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Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide
Author(s) -
Solomentsev Gleb Y.,
English Niall J.,
Mooney Damian A.
Publication year - 2012
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.22912
Subject(s) - chemistry , peptide , molecular dynamics , dipole , protein folding , helix (gastropod) , chemical physics , electromagnetic field , folding (dsp implementation) , crystallography , physics , computational chemistry , quantum mechanics , ecology , biochemistry , organic chemistry , snail , electrical engineering , biology , engineering
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. © 2012 Wiley Periodicals, Inc.