Application of Divergence Entropy to Characterize the Structure of the Hydrophobic Core in DNA Interacting Proteins

Entropy

Barbara Kalinowska¹  Mateusz Banach¹  Leszek Konieczny²  Irena Roterman¹ 

[1] Department of Bioinformatics and Telemedicine, Collegium Medium, Jagiellonian University, Lazarza 16, 31- 530 Krakow, Poland; E-Mails:;Chair of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31- 034 Krakow, Poland; E-Mail:

关键词: divergence entropy;    hydrophobicity;    fuzzy oil drop;    disordered proteins;    JARID2;    JARID1A;    JARID1B;    JARID1D;    ARID;    PHD;    jumonji;   

DOI  :  10.3390/e17031477

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2015 by the authors; licensee MDPI, Basel, Switzerland