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

TitleHydrophobic collapse in late-stage folding (in silico) of bovine pancreatic trypsin inhibitor
Publication TypeJournal Article
Year of Publication2006
AuthorsBrylinski M, Konieczny L, Roterman I
Date Published2006 Sep
KeywordsAnimals, Cattle, Computer Simulation, Hydrophobic and Hydrophilic Interactions, Models, Biological, Models, Molecular, Pancreas, Protein Folding, Trypsin Inhibitors

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.

Alternate JournalBiochimie
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