Conformational polymorphism of the PrP106-126 peptide in different environments: a molecular dynamics study.
Extensive molecular dynamic simulations (approximately 240 ns) have been used to investigate the conformational behavior of PrP106-126 prion peptide in four different environments (water, dimethyl sulfoxide, hexane, and trifluoroethanol) and under both neutral and acidic conditions. The conformational polymorphism of PrP106-126 in solution observed in the simulations supports the role of this fragment in the structural transition of the native to the abnormal form of prion protein in response to changes in the local environmental conditions. The peptide in solution is primarily unstructured. The simulations show an increased presence of helical structure in an apolar solvent, in agreement with the results from circular dichroism spectroscopy. In water solution, beta-sheet elements were observed between residues 108-112 and either residues 115-121 or 121-126. An alpha-beta transition was observed under neutral conditions. In DMSO, the peptide adopted an extended conformation, in agreement with nuclear magnetic resonance experiments.
Villa
Alessandra
A
Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands. villa@theochem.uni-frankfurt.de
Mark
Alan E
AE
Saracino
Gloria A A
GA
Cosentino
Ugo
U
Pitea
Demetrio
D
Moro
Giorgio
G
Salmona
Mario
M
D003198:Computer Simulation; D004121:Dimethyl Sulfoxide / Q000737:chemistry*; D006586:Hexanes / Q000737:chemistry*; D006801:Humans; D006863:Hydrogen-Ion Concentration; D009682:Magnetic Resonance Spectroscopy / Q000379:methods / Q000592:standards; D008956:Models, Chemical; D010446:Peptide Fragments / Q000737:chemistry*; D011328:Prions / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D012015:Reference Standards; D012680:Sensitivity and Specificity; D013997:Time Factors; D014270:Trifluoroethanol / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D006586:Hexanes; D010446:Peptide Fragments; D011328:Prions; C082632:prion protein (106-126); D014867:Water; D014270:Trifluoroethanol; D004121:Dimethyl Sulfoxide