Title

Recognition of protein complexation based on hydrophobicity distribution

Authors

Mateusz Banach^1,2, Irena Roterman^1,*

Affiliation

¹Department of Bioinformatics and Telemedicine, Collegium Medium – Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland; ²Faculty of Physics, Astronomy and Applied Computer Science – Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland

Email

myroterm@cyf-kr.edu.pl

Article Type

Hypothesis

Date

Received August 04, 2009; Accepted August 18, 2009; Published September 30, 2009

Abstract

The identification of the surface area able to generate the protein-protein complexation ligand and ion ligation is critical for the recognition of the biological function of particular proteins. The technique based on the analysis of the irregularity of hydrophobicity distribution is used as the criterion for the recognition of the interaction regions. Particularly, the exposure of hydrophobic residues on the surface of protein as well as the localization of the hydrophilic residues in the hydrophobic core is treated as potential area ready to interact with external molecules. The model based on the “fuzzy oil drop” approach treating the protein molecule as the drop of hydrophobicity concentrated in the central part of structure with the hydrophobicity close to zero on the surface according to 3-dimensional Gauss function. The comparison with the observed hydrophobicy in particular protein reveals some irregularities. These irregularities seem to represent the aim-oriented localization.

hydrophobicity distribution, protein complexation, fuzzy-oil-drop model

Citation

Banach & Roterman, Bioinformation 4(3): 98-100 (2009)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.