Nanosecond pulsed electric signals can affect electrostatic environment of proteins below the threshold of conformational effects: The case study of SOD1 with a molecular simulation study

An Infrared Nanospectroscopy Technique for the Study of Electric-Field-Induced Molecular Dynamics

Static electric fields play a considerable role in a variety of molecular nanosystems as diverse as single-molecule junctions, molecules supporting electrostatic catalysis, and biological cell membranes incorporating proteins. External electric fields can be applied to nanoscale samples with a conductive atomic force microscopy (AFM) probe in contact mode, but typically, no structural information is retrieved. Here we combine photothermal expansion infrared (IR) nanospectroscopy with electrostatic AFM probes to measure nanometric volumes where the IR field enhancement and the static electric field overlap spatially. We leverage the vibrational Stark effect in the polymer poly(methyl methacrylate) for calibrating the local electric field strength. In the relevant case of membrane protein bacteriorhodopsin, we observe electric-field-induced changes of the protein backbone conformation and residue protonation state. The proposed technique also has the potential to measure DC currents and IR spectra simultaneously, insofar enabling the monitoring of the possible interplay between charge transport and other effects.

Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field

Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.

Effect of Electric Field on α-Synuclein Fibrils: Revealed by Molecular Dynamics Simulations

The self-association of amylogenic proteins to the fibril form is considered a pivotal factor in the pathogenesis of neurodegenerative diseases, including Parkinson’s disease (PD). PD causes unintended or uncontrollable movements in its common symptoms. α-synuclein is the major cause of PD development and thus has been the main target of numerous studies to suppress and sequester its expression or effectively degrade it. Nonetheless, to date, there are no efficient and proven ways to prevent pathological protein aggregation. Recent investigations proposed applying an external electric field to interrupt the fibrils. This method is a non-invasive approach that has a certain benefit over others. We performed molecular dynamics (MD) simulations by applying an electric field on highly toxic fibrils of α-synuclein to gain a molecular-level insight into fibril disruption mechanisms. The results revealed that the applied external electric field induces substantial changes in the conformation of the α-synuclein fibrils. Furthermore, we show the threshold value for electric field strength required to completely disrupt the α-synuclein fibrils by opening the hydrophobic core of the fibril. Thus, our findings might serve as a valuable foundation to better understand molecular-level mechanisms of the α-synuclein fibrils disaggregation process under an applied external electric field.

Capturing the Polarization Response of Solvated Proteins under Constant Electric Fields in Molecular Dynamics Simulations

We capture and compare the polarization response of a solvated globular protein ubiquitin to static electric (E-fields) using atomistic molecular dynamics simulations. We collectively follow E-field induced changes, electrical and structural, occurring across multiple trajectories using the magnitude of the protein dipole vector (P_p ). E-fields antiparallel to P_p induce faster structural changes and more facile protein unfolding relative to parallel fields of the same strength. While weak E-fields (0.1-0.5 V/nm) do not unfold ubiquitin and produce a reversible polarization, strong E-fields (1-2 V/nm) unfold the protein through a pathway wherein the helix:β-strand interactions rupture before those for the β1-β5 clamp. Independent of E-field direction, high E-field induced structural changes are also reversible if the field is switched off before P_p exceeds 2 times its equilibrium value. We critically examine the dependence of water properties, protein rotational diffusion and E-field induced protein unfolding pathways on the thermostat/barostat parameters used in our simulations.

Mapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers

Protein kinases play central roles in cellular regulation by catalyzing the phosphorylation of target proteins. Kinases have inherent structural flexibility allowing them to switch between active and inactive states. Quantitative characterization of kinase conformational dynamics is challenging. Here, we use nanopore tweezers to assess the conformational dynamics of Abl kinase domain, which is shown to interconvert between two major conformational states where one conformation comprises three sub-states. Analysis of kinase-substrate and kinase-inhibitor interactions uncovers the functional roles of relevant states and enables the elucidation of the mechanism underlying the catalytic deficiency of an inactive Abl mutant G321V. Furthermore, we obtain the energy landscape of Abl kinase by quantifying the population and transition rates of the conformational states. These results extend the view on the dynamic nature of Abl kinase and suggest nanopore tweezers can be used as an efficient tool for other members of the human kinome.

Quantitative characterization of kinase conformational dynamics remains challenging. Here, the authors show that protein nanopore tweezers allow analyzing the conformational energy landscape and ligand binding of the Abl kinase domain.

