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.

Hydrogen bond perturbation in hen egg white lysozyme by external electromagnetic fields: a nonequilibrium molecular dynamics study.

Nonequilibrium molecular dynamics simulations of a charge-neutral mutant of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of external microwave fields (2.45 to 100 GHz) of an rms electric field intensity of 0.05 V Å(-1). A systematic study was carried out of the distributions of persistence times and energies of each intraprotein hydrogen bond in between breakage and reformation, in addition to overall persistence over 20 ns simulations, vis-á-vis equilibrium, zero-field conditions. It was found that localized translational motion for formally charged residues led to greater disruption of associated hydrogen bonds, although induced rotational motion of strongly dipolar residues also led to a degree of hydrogen bond perturbation. These effects were most apparent in the solvent exposed exterior of hen egg white lysozyme, in which the intraprotein hydrogen bonds tend to be weaker.

Nonequilibrium molecular dynamics study of electric and low-frequency microwave fields on hen egg white lysozyme.

Nonequilibrium molecular dynamics simulations of various mutants of hen egg white lysozyme have been performed at 300 K and 1 bar in the presence of both external static electric and low-frequency microwave (2.45 GHz) fields of varying intensity. Significant nonthermal field effects were noted, such as marked changes in the protein's secondary structure relative to the zero-field state, depending on the field conditions, mutation, and orientation with respect to the applied field. This occurred primarily as a consequence of alignment of the protein's total dipole moment with the external field, although the dipolar alignment of water molecules in both the solvation layer and the bulk was also found to be influential. Substantial differences in behavior were found for proteins with and without overall net charges, particularly with respect to translational motion. Localized motion and perturbation of hydrogen bonds were also found to be evident for charged residues.