Terahertz underdamped vibrational motion governs protein-ligand binding in solution

Insights into the terahertz response of L-glutamic acid and its receptor

L-Glutamic acid (L-Glu) is a basic unit of proteins and also serves as an important neurotransmitter in the central nervous system. Its structural properties are critical for biological functions and selective receptor recognition. Although this molecule has been extensively studied, the low frequency vibrational behavior that is closely related to conformational changes and the intermolecular interactions between L-Glu and its receptors are still unclear. In this study, we acquired the fingerprint spectrum of L-Glu by using air plasma terahertz (THz) time-domain spectroscopy in the 0.5-18 THz range. The low frequency vibrational characteristics of L-Glu were investigated through density functional theory (DFT) calculations. The THz responses of the ligand binding domain of the NMDAR-L-Glu complex were studied by the ONIOM method, with a focus on discussing the normal modes and interactions of ligand L-Glu and water molecules. The results illustrate that THz spectroscopy exhibits a sensitive response to the influence of L-Glu on the structure of the NMDAR. The water molecules in proteins have various strong vibration modes in the THz band, showing specificity, diversity and complexity of vibrational behavior. There is potential for influencing and regulating the structural stability of the NMDAR-L-Glu complex through water molecules.

Tubulin Vibration Modes Are in the Subterahertz Range, and Their Electromagnetic Absorption Is Affected by Water

Many proteins are thought to coordinate distant sites in their structures through a concerted action of global structural vibrations. However, the direct experimental spectroscopic detection of these vibration modes is rather elusive. We used normal-mode analysis to explore the dominant vibration modes of an all-atom model of the tubulin protein and described their characteristics using a large ensemble of tubulin structures. We quantified the frequency range of the normal vibrational modes to be in the subterahertz band, specifically between ∼40 and ∼160 GHz. Adding water layers to the model increases the frequencies of the low-frequency modes and narrows the frequency variations of the modes among the protein ensemble. We also showed how the electromagnetic absorption of tubulin vibration modes is affected by vibrational damping. These results contribute to our understanding of tubulin's vibrational and electromagnetic properties and provide a foundation for future attempts to control protein behavior via external electromagnetic fields.

Insights into Modeling Approaches in Chemistry: Assessing Ligand-Protein Binding Thermodynamics Based on Rigid-Flexible Model Molecules

In the field of chemistry, model compounds find extensive use for investigating complex objects. One prime example of such object is the protein-ligand supramolecular interaction. Prediction the enthalpic and entropic contribution to the free energy associated with this process, as well as the structural and dynamic characteristics of protein-ligand complexes poses considerable challenges. This review exemplifies modeling approaches used to study protein-ligand binding (PLB) thermodynamics by employing pairs of conformationally constrained/flexible model molecules. Strategically designing the model molecules can reduce the number of variables that influence thermodynamic parameters. This enables scientists to gain deeper insights into the enthalpy and entropy of PLB, which is relevant for medicinal chemistry and drug design. The model studies reviewed here demonstrate that rigidifying ligands may induce compensating changes in the enthalpy and entropy of binding. Some "rules of thumb" have started to emerge on how to minimize entropy-enthalpy compensation and design efficient rigidified or flexible ligands.

Lifting Hofmeister's Curse: Impact of Cations on Diffusion, Hydrogen Bonding, and Clustering of Water

Water plays a role in the stability, reactivity, and dynamics of the solutes that it contains. The presence of ions alters this capacity by changing the dynamics and structure of water. However, our understanding of how and to what extent this occurs is still incomplete. Here, a study of the low-frequency Raman spectra of aqueous solutions of various cations by using optical Kerr-effect spectroscopy is presented. This technique allows for the measurement of the changes that ions cause in both the diffusive dynamics and the vibrations of the hydrogen-bond structure of water. It is found that when salts are added, some of the water molecules become part of the ion solvation layers, while the rest retain the same diffusional properties as those of pure water. The slowing of the dynamics of the water molecules in the solvation shell of each ion was found to depend on its charge density at infinite dilution conditions and on its position in the Hofmeister series at higher concentrations. It is also observed that all cations weaken the hydrogen-bond structure of the solution and that this weakening depends only on the size of the cation. Finally, evidence is found that ions tend to form amorphous aggregates, even at very dilute concentrations. This work provides a novel approach to water dynamics that can be used to better study the mechanisms of solute nucleation and crystallization, the structural stability of biomolecules, and the dynamic properties of complex solutions, such as water-in-salt electrolytes.

Examining DNA breathing with pyDNA-EPBD

MOTIVATION

The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion. This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others.

RESULTS

We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop-Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo algorithm.

AVAILABILITY AND IMPLEMENTATION

pyDNA-EPBD is supported across most operating systems and is freely available at https://github.com/lanl/pyDNA_EPBD. Extensive documentation can be found at https://lanl.github.io/pyDNA_EPBD/.

Intra-protein interacting collective modes in the terahertz frequency region

Understanding how proteins work requires a thorough understanding of their internal dynamics. Proteins support a wide range of motions, from the femtoseconds to seconds time scale, relevant to crucial biological functions. In this context, the term "protein collective dynamics" refers to the complex patterns of coordinated motions of numerous atoms throughout the protein in the sub-picosecond time scale (terahertz frequency region). It is hypothesized that these dynamics have a substantial impact on the regulation of functional dynamical mechanisms, including ligand binding and allosteric signalling, charge transport direction, and the regulation of thermodynamic and thermal transport properties. Using the theoretical framework of hydrodynamics, the collective dynamics of proteins had previously been described in a manner akin to that of simple liquids, i.e. in terms of a single acoustic-like excitation, related to intra-protein vibrational motions. Here, we employ an interacting-mode model to analyse the results from molecular dynamics simulations and we unveil that the vibrational landscape of proteins is populated by multiple acoustic-like and low-frequency optic-like modes, with mixed symmetry and interfering with each other. We propose an interpretation at the molecular level of the observed scenario that we relate to the side-chains and the hydrogen-bonded networks dynamics. The present insights provide a perspective for understanding the molecular mechanisms underlying the energy redistribution processes in the interior of proteins.

