Biomolecular response to hour-long ultralow field microwave radiation: An effective coarse-grained model simulation

Various electronic devices, which we commonly use, radiate microwaves. Such external perturbation influences the functionality of biomolecules. In an ultralow field, the cumulative response of a molecule is expected only over a time scale of hours. To study the structural dynamics of biomolecules over hours, we adopt a simple methodology for constructing the coarse-grained structure of the protein molecule and solve the Langevin equation under different working potentials. In this approach, each amino acid residue of a biomolecule is mapped onto a number of beads, a few for the backbone, and few for the side chain, depending on the complexity of its chemical structure. We choose the force field in such a way that the dynamics of the protein molecule in the presence of ultralow radiation field of microvolt/nm could be followed over the time frame of 2 h. We apply the model to describe a biomolecule, hen egg white lysozyme, and simulate its structural evolution under ultralow strength electromagnetic radiation. The simulation revealed the finer structural details, like the extent of exposure of bioactive residues and the state of the secondary structures of the molecule, further confirmed from spectroscopic measurements [details are available in Phys. Rev. E 97, 052416 (2018) and briefly described here]. Though tested for a specific system, the model is quite general. We believe that it harnesses the potential in studying the structural dynamics of any biopolymer under external perturbation over an extended time scale.

Figure 1

Schematic diagrams to compare (a) the time scale followed by Voth [26, 27, 28, 29] and Martini CG model [23, 24, 25] and the same used in this study, and (b) the radiation power and time scale used by us and others to study the nonthermal effect of radiation, using false color scales.

Figure 2

(a) Chemical structure of arginine (Arg) residue of HEWL. (b) The positions of beads (red) and bonds (black) for Arg in the CG model in the backdrop of the stick representation of the same chemical structure shown in (a).

Figure 3

(a) Reduced representations for all amino acid residues of HEWL. (b) Atomistic structure of the HEWL following the PDB file of 6LYZ. (c) Reduced structure of HEWL protein.

Figure 4

A sketch to describe some of the FFs in our model, using the cartoon diagrams of three residues, marked as 1, 2, and 3 (not along the chain). The beads in each residue are connected by covalent bonds, represented by olive colored springs, to form the CG structure. The noncovalent interactions between a reference bead (red) in the residue (1) and beads (blue) representing two other amino acid residues (2 and 3) act within the cutoff radius $r_c$ (cyan shaded area).

Figure 5

Characteristic Raman spectra of (a) native HEWL and (b) the sample irradiated for 30 min are shown by solid black lines. Deconvoluted components are shown by green lines, and the net fitted spectra by solid red lines.

Figure 6

Simulated time (dimensionless) variation of (a) $\mathrm{\Delta }{R}_1$ (blue + symbols and right scale) and $R_2$ (green color filled sphere and left scale) as defined in the text, (b) time derivative of $R_2$ (black symbols) and low-pass filtered derivative (solid red line), (c) ΔASA (black symbols) and low-pass filtered ΔASA (solid red line). $\mathrm{\Delta }{R}_1, \mathrm{\Delta }{R}_2, d{R}_2/dt$, ΔASA are dimensionless simulated parameters. (d) Spectroscopically measured variation of the peak width (${\mathrm{\Gamma }}_{1447}$) of ${\mathrm{CH}}_2$ vibration at $1447\mathrm{c}{\mathrm{m}}^{-1}$, indicating a change in the topology of the molecule in the radiation field (symbols are experimental data points, and the solid line joins the data points). Error bar to each data point is the standard deviation of ${\mathrm{\Gamma }}_{1447}$ as a fitting parameter, obtained from the curve fitting procedure.

Figure 7

(a) ϕ angle and (b) ψ angle distributions in the modeled protein structure at simulation time $t_s=0$. Solid red lines are fitted curve using a Gaussian function for unimodal distribution of the ϕ angle and two Gaussian functions for a bimodal distribution of ψ angle. The same at other simulation times (with $\times {10}^6$ and mentioned in the panels) are plotted in (c)–(l). Simulated secondary structures at the corresponding time are shown in the extreme right panel.

Figure 8

(a) Simulated time (dimensionless) variation of $\mathrm{\Delta }{\mathrm{ASA}}_{\mathrm{Trp}}$ (dimensionless) of Trp molecule (connecting black filled symbols) and low-pass filtered data points (solid red line). (b) Spectroscopically measured variation of peak intensity (${\mathrm{I}}_{760}$) of the Raman mode of Trp at $760\mathrm{c}{\mathrm{m}}^{-1}$ from analysis of the Raman spectra in Fig. S1 [61], indicating modulation in the exposure of the residues with time in the radiation field (symbols are experimental data points and the solid line joins the data points). The error bar to each data point is the standard deviation of the peak intensity as the free fitting parameter in the curve fitting procedure.