Localization of ligand binding site in proteins identified in silico

TitleLocalization of ligand binding site in proteins identified in silico
Publication TypeJournal Article
Year of Publication2007
AuthorsBrylinski M, Kochanczyk M, Broniatowska E, Roterman I
JournalJ Mol Model
Volume13
Issue6-7
Pagination665-75
Date Published2007 Jul
ISSN0948-5023
KeywordsBinding Sites, Computer Simulation, Hydrophobic and Hydrophilic Interactions, Knowledge Bases, Ligands, Models, Chemical, Models, Molecular, Protein Binding, Protein Folding, Protein Structure, Secondary, Proteins
Abstract

Knowledge-based models for protein folding assume that the early-stage structural form of a polypeptide is determined by the backbone conformation, followed by hydrophobic collapse. Side chain-side chain interactions, mostly of hydrophobic character, lead to the formation of the hydrophobic core, which seems to stabilize the structure of the protein in its natural environment. The fuzzy-oil-drop model is employed to represent the idealized hydrophobicity distribution in the protein molecule. Comparing it with the one empirically observed in the protein molecule reveals that they are not in agreement. It is shown in this study that the irregularity of hydrophobic distributions is aim-oriented. The character and strength of these irregularities in the organization of the hydrophobic core point to the specificity of a particular protein's structure/function. When the location of these irregularities is determined versus the idealized fuzzy-oil-drop, function-related areas in the protein molecule can be identified. The presented model can also be used to identify ways in which protein-protein complexes can possibly be created. Active sites can be predicted for any protein structure according to the presented model with the free prediction server at http://www.bioinformatics.cm-uj.krakow.pl/activesite. The implication based on the model presented in this work suggests the necessity of active presence of ligand during the protein folding process simulation.

Alternate JournalJournal of Molecular Modeling
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