Investigations on Na+, K+-ATPase energy consumption in ion flow of hydrophilic pores by THz unipolar stimulation

Terahertz science and technology has recently shown new application prospects in artificial intelligence. It is found that terahertz unipolar stimulation can activate cell membrane hydrophilic pores. However, the behaviors of Na+, K+-ATPase and energy consumption during this period remain unknown. This paper investigates these behaviors by Na+, K+-ATPase and electroporation models, based on the interaction theory between terahertz fields and ions at the cellular level. The effective diameters of life ions are considered in the aqueous solution. From results, Na+, K+-ATPases can be activated and stay for a while before close after the stimulation. Their life ion flows are far lower than the flows via the pores. And their power dissipation is as low as 10-11 W in both rat neostriatal neurons and guinea pig ventricular myocytes. The results keep tenable in 0.1-1.2 THz. These lay the basis for investigations of information communication mechanisms in cells under terahertz stimulation.

Examining DNA Breathing with pyDNA-EPBD

Motivation

The two strands of the DNA double helix locally and spontaneously separate and recombine in living cells due to the inherent thermal DNA motion.This dynamics results in transient openings in the double helix and is referred to as "DNA breathing" or "DNA bubbles." The propensity to form local transient openings is important in a wide range of biological processes, such as transcription, replication, and transcription factors binding. However, the modeling and computer simulation of these phenomena, have remained a challenge due to the complex interplay of numerous factors, such as, temperature, salt content, DNA sequence, hydrogen bonding, base stacking, and others.

Results

We present pyDNA-EPBD, a parallel software implementation of the Extended Peyrard-Bishop- Dauxois (EPBD) nonlinear DNA model that allows us to describe some features of DNA dynamics in detail. The pyDNA-EPBD generates genomic scale profiles of average base-pair openings, base flipping probability, DNA bubble probability, and calculations of the characteristically dynamic length indicating the number of base pairs statistically significantly affected by a single point mutation using the Markov Chain Monte Carlo (MCMC) algorithm.

Frequency-Selective Anharmonic Mode Analysis of Thermally Excited Vibrations in Proteins

Low-frequency molecular vibrations at far-infrared frequencies are thermally excited at room temperature. As a consequence, thermal fluctuations are not limited to the immediate vicinity of local minima on the potential energy surface, and anharmonic properties cannot be ignored. The latter is particularly relevant in molecules with multiple conformations, such as proteins and other biomolecules. However, existing theoretical and computational frameworks for the analysis of molecular vibrations have so far been limited by harmonic or quasi-harmonic approximations, which are ill-suited to describe anharmonic low-frequency vibrations. Here, we introduce a fully anharmonic analysis of molecular vibrations based on a time correlation formalism that eliminates the need for harmonic or quasi-harmonic approximations. We use molecular dynamics simulations of a small protein to demonstrate that this new approach, in contrast to harmonic and quasi-harmonic normal modes, correctly identifies the collective degrees of freedom associated with molecular vibrations at any given frequency. This allows us to unambiguously characterize the anharmonic character of low-frequency vibrations in the far-infrared spectrum.

Phonon Polaritonics in Broad Terahertz Frequency Range with Quantum Paraelectric SrTiO3

Photonics in the frequency range of 5-15 terahertz (THz) potentially open a new realm of quantum materials manipulation and biosensing. This range, sometimes called "the new terahertz gap", is traditionally difficult to access due to prevalent phonon absorption bands in solids. Low-loss phonon-polariton materials may realize sub-wavelength, on-chip photonic devices, but typically operate in mid-infrared frequencies with narrow bandwidths and are difficult to manufacture on a large scale. Here, for the first time, quantum paraelectric SrTiO3 enables broadband surface phonon-polaritonic devices in 7-13 THz. As a proof of concept, polarization-independent field concentrators are designed and fabricated to locally enhance intense, multicycle THz pulses by a factor of 6 and increase the spectral intensity by over 90 times. The time-resolved electric field inside the concentrators is experimentally measured by THz-field-induced second harmonic generation. Illuminated by a table-top light source, the average field reaches 0.5 GV m-1 over a large volume resolvable by far-field optics. These results potentially enable scalable THz photonics with high breakdown fields made of various commercially available phonon-polariton crystals for studying driven phases in quantum materials and nonlinear molecular spectroscopy.

Investigating the function and design of molecular materials through terahertz vibrational spectroscopy

Terahertz spectroscopy has proved to be an essential tool for the study of condensed phase materials. Terahertz spectroscopy probes the low-frequency vibrational dynamics of atoms and molecules, usually in the condensed phase. These nuclear dynamics, which typically involve displacements of entire molecules, have been linked to bulk phenomena ranging from phase transformations to semiconducting efficiency. The terahertz region of the electromagnetic spectrum has historically been referred to as the 'terahertz gap', but this is a misnomer, as there exist a multitude of methods for accessing terahertz frequencies, and now there are cost-effective instruments that have made terahertz studies much more user-friendly. This Review highlights some of the most exciting applications of terahertz vibrational spectroscopy so far, and provides an in-depth overview of the methods of this technique and its utility to the study of the chemical sciences.

Nonthermal acceleration of protein hydration by sub-terahertz irradiation

The collective intermolecular dynamics of protein and water molecules, which overlap in the sub-terahertz (THz) frequency region, are relevant for expressing protein functions but remain largely unknown. This study used dielectric relaxation (DR) measurements to investigate how externally applied sub-THz electromagnetic fields perturb the rapid collective dynamics and influence the considerably slower chemical processes in protein-water systems. We analyzed an aqueous lysozyme solution, whose hydration is not thermally equilibrated. By detecting time-lapse differences in microwave DR, we demonstrated that sub-THz irradiation gradually decreases the dielectric permittivity of the lysozyme solution by reducing the orientational polarization of water molecules. Comprehensive analysis combining THz and nuclear magnetic resonance spectroscopies suggested that the gradual decrease in the dielectric permittivity is not induced by heating but is due to a slow shift toward the hydrophobic hydration structure in lysozyme. Our findings can be used to investigate hydration-mediated protein functions based on sub-THz irradiation.

