydrophobic core—a result of hydrophobic interactions within the protein body. In some proteins (especially extracellular ones) additional stabilization is provided by covalent bonds between selected Cys residues, commonly referred to as disulfide bonds. The mutual interplay of both factors and their respective contributions to stabilization are the focus of this work. The assessment of the effects of disulfide bonds isinterpreted by Fuzzy Oil Drop (FOD) model in which individual polypeptide chain fragments (including fragments which participate in SS bonds) can be evaluated in the context of their influence upon tertiary structural stabilization by comparing their corresponding theoretical and idealized hydrophobicity density distributions. The proteins were identified with both factors reinforcing each other, as well as proteins where they seem to counteract each other. The analysis presents a number of enzymes, including ribonuclease, lysozyme, disulfide isomerase and phospholipase. View Full-Text
Keywords: Kullback–Leibler entropy; protein structure; hydrophobicity; disulfide bonds; tertiary structure stabilization; enzymes Kullback–Leibler entropy; protein structure; hydrophobicity; disulfide bonds; tertiary structure stabilization; enzymes
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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MDPI and ACS Style

Banach, M.; Kalinowska, B.; Konieczny, L.; Roterman, I. Role of Disulfide Bonds in Stabilizing the Conformation of Selected Enzymes—An Approach Based on Divergence Entropy Applied to the Structure of Hydrophobic Core in Proteins. Entropy 2016, 18, 67.

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