PHYS 547 |
| A stabilizing dipole exists throughout any polypeptide helix. Polar side chain properties contribute to this effect through increased electronegativity; non-polar side chains are destabilizing. We previously performed molecular dynamics (MD) simulations via CHARMM, which illustrated the stabilization of gas-phase polyalanine helices via N-terminal cysteine-capping. We report results of Replica Exchange Molecular Dynamics (REX-MD) simulations to study this enhancement in biologically relevant helical moieties. We examined a helical segment from YAP1 alcohol oxidase from Saccharomyces cerevisiae in this study. We showed that the presence of an N-terminal cysteine increased the likelihood of successful folding in properly simulated solvent environments. Standard CHARMM techniques were used to minimize these structures. A Generalized Born (GB) force field was utilized to implicitly mimic solvent properties of water and we also performed an explicit simulation using TIP3 water molecules. Energetic and structural output detected any stabilizing affects instilled in the sequence. |
|
PHYS Poster Session - General Theory
7:30 PM-10:00 PM, Wednesday, April 9, 2008 Morial Convention Center -- Hall A, Poster
Sci-Mix
Division of Physical Chemistry |