The collective vibrational modes of dihydropyridine in nifedipine studied by terahertz spectroscopy

Cardiovascular pharmaceuticals have drawn huge attention in drug development. Nifedipine (NFD) is an important member of calcium channel blockers (CCB) with the structural characteristic of dihydropyridine (DHP), but the binding mechanism to its target remains an open question. Even though several analytical techniques have been used for structural characterizations, the information of collective vibrational behavior is still lacking. In this work, we use terahertz (THz) spectroscopy to investigate the spectral fingerprints of NFD, and quantitatively evaluate the temperature-induced frequency shifts. Combined with quantum chemical calculations, each THz fingerprint is attributed to specific collective vibrational modes. The collective vibrations of DHP are mainly distributed below 2.5 THz, which provides complementary information to understand the behavior of rigid DHP ring. The rotation of methyl group and the wagging of nitrophenyl group are widely distributed in the range of 1.0-4.0 THz, which is helpful for the conformational recognition between NFD and target molecule. THz spectroscopy is demonstrated to be suitable for characterizing the collective vibrational modes of DHP and elucidating the drug-target binding behavior from the perspective of noncovalent interactions. It has the potential to become a non-invasive technology for conformational analysis and pharmaceutical development.

Selectivity of Protein Interactions Stimulated by Terahertz Signals

It has been established that Terahertz (THz) band signals can interact with biomolecules through resonant modes. Specifically, of interest here, protein activation. Our research goal is to show how directing the mechanical signaling inside protein molecules using THz signals can control changes in their structure and activate associated biochemical and biomechanical events. To establish that, we formulate a selectivity metric that quantifies the system performance and captures the capability of the nanoantenna to induce a conformational change in the desired protein molecule/population. The metric provides a score between -1 and 1 that indicates the degree of control we have over the system to achieve targeted protein interactions. To develop the selectivity measure, we first use the Langevin stochastic equation driven by an external force to model the protein behavior. We then determine the probability of protein folding by computing the steady-state energy of the driven protein and then generalize our model to account for protein populations. Our numerical analysis results indicate that a maximum selectivity score is attained when only the targeted population experiences a folding behavior due to the impinging THz signal. From the achieved selectivity values, we conclude that the system response not only depends on the resonant frequency but also on the system controlling parameters namely, the nanoantenna force, the damping constant, and the abundance of each protein population. Based on the selectivity metric, the nanoantenna must be tuned to a frequency that is not necessarily the resonant frequency of the protein. The presented work sheds light on the potential associated with the electromagnetic-based control of protein networks, which could lead to a plethora of applications in the medical field ranging from bio-sensing to targeted therapy.

Correlated Evolution of Low-Frequency Vibrations and Function in Enzymes

Previous studies of the flexibility of ancestral proteins suggest that proteins evolve their function by altering their native state ensemble. Here, we propose a more direct method to analyze such changes during protein evolution by comparing thermally activated vibrations at frequencies below 6 THz, which report on the dynamics of collective protein modes. We analyzed the backbone vibrational density of states of ancestral and extant β-lactamases and thioredoxins and observed marked changes in the vibrational spectrum in response to evolution. Coupled with previously observed changes in protein flexibility, the observed shifts of vibrational mode densities suggest that protein dynamics and dynamical allostery are critical factors for the evolution of enzymes with specialized catalytic and biophysical properties.

Raman Spectroscopy as a Tool to Study the Pathophysiology of Brain Diseases

The Raman phenomenon is based on the spontaneous inelastic scattering of light, which depends on the molecular characteristics of the dispersant. Therefore, Raman spectroscopy and imaging allow us to obtain direct information, in a label-free manner, from the chemical composition of the sample. Since it is well established that the development of many brain diseases is associated with biochemical alterations of the affected tissue, Raman spectroscopy and imaging have emerged as promising tools for the diagnosis of ailments. A combination of Raman spectroscopy and/or imaging with tagged molecules could also help in drug delivery and tracing for treatment of brain diseases. In this review, we first describe the basics of the Raman phenomenon and spectroscopy. Then, we delve into the Raman spectroscopy and imaging modes and the Raman-compatible tags. Finally, we center on the application of Raman in the study, diagnosis, and treatment of brain diseases, by focusing on traumatic brain injury and ischemia, neurodegenerative disorders, and brain cancer.

Low-THz Vibrations of Biological Membranes

A growing body of work has linked key biological activities to the mechanical properties of cellular membranes, and as a means of identification. Here, we present a computational approach to simulate and compare the vibrational spectra in the low-THz region for mammalian and bacterial membranes, investigating the effect of membrane asymmetry and composition, as well as the conserved frequencies of a specific cell. We find that asymmetry does not impact the vibrational spectra, and the impact of sterols depends on the mobility of the components of the membrane. We demonstrate that vibrational spectra can be used to distinguish between membranes and, therefore, could be used in identification of different organisms. The method presented, here, can be immediately extended to other biological structures (e.g., amyloid fibers, polysaccharides, and protein-ligand structures) in order to fingerprint and understand vibrations of numerous biologically-relevant nanoscale structures.

Understanding the emergence of the boson peak in molecular glasses

A common feature of glasses is the "boson peak", observed as an excess in the heat capacity over the crystal or as an additional peak in the terahertz vibrational spectrum. The microscopic origins of this peak are not well understood; the emergence of locally ordered structures has been put forward as a possible candidate. Here, we show that depolarised Raman scattering in liquids consisting of highly symmetric molecules can be used to isolate the boson peak, allowing its detailed observation from the liquid into the glass. The boson peak in the vibrational spectrum matches the excess heat capacity. As the boson peak intensifies on cooling, wide-angle x-ray scattering shows the simultaneous appearance of a pre-peak due to molecular clusters consisting of circa 20 molecules. Atomistic molecular dynamics simulations indicate that these are caused by over-coordinated molecules. These findings represent an essential step toward our understanding of the physics of vitrification.

Dimensional Design for Surface-Enhanced Raman Spectroscopy

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that enables specific identification of target analytes with sensitivity down to the single-molecule level by harnessing metal nanoparticles and nanostructures. Excitation of localized surface plasmon resonance of a nanostructured surface and the associated huge local electric field enhancement lie at the heart of SERS, and things will become better if strong chemical enhancement is also available simultaneously. Thus, the precise control of surface characteristics of enhancing substrates plays a key role in broadening the scope of SERS for scientific purposes and developing SERS into a routine analytical tool. In this review, the development of SERS substrates is outlined with some milestones in the nearly half-century history of SERS. In particular, these substrates are classified into zero-dimensional, one-dimensional, two-dimensional, and three-dimensional substrates according to their geometric dimension. We show that, in each category of SERS substrates, design upon the geometric and composite configuration can be made to achieve an optimized enhancement factor for the Raman signal. We also show that the temporal dimension can be incorporated into SERS by applying femtosecond pulse laser technology, so that the SERS technique can be used not only to identify the chemical structure of molecules but also to uncover the ultrafast dynamics of molecular structural changes. By adopting SERS substrates with the power of four-dimensional spatiotemporal control and design, the ultimate goal of probing the single-molecule chemical structural changes in the femtosecond time scale, watching the chemical reactions in four dimensions, and visualizing the elementary reaction steps in chemistry might be realized in the near future.

