Name
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. |
Year | DOI | Venue |
|---|---|---|
2006 | 10.1016/j.compbiolchem.2006.04.007 | Computational Biology and Chemistry |
Keywords | Field | DocType |
lattice model,protein folding,simulated folding procedure,driving force,hydrophobic collapse,hydrophobic character,hydrophobic core,late-stage folding,external hydrophobic force field,external force field,protein structure prediction,folding process,structural change,probability distribution,force field,amino acid,degree of freedom,three dimensional,energy minimization | Protein structure prediction,Protein folding,Thermodynamics,Hydrophobic collapse,Crystallography,Chemistry,Lattice protein,Downhill folding,Folding funnel,Contact order,Genetics,Energy minimization | Journal |
Volume | Issue | ISSN |
30 | 4 | 1476-9271 |
Citations | PageRank | References |
7 | 1.33 | 10 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Michal Brylinski | 1 | 124 | 12.16 |
| Leszek Konieczny | 2 | 67 | 22.55 |
| Irena Roterman | 3 | 78 | 30.08 |