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Entropy 2015, 17(3), 1477-1507; doi:10.3390/e17031477

Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting 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, 30-348 Łojasiewicza 11, Krakow, Poland
3
Chair of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland
*
Author to whom correspondence should be addressed.
Academic Editor: Wayne Dawson
Received: 4 September 2014 / Revised: 11 March 2015 / Accepted: 17 March 2015 / Published: 23 March 2015
(This article belongs to the Special Issue Entropy and RNA Structure, Folding and Mechanics)
View Full-Text   |   Download PDF [1576 KB, uploaded 23 March 2015]   |  

Abstract

The fuzzy oil drop model, a tool which can be used to study the structure of the hydrophobic core in proteins, has been applied in the analysis of proteins belonging to the jumonji group—JARID2, JARID1A, JARID1B and JARID1D—proteins that share the property of being able to interact with DNA. Their ARID and PHD domains, when analyzed in the context of the fuzzy oil drop model, are found to exhibit structural variability regarding the status of their secondary folds, including the β-hairpin which determines their biological function. Additionally, the structure of disordered fragments which are present in jumonji proteins (as confirmed by the DisProt database) is explained on the grounds of the hydrophobic core model, suggesting that such fragments contribute to tertiary structural stabilization. This conclusion is supported by divergence entropy measurements, expressing the degree of ordering in each protein’s hydrophobic core. View Full-Text
Keywords: divergence entropy; hydrophobicity; fuzzy oil drop; disordered proteins; JARID2; JARID1A; JARID1B; JARID1D; ARID; PHD; jumonji divergence entropy; hydrophobicity; fuzzy oil drop; disordered proteins; JARID2; JARID1A; JARID1B; JARID1D; ARID; PHD; jumonji
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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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MDPI and ACS Style

Kalinowska, B.; Banach, M.; Konieczny, L.; Roterman, I. Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins. Entropy 2015, 17, 1477-1507.

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