Gauss-function-based model of hydrophobicity density in proteins

TitleGauss-function-based model of hydrophobicity density in proteins
Publication TypeJournal Article
Year of Publication2006
AuthorsKonieczny L, Brylinski M, Roterman I
JournalIn Silico Biol
Volume6
Issue1-2
Pagination15-22
Date Published2006
ISSN1386-6338
KeywordsComputer Simulation, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Membrane Proteins, Models, Molecular, Normal Distribution, Protein Conformation, Protein Folding, Proteins, Thermoplasma
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.

Alternate JournalIn Silico Biology (Gedrukt)
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