A rationale for non-linear responses to strong electric fields in molecular dynamics simulations

Many approaches for calculation of the field-dependent electric properties of water solutions rely on the Onsager and Kirkwood theories of polar dielectrics. Such basic theories implicitly consider the electric field intensity to fulfill the so-called 'weak field conditions', i.e. to produce a linear response in the system. In this work we made use of molecular dynamics simulations to investigate possible non-linear effects induced by high intensity electric fields, specifically continuous wave bursts with nanosecond duration, comparing them with the ones predicted by the theory. We found that field intensities above 0.15 V nm^-1 produce remarkable nonlinear responses in the whole 100 MHz-100 GHz frequency window considered, with the onset of higher order polarization signals, which are the clear fingerprint of harmonic distorsions. That non-linear response turned out to depend on the considered frequency. We finally show that MD outcomes are consistent with a modelization based on an extended formulation of the Langevin function including a frequency-dependent parameter.

In-Cell Structural Biology by NMR: The Benefits of the Atomic Scale

In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.

Electromagnetic bioeffects: a multiscale molecular simulation perspective

Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.

Pulsed Power Applications for Protein Conformational Change and the Permeabilization of Agricultural Products

Pulsed electric fields (PEFs), which are generated by pulsed power technologies, are being tested for their applicability in food processing through protein conformational change and the poration of cell membranes. In this article, enzyme activity change and the permeabilization of agricultural products using pulsed power technologies are reviewed as novel, nonthermal food processes. Compact pulsed power systems have been developed with repetitive operation and moderate output power for application in food processing. Firstly, the compact pulsed power systems for the enzyme activity change and permeabilization are outlined. Exposure to electric fields affects hydrogen bonds in the secondary and tertiary structures of proteins; as a result, the protein conformation is induced to be changed. The conformational change induces an activity change in enzymes such as α-amylase and peroxidase. Secondly, the conformational change in proteins and the induced protein functional change are reviewed. The permeabilization of agricultural products is caused through the poration of cell membranes by applying PEFs produced by pulsed discharges. The permeabilization of cell membranes can be used for the extraction of nutrients and health-promoting agents such as polyphenols and vitamins. The electrical poration can also be used as a pre-treatment for food drying and blanching processes. Finally, the permeabilization of cell membranes and its applications in food processing are reviewed.

The SARS-CoV-2 spike protein is vulnerable to moderate electric fields

Most of the ongoing projects aimed at the development of specific therapies and vaccines against COVID-19 use the SARS-CoV-2 spike (S) protein as the main target. The binding of the spike protein with the ACE2 receptor (ACE2) of the host cell constitutes the first and key step for virus entry. During this process, the receptor binding domain (RBD) of the S protein plays an essential role, since it contains the receptor binding motif (RBM), responsible for the docking to the receptor. So far, mostly biochemical methods are being tested in order to prevent binding of the virus to ACE2. Here we show, with the help of atomistic simulations, that external electric fields of easily achievable and moderate strengths can dramatically destabilise the S protein, inducing long-lasting structural damage. One striking field-induced conformational change occurs at the level of the recognition loop L3 of the RBD where two parallel beta sheets, believed to be responsible for a high affinity to ACE2, undergo a change into an unstructured coil, which exhibits almost no binding possibilities to the ACE2 receptor. We also show that these severe structural changes upon electric-field application also occur in the mutant RBDs corresponding to the variants of concern (VOC) B.1.1.7 (UK), B.1.351 (South Africa) and P.1 (Brazil). Remarkably, while the structural flexibility of S allows the virus to improve its probability of entering the cell, it is also the origin of the surprising vulnerability of S upon application of electric fields of strengths at least two orders of magnitude smaller than those required for damaging most proteins. Our findings suggest the existence of a clean physical method to weaken the SARS-CoV-2 virus without further biochemical processing. Moreover, the effect could be used for infection prevention purposes and also to develop technologies for in-vitro structural manipulation of S. Since the method is largely unspecific, it can be suitable for application to other mutations in S, to other proteins of SARS-CoV-2 and in general to membrane proteins of other virus types.

The SARS-CoV-2 Spike protein is essential for viral infectivity and binds to the host receptor ACE2. Here, the authors present MD simulations of the Spike protein and its variants of concern and observe that the Spike protein is destabilised by moderate static electric fields, and undergoes field-induced conformational changes that hinder binding to ACE2.

Molecular dynamics evidence for nonthermal effects of electric fields on pectin methylesterase activity

Experimental studies relevant to the nonthermal effects of electric fields on biological systems are emerging. However, these effects are poorly understood at the molecular level. The present study investigates pectin methylesterase, a cell wall modifying enzyme in plants, exposed to various electric field strengths. Molecular dynamics (MD) of the enzyme were studied with and without (thermal-only) electric field applications. The measurements were interpreted on the basis of equivalent energy input to gain insights into the effect of electric field treatment time at a constant temperature (50 °C). Results reveal that electric fields exert nonthermal effects on both local and global protein structure. In 1 μs simulations, the results show significant (P ≤ 0.05) shrinkage of the catalytic domain and shortening of enzyme-water hydrogen bond lifetime by a 50 V cm-1 electric field. Unwinding of the helical segments, altered intra- and intermolecular hydrogen bond patterns, and increased hydration are also caused by the 50 V cm-1 electric field. This study serves to understand the electric field influence on the functional role of proteins.

