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3 Bio-Algorithms and Med-Systems

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The variability of protein structure with respect to the hydrophobic core

Banach M., Wiśniowski Z., Kalinowska B., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

2017

Vol. 13, no. 2

63--67

The application of the fuzzy oil drop model to the analysis of protein structure is shown using two proteins. The selection of these two examples is due to their opposite character. Two proteins were selected representing very high order and very high disorder with respect to the organized uni-central hydrophobic core in proteins (one centrally localized concentration of high hydrophobicity). These two cases are to show examples of the large spectrum of variability of local organization of the hydrophobic core in proteins. The importance of the observation presented in this paper is significant with respect to large sets of proteins discussed in separate publications.

Structure of hydrophobic core in plant carboxylesterase

Banach M., Konieczny L., Wiśniowski Z., Roterman I.

Bio-Algorithms and Med-Systems

2017

Vol. 13, no. 1

13--16

The fuzzy oil drop model was applied to characterize the hydrophobic core structure in plant carboxylesterase. The characteristics revealed the status of β-sheets in the central part of the molecule as discordant as opposed to the expected hydrophobicity distribution. Particularly, the β-strands and helices in close proximity to the enzymatic residues recognized as discordant with respect to the ideal hydrophobicity distribution of hydrophobic core are of high importance. It is assumed that this local irregularity is the form of coding the specificity of enzymes. The protein under consideration appears to be the next example proving this assumption.

Structural role of exon-coded fragments in proteins

Piwowar M., Banach M., Konieczny L., Roterman I.

Bio-Algorithms and Med-Systems

2013

Vol. 9, no. 3

103--114

This article describes the role of protein fragments encoded by individual exons. Structural analysis of the hydrophobic core on the basis of the “fuzzy oil drop” model – in whole molecules as well as in fragments encoded by specific exons – indicates that, in each protein, at least one exon encodes a fragment, which is consistent with the theoretical distribution of hydrophobicity density. Quantitative assessment of the properties of such exons in selected proteins enables the model to be applied in identifying the structural (stabilizing) role of polypeptide chains encoded by individual exons. This is viewed as a preliminary step toward future exploitation of this technique in studying the alternative splicing phenomenon.