Affiliations: Institute of Biochemistry, Collegium Medicum,
Jagiellonian University, Kopernika 7, 31-034 Cracow, Poland. E-mail:
[email protected] | Department of Bioinformatics and Telemedicine,
Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Cracow,
Poland, and Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060
Cracow, Poland. E-mail: [email protected]' | Department of Bioinformatics and Telemedicine,
Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Cracow,
Poland, and Faculty of Physics, Jagiellonian University, Reymonta 4, 30-060
Krakow, Poland. E-mail: [email protected]
Note: [] Corresponding author
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
