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Open AccessArticle

Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy

1
Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
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Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland
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Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Lojasiewicza 11, 30-348 Krakow, Poland
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Chair of Medical Biochemistry, Medical College, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland
*
Author to whom correspondence should be addressed.
Symmetry 2020, 12(2), 273; https://doi.org/10.3390/sym12020273
Received: 12 January 2020 / Revised: 4 February 2020 / Accepted: 6 February 2020 / Published: 11 February 2020
Proteins with a high degree of sequence similarity representing different structures provide a key to understand how protein sequence codes for 3D structure. An analysis using the fuzzy oil drop model was carried out on two pairs of proteins with different secondary structures and with high sequence identities. It has been shown that distributions of hydrophobicity for these proteins are approximated well using single 3D Gaussian function. In other words, the similar sequences fold into different 3D structures, however, alternative structures also have symmetric and monocentric hydrophobic cores. It should be noted that a significant change in the helical to beta-structured form in the N-terminal section takes places in the fragment much preceding the location of the mutated regions. It can be concluded that the final structure is the result of a complicated synergy effect in which the whole chain participates simultaneously.
Keywords: homology; protein structure; hydrophobic core; hydrophobicity; synergy; spherical symmetry homology; protein structure; hydrophobic core; hydrophobicity; synergy; spherical symmetry
MDPI and ACS Style

Fabian, P.; Stapor, K.; Banach, M.; Ptak-Kaczor, M.; Konieczny, L.; Roterman, I. Alternative Hydrophobic Core in Proteins—The Effect of Specific Synergy. Symmetry 2020, 12, 273.

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