Hydrophobic collapse in (in silico) protein folding

TitleHydrophobic collapse in (in silico) protein folding
Publication TypeJournal Article
Year of Publication2006
AuthorsBrylinski M, Konieczny L, Roterman I
JournalComput Biol Chem
Volume30
Issue4
Pagination255-67
Date Published2006 Aug
ISSN1476-9271
KeywordsAmino Acids, Computational Biology, Computer Simulation, Hydrophobic and Hydrophilic Interactions, Ligands, Models, Chemical, Models, Molecular, Oils, Particle Size, Protein Folding, Proteins
Abstract

A model of hydrophobic collapse, which is treated as the driving force for protein folding, is presented. This model is the superposition of three models commonly used in protein structure prediction: (1) 'oil-drop' model introduced by Kauzmann, (2) a lattice model introduced to decrease the number of degrees of freedom for structural changes and (3) a model of the formation of hydrophobic core as a key feature in driving the folding of proteins. These three models together helped to develop the idea of a fuzzy-oil-drop as a model for an external force field of hydrophobic character mimicking the hydrophobicity-differentiated environment for hydrophobic collapse. All amino acids in the polypeptide interact pair-wise during the folding process (energy minimization procedure) and interact with the external hydrophobic force field defined by a three-dimensional Gaussian function. The value of the Gaussian function usually interpreted as a probability distribution is treated as a normalized hydrophobicity distribution, with its maximum in the center of the ellipsoid and decreasing proportionally with the distance versus the center. The fuzzy-oil-drop is elastic and changes its shape and size during the simulated folding procedure.

Alternate JournalComputational Biology and Chemistry
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