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Open AccessArticle

Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity

1
Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Łazarza 16, 31-530 Krakow, Poland
2
Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Kraków, Poland
*
Author to whom correspondence should be addressed.
Symmetry 2019, 11(10), 1215; https://doi.org/10.3390/sym11101215
Received: 18 August 2019 / Revised: 10 September 2019 / Accepted: 21 September 2019 / Published: 30 September 2019
(This article belongs to the Special Issue Symmetry in Protein Structure and Bioinformatics)
The solenoid is a highly ordered structure observed in proteins, characterized by a set of symmetries. A group of enzymes—lyases containing solenoid fragments—was subjected to analysis with focus on their distribution of hydrophobicity/hydrophilicity, applying the fuzzy oil drop model. The model differentiates between a monocentric distribution hydrophobic core (spherical symmetry—mathematically modeled by a 3D Gaussian) and linear propagation of hydrophobicity (symmetry based on translation of structural units, i.e., chains—evident in amyloids). The linearly ordered solenoid carries information that affects the structure of the aqueous solvent in its neighborhood. Progressive disruption of its symmetry (via incorporation of asymmetrical fragments of varying size) appears to facilitate selective interaction with the intended substrate during enzymatic catalysis. View Full-Text
Keywords: symmetry; dissymmetry; specificity; hydrophobicity; hydrophilicity; hydrophobic core; fuzzy oil drop model; lyases; active site; structuralization of water; force field symmetry; dissymmetry; specificity; hydrophobicity; hydrophilicity; hydrophobic core; fuzzy oil drop model; lyases; active site; structuralization of water; force field
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Banach, M.; Konieczny, L.; Roterman, I. Symmetry and Dissymmetry in Protein Structure—System-Coding Its Biological Specificity. Symmetry 2019, 11, 1215.

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