Hydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor

Biochimie
M BrylińskiI Roterman

Abstract

Hydrophobic collapse is commonly considered as a process of significance for protein folding. Many models have been applied for description of this event. A model introducing an external force field mimicking the hydrophobic environment and simultaneously the driving force for the folding process is presented in this paper. Bovine pancreatic trypsin inhibitor (BPTI) was taken as a test protein. An early-stage folding (in silico) model presented elsewhere was used to create the starting structure for hydrophobic collapse. The resulting structure was energy-refined using molecular dynamics simulation in an explicit solvent. The similarity versus the crystal structure of BPTI is estimated using visual analysis, residue-residue contacts, phi, psi angle distributions, RMSD, accessible solvent area, radii of gyration and hydrodynamic radii. A program allowing creation of early-stage folding structural forms to be created for any protein is available from http://bioinformatics.cm-uj.krakow.pl/earlystage. The program for late-stage folding simulation is available on request.

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Citations

Mar 31, 2007·Journal of Molecular Modeling·Michal BrylinskiIrena Roterman
Jan 20, 2010·Journal of Molecular Modeling·Katarzyna PrymulaIrena Roterman
May 29, 2007·PLoS Computational Biology·Michał BrylińskiIrena Roterman
Apr 29, 2009·International Journal of Molecular Sciences·Mateusz BanachIrena Roterman
Sep 29, 2011·International Journal of Molecular Sciences·Irena RotermanWiktor Jurkowski
Mar 9, 2011·Bioinformation·Mateusz BanachIrena Roterman
Jul 20, 2011·Bioinformation·Damian MarchewkaIrena Roterman
May 21, 2009·Proteins·Veronica Zobnina, Irena Roterman
Feb 18, 2010·Protein Science : a Publication of the Protein Society·Olivia Doppelt-AzeroualAlexandre G de Brevern
Jun 27, 2006·Computational Biology and Chemistry·Michal BrylinskiIrena Roterman

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