Route to flexible metamaterial terahertz biosensor based on multi-resonance dips

A flexible terahertz (THz) metamaterial biosensor is theoretically and experimentally investigated. The metamaterial unit cell of the periodic structure array was simply composed of three non-overlapping cut wires with different length parameters on a flexible thin-film (parylene-C) to improve sensitivity. The biosensor sample was fabricated using a lithography process and characterized by a THz time-domain spectroscopy (TDS) system. The metamaterial exhibited multi-resonance dips in transmission spectrum at 0.6-2.0 THz, which can self-correct errors in biosensing. Numerical results show that the Q-factor, figure of merit (FOM) and sensitivity can change in dynamic ranges with the geometric parameters (space and width) of three-cut-wire metamaterial. When space distance was 40 µm and other parameters were default, the sensitivity, FOM and Q-factor reached 710 GHz/RIU (Refractive Index Unit), 9, and 20, respectively. Therefore, through proper design and preparation, the metamaterial can be applied to biochemical detection.

Probing terahertz dynamics of multidomain protein in cell-like confinement

The development of meaningful descriptions of multidomain proteins exhibiting complex inter-domain dynamics modes is a key challenge for understanding their roles in molecular recognition and signalling processes. Here we developed a generally applicable approach for probing the low frequency collective hydration dynamics of multidomain proteins that uses terahertz spectroscopy of a protein molecule confined in a phospholipid reverse micelles environment (named Droplet THz). With the combination of normal mode analysis, we demonstrated the binding of calcium ions modulates the local inter-domain motion of the human coagulant factor VIII protein in a concentration-dependent manner. These findings highlight the Droplet THz as a valuable tool for dissecting the ultrafast dynamics of domain motion in the multidomain proteins and suggest a modulating mechanism of calcium ions on the structural flexibility and function of human coagulant proteins.

Tuning symmetry-protected quasi bound state in the continuum using terahertz meta-atoms of rotational and reflectional symmetry

Conventionally, a symmetry-protected quasi bound state of the continuum (BIC) becomes achievable by breaking the C₂ symmetry of meta-atoms. Our work exhibits a novel approach to achieving dual band quasi-BIC by breaking the C_2v symmetry into C_s symmetry. Also, we show that a single band quasi-BIC can be achieved by breaking the C_2v symmetry into C₂ symmetry. Our metasurface of C_2v symmetry is composed of double gaps split ring resonator (DSRR), and it degrades to C₂ symmetry when the double gaps are displaced in opposite directions. One band quasi-BIC can be observed occurring at around 0.36 and 0.61 THz respectively with the metasurface excited by x- and y-polarized terahertz radiation, respectively. A couple of dark dipole oscillator dominates the quasi-BIC at 0.36 THz, while a quadruple-like oscillator dominates the quasi-BIC at 0.61 THz. The damping ratio and coupling coefficients of the above single quasi-BIC are close to the orthogonal polarization of the incident terahertz wave. However, the metasurface of the DSRR array degrades down to C_s symmetry when the double gaps are displaced in the same directions. A dual band quasi-BIC (0.23 THz and 0.62 THz) is found to be sensitive to the y-polarized terahertz radiation. It is found that the inductive-capacitive (LC) resonance results in quasi-BIC at 0.23 THz, while a quadrupole-like oscillation results in quasi-BIC at 0.62 THz. The quasi-BIC at 0.62 THz has a higher coupling coefficient and lower damping ratio than quasi-BIC at 0.23 THz in a metasurface of C_s symmetry. The realization of the above locally symmetric breaking on the quasi-BIC of terahertz metasurfaces is helpful for the innovation of multi-band terahertz biosensors.

Intermolecular Dynamics of Positively and Negatively Charged Aromatics and Their Isoelectronic Neutral Analogs in Aqueous Solutions

In this study, we investigated the temperature dependence of intermolecular vibrations and orientational dynamics in the aqueous solutions of imidazole hydrochloride, imidazole, sodium triazolide, and triazole using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES) and steady-state Raman spectroscopy. The difference low-frequency Raman spectra under 250 cm-1 of the aqueous solutions relative to the neat water showed that the spectral shoulder in the high-frequency region at 60-100 cm-1, assigned to the libration of an aromatic ring, was higher in frequency for the imidazolium cation but lower for the triazolide anion than those of the respective neutral aromatics. The results of the ab initio quantum chemistry calculations of the clusters of the aromatics and water molecule(s) were consistent with the experimental spectra of the aqueous solutions. Further, the results of the temperature-dependent experiments showed that the signal intensity in the low-frequency region below 50 cm-1 increased for all solutions with an increase in temperature. In contrast, the spectral density in the high-frequency region above 80 cm-1 exhibited almost no shift for the 1.0 M solutions, while a significant red shift was observed for the 5.0 M solutions. In addition, the temperature-dependent densities, viscosities, and surface tensions were characterized for the aqueous aromatic solutions from 293 to 353 K.

CHESS: The future direct geometry spectrometer at the second target station

CHESS, chopper spectrometer examining small samples, is a planned direct geometry neutron chopper spectrometer designed to detect and analyze weak signals intrinsic to small cross sections (e.g., small mass, small magnetic moments, or neutron absorbing materials) in powders, liquids, and crystals. CHESS is optimized to enable transformative investigations of quantum materials, spin liquids, thermoelectrics, battery materials, and liquids. The broad dynamic range of the instrument is also well suited to study relaxation processes and excitations in soft and biological matter. The 15 Hz repetition rate of the Second Target Station at the Spallation Neutron Source enables the use of multiple incident energies within a single source pulse, greatly expanding the information gained in a single measurement. Furthermore, the high flux grants an enhanced capability for polarization analysis. This enables the separation of nuclear from magnetic scattering or coherent from incoherent scattering in hydrogenous materials over a large range of energy and momentum transfer. This paper presents optimizations and technical solutions to address the key requirements envisioned in the science case and the anticipated uses of this instrument.

