Effects of external electromagnetic fields on the conformational sampling of a short alanine peptide

Molecular dynamics simulations explore effects of electric field orientations on spike proteins of SARS-CoV-2 virions

Emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its current worldwide spread have caused a pandemic of acute respiratory disease COVID-19. The virus can result in mild to severe, and even to fatal respiratory illness in humans, threatening human health and public safety. The spike (S) protein on the surface of viral membrane is responsible for viral entry into host cells. The discovery of methods to inactivate the entry of SARS-CoV-2 through disruption of the S protein binding to its cognate receptor on the host cell is an active research area. To explore other prevention strategies against the quick spread of the virus and its mutants, non-equilibrium molecular dynamics simulations have been employed to explore the possibility of manipulating the structure–activity of the SARS-CoV-2 spike glycoprotein by applying electric fields (EFs) in both the protein axial directions and in the direction perpendicular to the protein axis. We have found out the application of EFs perpendicular to the protein axis is most effective in denaturing the HR2 domain which plays critical role in viral-host membrane fusion. This finding suggests that varying irradiation angles may be an important consideration in developing EF based non-invasive technologies to inactivate the virus.

Conformational Dynamics of Glucagon-like Peptide-2 with Different Electric Field

Molecular dynamics (MD) simulation was used to study the influence of electric field on Glucagon-like Peptide-2 (GLP-2). Different electric field strengths (0 V/nm ≤ E ≤ 1 V/nm) were mainly carried out on GLP-2. The structural changes in GLP-2 were analyzed by the Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Radius of Gyration (Rg), Solvent Accessible Surface Area (SASA), Secondary Structure and the number of hydrogen bonds. The stable α—helix structure of GLP-2 was unwound and transformed into an unstable Turn and Coil structure since the stability of the GLP-2 protein structure was reduced under the electric field. Our results show that the degree of unwinding of the GLP-2 structure was not linearly related to the electric field intensity. E = 0.5 V/nm was a special point where the degree of unwinding of the GLP-2 structure reached the maximum at this electric field strength. Under a weak electric field, E < 0.5 V/nm, the secondary structure of GLP-2 becomes loose, and the entropy of the chain increases. When E reaches a certain value (E > 0.5 V/nm), the electric force of the charged residues reaches equilibrium, along the z-direction. Considering the confinement of moving along another direction, the residue is less free. Thus, entropy decreases and enthalpy increases, which enhance the interaction of adjacent residues. It is of benefit to recover hydrogen bonds in the middle region of the protein. These investigations, about the effect of an electric field on the structure of GLP-2, can provide some theoretical basis for the biological function of GLP-2 in vivo.

Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies

The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary structure analysis were used to assess the protein samples’ structural characteristics. In the simulation, we found that the higher frequency of the electric field influences the rapid response to the secondary structural transitions. However, the conformational changes measured by RMSD are diminished by applying the electrical field with a higher frequency. During the dipole moment analysis, we found that the magnitude and frequency of the dipole moment was directly related to the strength and frequency of the external electric field. In terms of the type of electric fields, we found that the average values of RMSD and RMSF of whole molecular protein are larger when the protein is exposed in the pulsed electric field. Concerning the typical sample 1BBL, the secondary structure analysis showed that two alpha-helix segments both transit to turns or random coils almost simultaneously when it is exposed in a pulsed electric field. Meanwhile, two segments present the different characteristic times when the transition occurs in the condition of an oscillating electric field. This study also demonstrated that the protein with fewer charged residues or more residues in forming α-helical structures display the higher conformational stability. These conclusions, achieved using MD simulations, provide a theoretical understanding of the effect of the frequency and expression form of external electric fields on the conformational changes of the all-α proteins with charged residues and the guidance for anticipative applications.

