Is the hydrophobic core a universal structural element in proteinsReport as inadecuate

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Journal of Molecular Modeling

, 23:205

First Online: 16 June 2017Received: 06 December 2016Accepted: 09 May 2017DOI: 10.1007-s00894-017-3367-z

Cite this article as: Kalinowska, B., Banach, M., Wiśniowski, Z. et al. J Mol Model 2017 23: 205. doi:10.1007-s00894-017-3367-z


The hydrophobic core, when subjected to analysis based on the fuzzy oil drop model, appears to be a universal structural component of proteins irrespective of their secondary, supersecondary, and tertiary conformations. A study has been performed on a set of nonhomologous proteins representing a variety of CATH categories. The presence of a well-ordered hydrophobic core has been confirmed in each case, regardless of the protein’s biological function, chain length or source organism. In light of fuzzy oil drop FOD analysis, various supersecondary forms seem to share a common structural factor in the form of a hydrophobic core, emerging either as part of the whole protein or a specific domain. The variable status of individual folds with respect to the FOD model reflects their propensity for conformational changes, frequently associated with biological function. Such flexibility is expressed as variable stability of the hydrophobic core, along with specific encoding of potential conformational changes which depend on the properties of helices and β-folds.

KeywordsProtein folding Hydrophobicity Hydrophobic core 

Author: Barbara Kalinowska - Mateusz Banach - Zdzisław Wiśniowski - Leszek Konieczny - Irena Roterman


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