Quantitative Analysis of Dynamic Allostery

Dynamic allostery refers to one important class of allosteric regulation that does not involve noticeable conformational changes upon effector binding. In recent years, many "quasi"-dynamic allosteric proteins have been found to only experience subtle conformational changes during allosteric regulation. However, as enthalpic and entropic contributions are coupled to each other and even tiny conformational changes could bring in noticeable free energy changes, a quantitative description is essential to understand the contribution of pure dynamic allostery. Here, by developing a unified anisotropic elastic network model (uANM) considering both side-chain information and ligand heavy atoms, we quantitatively estimated the contribution of pure dynamic allostery in a dataset of known allosteric proteins by excluding the conformational changes upon ligand binding. We found that the contribution of pure dynamic allostery is generally small (much weaker than previously expected) and robustly exhibits an allosteric activation effect, which exponentially decays with the distance between the substrate and the allosteric ligand. We further constructed toy models to study the determinant factors of dynamic allostery in monomeric and oligomeric proteins using the uANM. Analysis of the toy models revealed that a short distance, a small angle between the two ligands, strong protein-ligand interactions, and weak protein internal interactions lead to strong dynamic allostery. Our study provides a quantitative estimation of pure dynamic allostery and facilitates the understanding of dynamic-allostery-controlled biological processes and the design of allosteric drugs and proteins.

Intermolecular Dynamics and Structure in Aqueous Lidocaine Hydrochloride Solutions

We investigated the intermolecular dynamics and static structure in the aqueous solutions of lidocaine hydrochloride (LDHCl) in the concentration range of [LDHCl] = 0-2.00 M using femtosecond Raman-induced Kerr effect spectroscopy (fs-RIKES), small- and wide-angle X-ray scattering (SWAXS), and dynamic light scattering (DLS). For the fs-RIKES experiments, the concentration dependence of the difference low-frequency spectra of the aqueous LDHCl solutions relative to the neat water, which was mainly due to the intermolecular vibrations, was characterized using an exponential function with a characteristic concentration of ∼1 M. For the SWAXS experiments, we observed a manifestation of an excess scattering component centered within a range of 8-10 nm^-1 in the aqueous LDHCl solutions. The results of Fourier inversion and further deconvolution analyses unambiguously demonstrated that lidocaines assemble into a nanometer-sized micelle-like structure with the innermost core (∼0.3 nm) and outer shell (∼0.5 nm), respectively. The DLS experiments also found nanometer-sized aggregates and further indicated evidence of the clusters of the aggregates. The results of viscosities, densities, and surface tensions of the solutions and the quantum chemistry calculations supported the unique features of the microscopic intermolecular interaction and the micelle-like aggregation.

Probing the existence of non-thermal Terahertz radiation induced changes of the protein solution structure

During the last decades discussions were taking place on the existence of global, non-thermal structural changes in biological macromolecules induced by Terahertz (THz) radiation. Despite numerous studies, a clear experimental proof of this effect for biological particles in solution is still missing. We developed a setup combining THz-irradiation with small angle X-ray scattering (SAXS), which is a sensitive method for detecting the expected structural changes. We investigated in detail protein systems with different shape morphologies (bovine serum albumin, microtubules), which have been proposed to be susceptible to THz-radiation, under variable parameters (THz wavelength, THz power densities up to 6.8 mW/cm², protein concentrations). None of the studied systems and conditions revealed structural changes detectable by SAXS suggesting that the expected non-thermal THz-induced effects do not lead to alterations of the overall structures, which are revealed by scattering from dissolved macromolecules. This leaves us with the conclusion that, if such effects are present, these are either local or outside of the spectrum and power range covered by the present study.

Protein-Ligand Binding Molecular Details Revealed by Terahertz Optical Kerr Spectroscopy: A Simulation Study

Picosecond fast motions and their involvement in the biochemical processes such as protein-ligand binding has engaged significant attention. Terahertz optical Kerr spectroscopy (OKE) has the superior potential to probe these fast motions directly. Application of OKE in protein-ligand binding study is, however, limited by the difficulty of quantitative atomistic interpretation, and the calculation of Kerr spectrum for entire solvated protein complex was considered not yet feasible, due to the lack of one consistent polarizable model for both configuration sampling and polarizability calculation. Here, we analyzed the biochemical relevance of OKE to the lysozyme-triacetylchitotriose binding based on the first OKE simulation using one consistent Drude polarizable model. An analytical multipole and induced dipole scheme was employed to calculate the off-diagonal Drude polarizability more efficiently and accurately. Further theoretical analysis revealed how the subtle twisting and stiffening of aromatic protein residues' spatial arrangement as well as the confinement of small water clusters between ligand and protein cavity due to the ligand binding can be examined using Kerr spectroscopy. Comparison between the signals of bound complex and that of uncorrelated protein/ligand demonstrated that binding action alone has reflection in the OKE spectrum. Our study indicated OKE as a powerful terahertz probe for protein-ligand binding chemistry and dynamics.

Complete Mapping of DNA‐Protein Interactions at the Single‐Molecule Level

DNA–protein interaction plays an essential role in the storage, expression, and regulation of genetic information. A 1D/3D facilitated diffusion mechanism has been proposed to explain the extraordinarily rapid rate of DNA‐binding protein (DBP) searching for cognate sequence along DNA and further studied by single‐molecule experiments. However, direct observation of the detailed chronological protein searching image is still a formidable challenge. Here, for the first time, a single‐molecule electrical monitoring technique is utilized to realize label‐free detection of the DBP–DNA interaction process based on high‐gain silicon nanowire field‐effect transistors (SiNW FETs). The whole binding process of WRKY domain and DNA has been visualized with high sensitivity and single‐base resolution. Impressively, the swinging of hydrogen bonds between amino acid residues and bases in DNA induce the dynamic collective motion of DBP–DNA. This in situ, label‐free electrical detection platform provides a practical experimental methodology for dynamic studies of various biomolecules.

Low frequency coherent Raman spectroscopy

We revisit low frequency coherent Raman spectroscopy (LF-CRS) and present a unified theoretical background that provides consistent physical pictures of LF-CRS signal generation. Our general framework allows to compute the signal to noise ratio in the multitude of possible LF-CRS, and more generally CRS, experimental implementations both in the spectral and time domain.

