Logo of Science Foundation Ireland  Logo of the Higher Education Authority, Ireland7 CapacitiesGPGPU Research Projects
Ireland's High-Performance Computing Centre | ICHEC
Home | News | Infrastructure | Outreach | Services | Research | Support | Education & Training | Consultancy | About Us | Login

Publication

Title:Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide
Authors:Gleb Y. Solomentsev, Niall J. English, Damian A. Mooney, 2012
Abstract: 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.
ICHEC Project:Electric and electromagnetic field effects on nanomaterial-protein systems
Publication:Journal of Computational Chemistry 33 (9), pp 917-923, April 2012
URL: http://dx.doi.org/10.1002/jcc.22912
Keywords: molecular dynamics; helix-coil transition; electromagnetic field; hydrogen bonding; conformational entropy
Status: Published

return to publications list