Sequence-Structure-Function Relation Characterized in silico

Article type: Research Article

Authors: Brylinski, Michal^; | Kochanczyk, Marek | Konieczny, Leszek | Roterman, Irena^;

Affiliations: Department of Bioinformatics and Telemedicine, Collegium Medicum – Jagiellonian University, Kopernika 17, 31-501 Krakow, Poland | Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland | Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Reymonta 4, 30-059 Krakow, Poland | Chair of Biochemistry, Collegium Medicum – Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland

Note: [] Corresponding author. E-mail: [email protected]

Abstract: Methods for biological function recognition in silico appeared to be useful also for identifying characteristics of structure-to-function relations. The introduction of a three-dimensional Gauss function was assumed to represent the hydrophobic core in a protein molecule. The discrepancy between idealized "fuzzy oil-drop" and the observed one in real proteins appeared to be localized in the ligation site or in the area of biological function related part of protein molecule. The examples of proteins presented in this paper reveal that the structure-function relation can be evaluated and characterized also using the profile of the difference in value between idealized and real hydrophobicity distribution along the polypeptide chain. The specificity of particular polypeptide chain fragments in respect to their biological function and their specific participation in active site creation is discussed in this paper. The scale allowing comparison of different proteins in respect to their ligand-binding sites characteristics is introduced.

Keywords: Hydrophobicity, biological function, active site, proteins of unknown biological function

Journal: In Silico Biology, vol. 6, no. 6, pp. 589-600, 2006