Orientations and water dynamics of photoinduced secondary charge-separated states for magnetoreception by cryptochrome

In the biological magnetic compass, blue-light photoreceptor protein of cryptochrome is thought to conduct the sensing of the Earth's magnetic field by photoinduced sequential long-range charge-separation (CS) through a cascade of tryptophan residues, W_A(H), W_B(H) and W_C(H). Mechanism of generating the weak-field sensitive radical pair (RP) is poorly understood because geometries, electronic couplings and their modulations by molecular motion have not been investigated in the secondary CS states generated prior to the terminal RP states. In this study, water dynamics control of the electronic coupling is revealed to be a key concept for sensing the direction of weak magnetic field. Geometry and exchange coupling (singlet-triplet energy gap: 2J) of photoinduced secondary CS states composed of flavin adenine dinucleotide radical anion (FAD^-•) and radical cation W_B(H)^+• in the cryptochrome DASH from Xenopus laevis were clarified by time-resolved electron paramagnetic resonance. We found a time-dependent energetic disorder in 2J and was interpreted by a trap CS state capturing one reorientated water molecule at 120 K. Enhanced electron-tunneling by water-libration was revealed for the terminal charge-separation event at elevated temperature. This highlights importance of optimizing the electronic coupling for regulation of the anisotropic RP yield on the possible magnetic compass senses.

Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes

Protein dynamics has been investigated since almost half a century, as it is believed to constitute the fundamental connection between structure and function. Elastic network models (ENMs) have been widely used to predict protein dynamics, flexibility and the biological mechanism, from which remarkable results have been found regarding the prediction of protein conformational changes. Starting from the knowledge of the reference structure only, these conformational changes have been usually predicted either by looking at the individual mode shapes of vibrations (i.e., by considering the free vibrations of the ENM) or by applying static perturbations to the protein network (i.e., by considering a linear response theory). In this paper, we put together the two previous approaches and evaluate the complete protein response under the application of dynamic perturbations. Harmonic forces with random directions are applied to the protein ENM, which are meant to simulate the single frequency-dependent components of the collisions of the surrounding particles, and the protein response is computed by solving the dynamic equations in the underdamped regime, where mass, viscous damping and elastic stiffness contributions are explicitly taken into account. The obtained motion is investigated both in the coordinate space and in the sub-space of principal components (PCs). The results show that the application of perturbations in the low-frequency range is able to drive the protein conformational change, leading to remarkably high values of direction similarity. Eventually, this suggests that protein conformational change might be triggered by external collisions and favored by the inherent low-frequency dynamics of the protein structure.

Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering

Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.

Femtosecond time-resolved X-ray solution scattering (fs-TRXSS) measurements provide information on the structural dynamics of proteins in solution. Here, the authors present a structure refinement method for the analysis of fs-TRXSS data and use it to characterise the ultrafast structural changes of homodimeric haemoglobin.

Tracking Ultrafast Structural Dynamics by Time-Domain Raman Spectroscopy

In traditional Raman spectroscopy, narrow-band light is irradiated on a sample, and its inelastic scattering, i.e., Raman scattering, is detected. The energy difference between the Raman scattering and the incident light corresponds to the vibrational energy of the molecule, providing the Raman spectrum that contains rich information about the molecular-level properties of the materials. On the other hand, by using ultrashort optical pulses, it is possible to induce Raman-active coherent nuclear motion of the molecule and to observe the molecular vibration in real time. Moreover, this time-domain Raman measurement can be combined with femtosecond photoexcitation, triggering chemical changes, which enables tracking ultrafast structural dynamics in a form of “time-resolved” time-domain Raman spectroscopy, also known as time-resolved impulsive stimulated Raman spectroscopy. With the advent of stable, ultrashort laser pulse sources, time-resolved impulsive stimulated Raman spectroscopy now realizes high sensitivity and a wide detection frequency window from THz to 3000 cm^–1, and has seen success in unveiling the molecular mechanisms underlying the efficient functions of complex molecular systems. In this Perspective, we overview the present status of time-domain Raman spectroscopy, particularly focusing on its application to the study of femtosecond structural dynamics. We first explain the principle and a brief history of time-domain Raman spectroscopy and then describe the apparatus and recent applications to the femtosecond dynamics of complex molecular systems, including proteins, molecular assemblies, and functional materials. We also discuss future directions for time-domain Raman spectroscopy, which has reached a status allowing a wide range of applications.

Broadband terahertz signatures and vibrations of dopamine

Dopamine (DA) is an essential neurotransmitter and hormone of the nervous system, its structural and conformational properties play critical roles in biological functions and signal transmission processes. Although this neuroactive molecule has been studied extensively, the low-frequency vibration features that are closely related to the conformation and molecular interactions in the terahertz (THz) band still remain unclear. In this study, a broadband THz time-domain spectroscopy (THz-TDS) system in the frequency band of 0.5-18 THz was used to characterize the unique THz fingerprint of DA. In addition, density functional theory (DFT) calculations were performed to analyze the vibrational properties of DA. The results suggest that each THz resonant absorption peak of DA corresponds to specific vibrational modes, and the collective vibration also exists in the broadband THz range. Moreover, the interactions between the DA ligand and the D2 and D3 receptors were investigated by docking, and the simulated THz spectra were obtained. The results indicate the dominant role of hydrogen bonding interactions and the specificity of molecular conformation. This work may help to understand the resonance coupling between THz electromagnetic waves and neurotransmitters.

Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin

Water dynamics in the hydration layers of biomolecules play crucial roles in a wide range of biological functions. A hydrated protein contains multiple components of diffusional and vibrational dynamics of water and protein, which may be coupled at ∼0.1-THz frequency (10-ps timescale) at room temperature. However, the microscopic description of biomolecular functions based on various modes of protein-water-coupled motions remains elusive. A novel approach for perturbing the hydration dynamics in the subterahertz frequency range and probing them at the atomic level is therefore warranted. In this study, we investigated the effect of klystron-based, intense 0.1-THz excitation on the slow dynamics of ubiquitin using NMR-based measurements of hydrogen-deuterium exchange. We demonstrated that the subterahertz irradiation accelerated the hydrogen-deuterium exchange of the amides located in the interior of the protein and hydrophobic surfaces while decelerating this exchange in the amides located in the surface loop and short 3₁₀ helix regions. This subterahertz-radiation-induced effect was qualitatively contradictory to the increased-temperature-induced effect. Our results suggest that the heterogeneous water dynamics occurring at the protein-water interface include components that are nonthermally excited by the subterahertz radiation. Such subterahertz-excited components may be linked to the slow function-related dynamics of the protein.