Local Electric Field Changes during the Photoconversion of the Bathy Phytochrome Agp2

Phytochromes switch between a physiologically inactive and active state via a light-induced reaction cascade, which is initiated by isomerization of the tetrapyrrole chromophore and leads to the functionally relevant secondary structure transition of a protein segment (tongue). Although details of the underlying cause-effect relationships are not known, electrostatic fields are likely to play a crucial role in coupling chromophores and protein structural changes. Here, we studied local electric field changes during the photoconversion of the dark state Pfr to the photoactivated state Pr of the bathy phytochrome Agp2. Substituting Tyr165 and Phe192 in the chromophore pocket by para-cyanophenylalanine (pCNF), we monitored the respective nitrile stretching modes in the various states of photoconversion (vibrational Stark effect). Resonance Raman and IR spectroscopic analyses revealed that both pCNF-substituted variants undergo the same photoinduced structural changes as wild-type Agp2. Based on a structural model for the Pfr state of F192pCNF, a molecular mechanical-quantum mechanical approach was employed to calculate the electric field at the nitrile group and the respective stretching frequency, in excellent agreement with the experiment. These calculations serve as a reference for determining the electric field changes in the photoinduced states of F192pCNF. Unlike F192pCNF, the nitrile group in Y165pCNF is strongly hydrogen bonded such that the theoretical approach is not applicable. However, in both variants, the largest changes of the nitrile stretching modes occur in the last step of the photoconversion, supporting the view that the proton-coupled restructuring of the tongue is accompanied by a change of the electric field.

Reproducibility in the unfolding process of protein induced by an external electric field

The dynamics of proteins are crucial for their function. However, commonly used techniques for studying protein structures are limited in monitoring time-resolved dynamics at high resolution. Combining electric fields with existing techniques to study gas-phase proteins, such as single particle imaging using free-electron lasers and gas-phase small angle X-ray scattering, has the potential to open up a new era in time-resolved studies of gas-phase protein dynamics. Using molecular dynamics simulations, we identify well-defined unfolding pathways of a protein, induced by experimentally achievable external electric fields. Our simulations show that strong electric fields in conjunction with short-pulsed X-ray sources such as free-electron lasers can be a new path for imaging dynamics of gas-phase proteins at high spatial and temporal resolution.

Elucidating the Effect of Static Electric Field on Amyloid Beta 1-42 Supramolecular Assembly

Amyloid-β (Aβ) aggregation is recognized to be a key toxic factor in the pathogenesis of Alzheimer disease, which is the most common progressive neurodegenerative disorder. In vitro experiments have elucidated that Aβ aggregation depends on several factors, such as pH, temperature and peptide concentration. Despite the research effort in this field, the fundamental mechanism responsible for the disease progression is still unclear. Recent research has proposed the application of electric fields as a non-invasive therapeutic option leading to the disruption of amyloid fibrils. In this regard, a molecular level understanding of the interactions governing the destabilization mechanism represents an important research advancement. Understanding the electric field effects on proteins, provides a more in-depth comprehension of the relationship between protein conformation and electrostatic dipole moment. The present study focuses on investigating the effect of static Electric Field (EF) on the conformational dynamics of Aβ fibrils by all-atom Molecular Dynamics (MD) simulations. The outcome of this work provides novel insight into this research field, demonstrating how the Aβ assembly may be destabilized by the applied EF.

Effects of an Electric Field on the Conformational Transition of the Protein: A Molecular Dynamics Simulation Study

The effect of the electric field on the conformational properties of the protein 1BBL was investigated by molecular dynamics simulations. Our simulation results clearly capture the structural transitions of the protein sample from helix to turn or random coil conformation induced by the increasing strength of the electric field. During our analysis, we found that the conformational stability is weakened, and the protein sample is stretched as an unfolded structure when it was exposed in a sufficiently high electric field. The characteristic time when the jump occurs in the time evolution curves of root mean square deviation (RMSD) and radius of gyration R_g decreases with increasing electric strength, which demonstrates the rapidly conformational transition that occurs. The number of intra-protein hydrogen bonds, which is the key factor for stabilizing the protein structure, is related to the overall size of the protein. The value of the dipole moment and characteristic time are both influenced by the strength, but are independent of the direction of the external field. The protein sample becomes rotated with the electric field direction. These conclusions provide a theoretical realization of understanding the protein conformational transition in an electric field and the guidance for anticipative applications.

