title: Sequence-structure-function relation characterized in silico.
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.
authors.affiliation: Department of Bioinformatics and Telemedicine, Collegium Medicum - Jagiellonian University, Kopernika, Krakow, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Brylinski
authors.forename: Marek
authors.initials: M
authors.lastname: Kochanczyk
authors.forename: Leszek
authors.initials: L
authors.lastname: Konieczny
authors.forename: Irena
authors.initials: I
authors.lastname: Roterman
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D030562:Databases, Protein; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D013816:Thermodynamics
chemical_list: D001426:Bacterial Proteins; D008024:Ligands