Generation of tailored terahertz waves from monolithic integrated metamaterials onto spintronic terahertz emitters

Recently emerging spintronic terahertz (THz) emitters, featuring many appreciable merits such as low-cost, high efficiency, ultrabroadband, and ease of integration, offer multifaceted capabilities not only in understanding the fundamental ultrafast magnetism physics but also for exploring multifarious practical applications. Integration of various flexible and tunable functions at the source such as polarization manipulation, amplitude tailoring, phase modulation, and radiation beam steering with the spintronic THz emitters and their derivatives can yield more compact and elegant devices. Here, we demonstrate a monolithic metamaterial integrated onto a W/CoFeB/Pt THz nanoemitter for a purpose-designed functionality of the electromagnetically induced transparency analog. Through elaborate engineering the asymmetry degree and geometric parameters of the metamaterial structure, we successfully verified the feasibility of monolithic modulations for the radiated THz waves. The integrated device was eventually compared with a set of stand-alone metamaterial positioning scenarios, and the negligible frequency difference between two of the positioning schemes further manifests almost an ideal realization of the proposed monolithic integrated metamaterial device with a spintronic THz emitter. We believe that such adaptable and scalable devices may make valuable contributions to the designable spintronic THz devices with pre-shaping THz waves and enable chip-scale spintronic THz optics, sensing, and imaging.

Low-Frequency Protein Motions Coupled to Catalytic Sites

This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.

Modal Analysis of the Lysozyme Protein Considering All-Atom and Coarse-Grained Finite Element Models

Proteins are the fundamental entities of several organic activities. They are essential for a broad range of tasks in a way that their shapes and folding processes are crucial to achieving proper biological functions. Low-frequency modes, generally associated with collective movements at terahertz (THz) and sub-terahertz frequencies, have been appointed as critical for the conformational processes of many proteins. Dynamic simulations, such as molecular dynamics, are vastly applied by biochemical researchers in this field. However, in the last years, proposals that define the protein as a simplified elastic macrostructure have shown appealing results when dealing with this type of problem. In this context, modal analysis based on different modelization techniques, i.e., considering both an all-atom (AA) and coarse-grained (CG) representation, is proposed to analyze the hen egg-white lysozyme. This work presents new considerations and conclusions compared to previous analyses. Experimental values for the B-factor, considering all the heavy atoms or only one representative point per amino acid, are used to evaluate the validity of the numerical solutions. In general terms, this comparison allows the assessment of the regional flexibility of the protein. Besides, the low computational requirements make this approach a quick method to extract the protein’s dynamic properties under scrutiny.

Direct comparison with terahertz metamaterials and surface-enhanced Raman scattering in a molecular-specific sensing performance

Signal enhancement of spectroscopies including terahertz time-domain spectroscopy (THz-TDS) and surface-enhanced Raman scattering (SERS) is a critical issue for effective molecular detection and identification. In this study, the sensing performance between THz-TDS and SERS individually accompanied by the proper plasmonic subwavelength structures was compared. For the precisely quantitative study on the optical properties of rhodamine 6G (R6G) dyes, SERS incorporates with the non-linearly enhanced Raman emissions at the molecular characteristic peaks while THz-TDS refers to the transmittance change and the shift of the spectral resonance. The local molecular density-dependent trade-off relationship between limit-of-detection and quenching was observed from both measurements. The specificity for two samples, R6G and methylene blue, is determined by the discriminations in spectral features such as the intensity ratio of assigned peaks in SERS and transmittance difference in THz-TDS. The comprehension of field enhancement by the specific nanostructures was supported by the finite-element method-based numerical computations. As a result, both spectroscopic techniques with the well-tailored nanostructures show great potential for highly sensitive, reproducible, label-free, and cost-effective diagnosis tools in the biomedical fields.

Kinetic coherence underlies the dynamics of disordered proteins

The dynamics of two proteins of similar size, the globular lysozyme and the intrinsically disordered Huntingtin interacting protein, has been simulated in three states resembling a globule, a pre-molten globule, and a molten globule. A coherence time τ has been defined, measuring the delay in the display of a stochastic behaviour after a perturbation of the system. This time has been computed for two sets of collective variables: the projection of the phase point onto the positions and momenta subspaces (τ_r and τ_p), and the principal components (PCs) of positions q and momenta π produced by a covariance analysis in these subspaces (τ_q and τ_π). In all states τ_p ≈ 3.5τ_r, and τ_π ≈ 3.5τ_q. The coherence times of individual PCs, τ^(l)_q and τ^(l)_π, have also been computed, and τ^(l)_π > τ^(l)_q in all states. The prevalence of τ_p over τ_r, or of τ_π over τ_q, drives the dynamics of the protein over a time range of ≈1–2 ps; moreover, a hidden synchronism appears to raise the momenta subspace's coherence above that of its individual PCs. In the transition of lysozyme to the molten globule the τ^(l)_q decrease but, unexpectedly, the τ^(l)_π increase; after this transition τ_p ≈ 5τ_r and τ_π ≈ 5τ_q. A gain of kinetic coherence accompanies thus the loss of structural coherence caused by the denaturation of the protein in the transition from globule to molten globule. The increase of the τ^(l)_π does not take place in the analogous transition of the Huntingtin protein. These results are compared with those of a similar analysis performed on three pseudo-proteins designed by scrambling the primary sequence of the Huntingtin interacting protein, and on two oligopeptides. The hidden synchronism appears to be a generic property of these polypeptides. The τ^(l)_π spectrum is similar in denaturated and in intrinsically disordered biomolecules; but the gain of kinetic coherence as a result of denaturation seems to be a specific property of the biologically functional lysozyme.

In the phase space of a globular or intrinsically disordered protein, the momenta's dynamics is less chaotic than the coordinates' dynamics. When a protein is denaturated, a gain in kinetic coherence accompanies the loss of structural coherence.