An NMR Confirmation for Increased Folded State Entropy Following Loop Truncation

Previous studies conducted on flexible loop regions in proteins revealed that the energetic consequences of changing loop length predominantly arise from the entropic cost of ordering a loop during folding. However, in an earlier study of human acylphosphatase (hmAcP) using experimental and computational approaches, we showed that thermodynamic stabilization upon loop truncation can be attributed mainly to the increased entropy of the folded state. Here, using 15N NMR spectroscopy, we studied the effect of loop truncation on hmAcP backbone dynamics on the picosecond-nanosecond timescale with the aim of confirming the effect of folded state entropy on protein stability. NMR-relaxation-derived N-H squared generalized order parameters reveal that loop truncation results in a significant increase in protein conformational flexibility. Comparison of these results with previously acquired all-atom molecular dynamics simulation, analyzed here in terms of squared generalized NMR order parameters, demonstrates general agreement between the two methods. The NMR study not only provides direct evidence for the enhanced conformational entropy of the folded state of hmAcP upon loop truncation but also gives a quantitative measure of the observed effects.

Generation and propagation of yeast prion [URE3] are elevated under electromagnetic field

In this study, we studied the effect of 2.0 GHz radio frequency electromagnetic field (RF-EMF) and 50 Hz extremely low frequency electromagnetic field (ELF-EMF) exposure on prion generation and propagation using two budding yeast strains, NT64C and SB34, as model organisms. Under exposure to RF-EMF or ELF-EMF, the de novo generation and propagation of yeast prions [URE3] were elevated in both strains. The elevation increased over time, and the effects of ELF-EMF occurred in a dose-dependent manner. The transcription and expression levels of the molecular chaperones Hsp104, Hsp70-Ssa1/2, and Hsp40-Ydj1 were not statistically significantly changed after exposure. Furthermore, the levels of ROS, as well as the activities of superoxide dismutase (SOD) and catalase (CAT), were significantly elevated after short-term, but not long-term exposure. This work demonstrated for the first time that EMF exposure could elevate the de novo generation and propagation of yeast prions and supports the hypothesis that ROS may play a role in the effects of EMF on protein misfolding. The effects of EMF on protein folding and ROS levels may mediate the broad effects of EMF on cell function.

Deconstruction of the human connexin 26 hemichannel due to an applied electric field; A molecular dynamics simulation study

Connexins are a 21-member membrane protein family constituting channels evolved in direct communication between adjacent cells by passaging cytoplasmic molecules and ions. Hexametrical assembly of connexin proteins in plasma membrane forms a wide aqueous pore known as connexin hemichannel. These hemichannels mediate cytoplasm and extracellular milieu communication both in many external tissues and in the central nervous system. In this study, a series of molecular dynamics simulations has been performed to investigate the effect of applied static and alternating electric fields on the stability and conformation of human connexin26 hemichannel. The root mean square deviations of C-alpha atoms, the dipole moment distribution, the number of inter-protein hydrogen bonds and the number of water-protein hydrogen bonds were used to assess connexin26 hemichannel stability. In the static field case, our results show that although the lowest field used in this study (0.1V/nm) does not lead to the hemichannel deconstruction, stronger fields (>0.1V/nm), however, disrupt the protein structure during the simulations time period. Furthermore, in the alternating case, compared to static field case, field effects on the connexin26 hemichannel conformation are reduced and consequently the protein maintains its native structure for longer times. Specifically, for the highest frequency used in this study (50GHz), the hemichannel keeps its structure even under the effect of the strongest field (0.4V/nm). According to our results, the protein secondary structure is preserved in the characteristic times determined for the protein deconstruction. Consequently, we suggest that the protein deconstruction is due to the tertiary and quaternary structure loss.

