- Article -
| In Silico Biology 6, 0002 (2006); ©2006, Bioinformation Systems e.V. |
Gauss-function-based model of hydrophobicity density in proteins
Leszek Konieczny1, Michal Brylinski2 and Irena Roterman3*
1 Institute of Biochemistry, Collegium Medicum – Jagiellonian University, Kopernika 7, 31-034 Cracow, Poland
Email: mbkoniec@cyf-kr.edu.pl
2 Department of Bioinformatics and Telemedicine, Collegium Medicum – Jagiellonian University, Kopernika 17, 31-501 Cracow, Poland
Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
Email: brylinsk@chemia.uj.edu.pl
3 Department of Bioinformatics and Telemedicine, Collegium Medicum – Jagiellonian University, Kopernika 17, 31-501 Cracow, Poland
Faculty of Physics, Jagiellonian University, Reymonta 4, 30-060 Krakow, Poland
Email: myroterm@cyf-kr.edu.pl
* Corresponding author
Edited by E. Wingender; received September 29, 2005; revised November 14, 2005; accepted November 26, 2005; published January 23, 2006
Abstract
The model adopting the three-dimensional Gauss function to express the hydrophobicity distribution in proteins is presented in this paper. The tendency to create the hydrophobic center during protein folding is expressed in form of an external force field of the form of three-dimensional Gauss function which directs the folding polypeptide to locate the hydrophobic residues in a central part of the molecule and hydrophilic ones exposed toward the molecular surface. The decrease of the differences between hydrophobicity distribution as it appears at each step of the folding simulation and the expected hydrophobicity distribution (three-dimensional Gauss function) is the convergence criterion together with traditional non-bonding interaction optimization. The model was applied to fold the hypothetical membrane protein (target protein in CASP6) TA0354_69_121 from Thermoplasma acidophilum.
Keywords: protein folding, hydrophobicity, hydrophobic collapse, Gauss function, CASP, protein structure prediction