Information Rates of Controlled Protein Interactions Using Terahertz Communication

In this work, we present a paradigm bridging electromagnetic (EM) and molecular communication through a stimuli-responsive intra-body model. It has been established that protein molecules, which play a key role in governing cell behavior, can be selectively stimulated using Terahertz (THz) band frequencies. By triggering protein vibrational modes using THz waves, we induce changes in protein conformation, resulting in the activation of a controlled cascade of biochemical and biomechanical events. To analyze such an interaction, we formulate a communication system composed of a nanoantenna transmitter and a protein receiver. We adopt a Markov chain model to account for protein stochasticity with transition rates governed by the nanoantenna force. Both two-state and multi-state protein models are presented to depict different biological configurations. Closed form expressions for the mutual information of each scenario is derived and maximized to find the capacity between the input nanoantenna force and the protein state. The results we obtain indicate that controlled protein signaling provides a communication platform for information transmission between the nanoantenna and the protein with a clear physical significance. The analysis reported in this work should further research into the EM-based control of protein networks.

Collective excitations in α-helical protein structures interacting with the water environment

Low-frequency vibrational excitations of protein macromolecules in the terahertz frequency region are suggested to contribute to many biological processes such as enzymatic catalysis, intra-protein energy/charge transport, recognition, and allostery. To explain high effectiveness of these processes, two possible mechanisms of the long-lived excitation were proposed by H. Fröhlich and A.S. Davydov, which relate to either vibrational modes or solitary waves, respectively. In this paper, we developed a quantum dynamic model of vibrational excitation in α-helical proteins interacting with the aqueous environment. In the model, we distinguished three coupled subsystems, i.e., (i) a chain of hydrogen-bonded peptide groups (PGs), interacting with (ii) the subsystem of the side-chain residuals which in turn interact with (iii) the environment, surrounding water responsible for dissipation and fluctuation in the system. It was shown that the equation of motion for phonon variables of the PG chain can be transformed to nonlinear Schrodinger equation which admits bifurcation into the solution corresponding to the weak-damped vibrational modes (Fröhlich-type regime) and Davydov solitons. A bifurcation parameter is derived through the strength of phonon-phonon interaction between the side-chains and hydration-shell water molecules. As shown, the energy of these excited states is pumped through the interaction of the side-chains with fluctuating water environment of the proteins. The suggested mechanism of the collective vibrational mode excitation is discussed in connection with the recent experiments on the long-lived collective protein excitations in the terahertz frequency region and vibrational energy transport pathways in proteins.

Low-Frequency (Gigahertz to Terahertz) Depolarized Raman Scattering Off n-Alkanes, Cycloalkanes, and Six-Membered Rings: A Physical Interpretation

Molecular liquids have long been known to undergo various distinct intermolecular motions, from fast librations and cage-rattling oscillations to slow orientational and translational diffusion. However, their resultant gigahertz to terahertz spectra are far from simple, appearing as broad shapeless bands that span many orders of magnitude of frequency, making meaningful interpretation troublesome. Ad hoc spectral line shape fitting has become a notoriously fine art in the field; a unified approach to handling such spectra is long overdue. Here we apply ultrafast optical Kerr-effect (OKE) spectroscopy to study the intermolecular dynamics of room-temperature n-alkanes, cycloalkanes, and six-carbon rings, as well as liquid methane and propane. This work provides stress tests and converges upon an experimentally robust model across simple molecular series and range of temperatures, providing a blueprint for the interpretation of the dynamics of van der Waals liquids. This will enable the interpretation of low-frequency spectra of more complex liquids.

Substrate Binding Stiffens Aspartate Aminotransferase by Altering the Enzyme Picosecond Vibrational Dynamics

Protein dynamics on various time scales from femtoseconds to milliseconds impacts biological function by driving proteins to conformations conducive to ligand binding and creating functional states in enzyme catalysis. Neutron vibrational spectroscopy carried out by measuring inelastic neutron scattering from protein molecules in combination with molecular simulations has the unique ability of detecting and visualizing changes in the picosecond protein vibrational dynamics due to ligand binding. Here we present neutron vibrational spectra of a homodimeric pyridoxal 5'-phosphate-dependent enzyme, aspartate aminotransferase, obtained from the open internal aldimine and closed external aldimine conformational states. We observe that in the external aldimine state the protein structure stiffens relative to the internal aldimine state, indicating rigidified vibrational dynamics on the picosecond time scale in the low-frequency regime of 5-50 cm^-1. Our molecular dynamics simulations indicate substantial changes in the picosecond dynamics of the enzyme secondary structure elements upon substrate binding, with the largest contributions from just two helices and the β-sheet.

A THz transparent 3D printed microfluidic cell for small angle x-ray scattering

Excitation frequencies in the terahertz (THz) range are expected to lead to functionally relevant domain movements within the biological macromolecules such as proteins. The possibility of examining such movements in an aqueous environment is particularly valuable since here proteins are not deprived of any motional degrees of freedom. Small angle x-ray scattering (SAXS) is a powerful method to study the structure and domain movements of proteins in solution. Here, we present a microfluidic cell for SAXS experiments, which is also transparent for THz radiation. Specifically, cell dimensions and material were optimized for both radiation sources. In addition, the polystyrene cell can be 3D printed and easily assembled. We demonstrate the practicality of our design for SAXS measurements on several proteins in solution.

Optomechanical detection of vibration modes of a single bacterium

Low-frequency vibration modes of biological particles, such as proteins, viruses and bacteria, involve coherent collective vibrations at frequencies in the terahertz and gigahertz domains. These vibration modes carry information on their structure and mechanical properties, which are good indicators of their biological state. In this work, we harnessed a particular regime in the physics of coupled mechanical resonators to directly measure these low-frequency mechanical resonances of a single bacterium. We deposit the bacterium on the surface of an ultrahigh frequency optomechanical disk resonator in ambient conditions. The vibration modes of the disk and bacterium hybridize when their associated frequencies are similar. We developed a general theoretical framework to describe this coupling, which allows us to retrieve the eigenfrequencies and mechanical loss of the bacterium low-frequency vibration modes (quality factor). Additionally, we analysed the effect of hydration on these vibrational modes. This work demonstrates that ultrahigh frequency optomechanical resonators can be used for vibrational spectrometry with the unique capability to obtain information on single biological entities.

Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.