Electromagnetic-field effects on structure and dynamics of amyloidogenic peptides

Electromagnetic fields (EMFs) are ever-present, and so is the need to better understand their influence on human health and biological matter in general. The interaction between a molecular system and external EMF can alter the structure, and dynamical behaviour, and, hence, biological function of proteins with uncertain health consequences. This urges a detailed investigation of EMF-induced effects on basic protein biophysics. Here, we used all-atom non-equilibrium molecular dynamics simulations to understand and quantify the response mechanisms of the amyloidogenic apoC-II(60-70) peptides to non-ionising radiation by modelling their behaviour under external electromagnetic and electric fields of different strengths. Our simulations show high strength fields (>0.04 V/nm) cause structural changes in apoC-II(60-70) due to the peptide dipole alignment along the applied field direction, which disrupts the inherent β-hairpin conformation known to be the intermediate state for fibril formation. The intermediate field-strength range (0.04-0.004 V/nm) causes a significant acceleration in peptide dynamics, which leads to the increased population of structures with fibril-inhibiting characteristics, such as the separated N- and C-termini and colocation of the aromatic residues at the same peptide face. In contrast, lower field strengths (<0.004 V/nm) promote the formation of the amyloid-prone hairpin structures relative to the ambient conditions. These findings suggest that intermediate-strength electromagnetic fields could be considered for designing alternative treatments of amyloid diseases, while the very high and low field strengths could be employed for engineering well-ordered fibrillar aggregates for non-medicinal applications.

Perspectives on external electric fields in molecular simulation: progress, prospects and challenges

In this review, the application of a wide variety of external electric fields in molecular simulation shall be discussed, including time-varying and electromagnetic, as well as the utility and potential impact and prospects for exploitation of such simulations for real-world and industrial end use. In particular, non-equilibrium molecular dynamics will be discussed, as well as challenges in addressing adequate thermostatting and scaling field amplitudes to more experimentally relevant levels. Attention shall be devoted to recent progress and advances in external fields in ab initio molecular simulation and dynamics, as well as elusive challenges thereof (and, to some extent, for molecular dynamics from empirical potentials), such as timescales required to observe low-frequency and intensity field effects. The challenge of deterministic molecular dynamics in external fields in sampling phase space shall be discussed, along with prospects for application of fields in enhanced-sampling simulations. Finally, the application of external electric fields to a wide variety of aqueous, nanoscale and biological systems will be discussed, often motivated by the possibility of exploitation in real-world applications, which serve to underpin our molecular-level understanding of field effects in terms of microscopic mechanisms, and possibly with a view to control thereof.

Real-time assessment of possible electromagnetic-field-induced changes in protein conformation and thermal stability

Previous studies on possible interactions of radiofrequency electromagnetic fields (RF EMFs) with proteins have suggested that RF EMFs might affect protein structure and folding kinetics. In this study, the isolated thermosensor protein GrpE of the Hsp70 chaperone system of Escherichia coli was exposed to EMFs of various frequencies and field strengths under strictly controlled conditions. Circular dichroism spectroscopy was used to monitor possible structural changes. Simultaneously, temperature was recorded at each point of observation. The coiled-coil part of GrpE has been reported to undergo a well-defined and fully reversible folding/unfolding transition, thus facilitating the differentiation between thermal and non-thermal effects of RF EMFs. Any direct effect of EMF on the conformation and/or stability would result in a shift of the conformational equilibrium of the protein at a given temperature. Possible immediate (t ≤ 0.1 s) and delayed (t ≥ 30 s) effects of RF EMFs were investigated with sinusoidal signals of 0.1, 1.0, and 1.9 GHz at various field strengths up to 5.0 kV/m and with GSM signals at 0.3 kV/m in the protein solution. Taking the overall uncertainty of the experimental system into account, possible RF EMF-induced shifts in the conformational equilibrium of less than 1% of its total range might have been detected. The results obtained with the different experimental protocols indicate, however, that the conformational equilibrium of GrpE is insensitive to electromagnetic fields in the tested range of frequency and field strength.

Electric field effects on alanine tripeptide in sodium halide solutions

The electric field effects on conformational properties of trialanine in different halide solutions were explored with long-scale molecular dynamics simulations. NaF, NaCl, NaBr and NaI solutions of low (0.2 M) and high (2 M) concentrations were exposed to a constant electric field of 1000 V/m. Generally, the electric field does not disturb trialanine's structure. Large structural changes appear only in the case of the supersaturated 2.0 M NaF solution containing NaF crystals. Although the electric field affects in a complex way, all the ions-water-peptide interactions, it predominantly affects the electroselectivity effect, which describes specific interactions such as the ion-pair formation.