Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide.
Non-equilibrium molecular dynamics simulations of a solvated 21-residue polyalanine (A21) peptide, featuring a high propensity for helix formation, have been performed at 300 K and 1 bar in the presence of external electromagnetic (e/m) fields in the microwave region (2.45 GHz) and an r.m.s. electric field intensity range of 0.01-0.05 V/Å. To investigate how the field presence affects transitions between the conformational states of a protein, we report 16 independent 40 ns-trajectories of A21 starting from both extended and fully folded states. We observe folding-behavior of the peptide consistent with prior simulation and experimental studies. The peptide displays a natural tendency to form stable elements of secondary structure which are stabilized by tertiary interactions with proximate regions of the peptide. Consistent with our earlier work, the presence of external e/m fields disrupts this behavior, involving a mechanism of localized dipolar alignment which serves to enhance intra-protein perturbations in hydrogen bonds (English, et al., J. Chem. Phys. 2010, 133, 091105), leading to more frequent transitions between shorter-lifetime states.
School of Chemical and Bioprocess Engineering, The Centre for Synthesis and Chemical Biology, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland.
Gleb Y
GY
Solomentsev
Niall J
NJ
English
Damian A
DA
Mooney
D004574:Electromagnetic Fields; D019277:Entropy; D006860:Hydrogen Bonding; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary
D010455:Peptides; C019529:polyalanine