Molecular dynamics simulation of the stability of a 22-residue alpha-helix in water and 30% trifluoroethanol.
A molecular dynamics (MD) simulation was performed on the alpha-helix H8-HC5, the C-terminal part of myoglobin (residue 132-153), under periodic boundary conditions in two different solutions, water and water with 30% (v/v) 2,2,2-trifluoroethanol (TFE), at 300 K to investigate the stability of the helix. In both simulations, the initial configuration was a canonical right-handed alpha-helix. In the course of the MD trajectory in water (200 ps), the helix clearly destabilized and began to unfold after 100 ps. In the TFE solution, two stable parts of helical regions were observed after 70 ps of a 200-ps MD simulation, supporting the notion that TFE acts as a structure-forming solvent.
Van Buuren
A R
AR
BIOSON Research Institute, Groningen, The Netherlands.
Berendsen
H J
HJ
D000595:Amino Acid Sequence; D003198:Computer Simulation; D004355:Drug Stability; D008969:Molecular Sequence Data; D009211:Myoglobin / Q000737:chemistry; D010446:Peptide Fragments / Q000737:chemistry; D017433:Protein Structure, Secondary; D012996:Solutions; D013816:Thermodynamics; D014270:Trifluoroethanol / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D009211:Myoglobin; D010446:Peptide Fragments; D012996:Solutions; D014867:Water; D014270:Trifluoroethanol