Electro-opening of a microtubule lattice in silico

Modulation of the structure and function of biomaterials is essential for advancing bio-nanotechnology and biomedicine. Microtubules (MTs) are self-assembled protein polymers that are essential for fundamental cellular processes and key model compounds for the design of active bio-nanomaterials. In this in silico study, a 0.5 μs-long all-atom molecular dynamics simulation of a complete MT with approximately 1.2 million atoms in the system indicated that a nanosecond-scale intense electric field can induce the longitudinal opening of the cylindrical shell of the MT lattice, modifying the structure of the MT. This effect is field-strength- and temperature-dependent and occurs on the cathode side. A model was formulated to explain the opening on the cathode side, which resulted from an electric-field-induced imbalance between electric torque on tubulin dipoles and cohesive forces between tubulin heterodimers. Our results open new avenues for electromagnetic modulation of biological and artificial materials through action on noncovalent molecular interactions.

Challenges in coupling atmospheric electricity with biological systems

The atmosphere is host to a complex electric environment, ranging from a global electric circuit generating fluctuating atmospheric electric fields to local lightning strikes and ions. While research on interactions of organisms with their electrical environment is deeply rooted in the aquatic environment, it has hitherto been confined to interactions with local electrical phenomena and organismal perception of electric fields. However, there is emerging evidence of coupling between large- and small-scale atmospheric electrical phenomena and various biological processes in terrestrial environments that even appear to be tied to continental waters. Here, we synthesize our current understanding of this connectivity, discussing how atmospheric electricity can affect various levels of biological organization across multiple ecosystems. We identify opportunities for research, highlighting its complexity and interdisciplinary nature and draw attention to both conceptual and technical challenges lying ahead of our future understanding of the relationship between atmospheric electricity and the organization and functioning of biological systems.

Polyelectrolyte in Electric Field: Disparate Conformational Behavior along an Aminopolysaccharide Chain

Electrical signals are increasingly used in fabrication of hydrogels (e.g., based on aminopolysaccharide chitosan) to guide the emergence of complex and anisotropic structure; however, how an imposed electric field affects the polymer chain conformation and orientation during the self-assembly process is not understood. Here, we applied nonequilibrium all-atom molecular dynamics simulations to explore the response of a charged chitosan chain comprising 5- or 20-monomer units to a constant uniform electric field in water and salt solution. While no conformational or orientational response was observed for the polyelectrolyte (PE) chains under the small electric fields within the simulation time, a field strength of 400 mV/nm induced significant changes. In water, a 5-mer chain is found to be slightly bent and oriented parallel to the field; however, surprisingly, a 20-mer chain displays candy-cane-like conformations whereby one half of the chain is collapsed and flexible, while the other half of the chain is stretched along the electric field. In salt solution, the disparity remains between the two halves of the 20-mer chain, although the backbone is extremely flexible with multiple bent regions and non-native conformations occur near the chain center in one of the three trajectories. The disparate conformational response along the polyelectrolyte chain may be attributed to the balancing forces between chain dynamics, electric polarization, counterion binding, and hydrodynamic pressure as well as friction. These findings reconcile existing experiments and theoretical studies and represent an important step toward understanding the complex roles of electric field and salt in controlling the structure and properties of soft matter.

Molecular dynamics simulation of the nanosecond pulsed electric field effect on kinesin nanomotor

Kinesin is a biological molecular nanomotor which converts chemical energy into mechanical work. To fulfill various nanotechnological tasks in engineered environments, the function of biological molecular motors can be altered by artificial chemical modifications. The drawback of this approach is the necessity of designing and creating a new motor construct for every new task. We propose that intense nanosecond-scale pulsed electric field could modify the function of nanomotors. To explore this hypothesis, we performed molecular dynamics simulation of a kinesin motor domain docked on a subunit of its microtubule track - a single tubulin heterodimer. In the simulation, we exposed the kinesin motor domain to intense (100 MV/m) electric field up to 30 ns. We found that both the magnitude and angle of the kinesin dipole moment are affected. Furthermore, we found that the electric field affects contact surface area between kinesin and tubulin, the structure and dynamics of the functionally important kinesin segments, including microtubule binding motifs as well as nucleotide hydrolysis site which power the nanomotor. These findings indicate that external intense nanosecond-scale electric field could alter kinesin behavior. Our results contribute to developing novel electromagnetic methods for modulating the function of biomolecular matter at the nanoscale.