Moving in the Right Direction: Protein Vibrations Steering Function

Mechanotransduction, cellular biophotonic activity, and signaling patterns for tissue regeneration

Signaling molecules exhibit mechanical oscillations, entailing precise vibrational directionalities. These steering signatures have profound functional implications and are intimately connected with the onset of molecular electric oscillations and biophoton emission. We discuss biophotonic activity as a form of endogenous photobiomodulation, orchestrating the mechano-sensing/-transduction in signaling players. We focus on exogenous photobiomodulation in the form of pulsed wave modulation of selected light wavelengths to direct endogenous biophotonic activity and molecular cellular dynamics. We highlight the relevance of this strategy to target and reprogram the developmental potential of tissue-resident stem cells in damaged tissues, affording precision regenerative medicine without the need for cell or tissue transplantation.

Harmonic and anharmonic studies on THz spectra of two vanillin polymorphs

Polymorphism commonly exists in organic molecular crystals. The fingerprint features in low-frequency vibrational range are important information reflecting different intermolecular interactions of polymorphs. Interpreting these features is very helpful to understand vibrational property of polymorphs and reveal the thermodynamic stability. In this work, the low-frequency vibrations of form I and II of vanillin are investigated using terahertz time-domain spectroscopy. Static DFT calculation and ab initio molecular dynamics (AIMD) are employed to interpret their low-frequency vibrations of both forms in harmonic and anharmonic ways, respectively. Their low-frequency vibration characteristics in harmonic calculations are discussed, and anharmonic mode couplings between OH bond stretch and the stretching and bending motion of hydrogen bonds are uncovered. Moreover, the thermodynamic energies including electronic potential energy and vibrational/kinetic energy arising from nuclear motions are calculated. The result reveals that the stability order of the two forms is mainly dependent on their electric potential energy difference.

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.

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.

Vibrational Analysis of Hydration-Layer Water around Ubiquitin, Unpeeled Layer by Layer: Molecular-Dynamics Perceptions

Classical molecular-dynamics simulations have been performed to examine the interplay between ubiquitin and its hydration-water sub-layers, chiefly from a vibrational-mode and IR viewpoint-where we analyse individual sub-layers characteristics. The vibrational Density of States (VDOS) revealed that the first solvation sub-shell indicates a confined character therein. For layers of increasing distance from the surface, the adoption of greater bulk-like spectral behaviour was evident, suggesting that vibrational harmonisation to bulk occurs within 6-7 Å of the surface.

Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering

Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ∼20-50 cm-1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.

Label-free laser spectroscopy for respiratory virus detection: A review

Infectious diseases are among the most severe threats to modern society. Current methods of virus infection detection based on genome tests need reagents and specialized laboratories. The desired characteristics of new virus detection methods are noninvasiveness, simplicity of implementation, real-time, low cost and label-free detection. There are two groups of methods for molecular biomarkers' detection and analysis: (i) a sample physical separation into individual molecular components and their identification, and (ii) sample content analysis by laser spectroscopy. Variations in the spectral data are typically minor. It requires the use of sophisticated analytical methods like machine learning. This review examines the current technological level of laser spectroscopy and machine learning methods in applications for virus infection 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.

Cell Responsiveness to Physical Energies: Paving the Way to Decipher a Morphogenetic Code

We discuss emerging views on the complexity of signals controlling the onset of biological shapes and functions, from the nanoarchitectonics arising from supramolecular interactions, to the cellular/multicellular tissue level, and up to the unfolding of complex anatomy. We highlight the fundamental role of physical forces in cellular decisions, stressing the intriguing similarities in early morphogenesis, tissue regeneration, and oncogenic drift. Compelling evidence is presented, showing that biological patterns are strongly embedded in the vibrational nature of the physical energies that permeate the entire universe. We describe biological dynamics as informational processes at which physics and chemistry converge, with nanomechanical motions, and electromagnetic waves, including light, forming an ensemble of vibrations, acting as a sort of control software for molecular patterning. Biomolecular recognition is approached within the establishment of coherent synchronizations among signaling players, whose physical nature can be equated to oscillators tending to the coherent synchronization of their vibrational modes. Cytoskeletal elements are now emerging as senders and receivers of physical signals, "shaping" biological identity from the cellular to the tissue/organ levels. We finally discuss the perspective of exploiting the diffusive features of physical energies to afford in situ stem/somatic cell reprogramming, and tissue regeneration, without stem cell transplantation.

Joint neutron/molecular dynamics vibrational spectroscopy reveals softening of HIV-1 protease upon binding of a tight inhibitor

Biomacromolecules are inherently dynamic, and their dynamics are interwoven into function. The fast collective vibrational dynamics in proteins occurs in the low picosecond timescale corresponding to frequencies of ∼5-50 cm^-1. This sub-to-low THz frequency regime covers the low-amplitude collective breathing motions of a whole protein and vibrations of the constituent secondary structure elements, such as α-helices, β-sheets and loops. We have used inelastic neutron scattering experiments in combination with molecular dynamics simulations to demonstrate the vibrational dynamics softening of HIV-1 protease, a target of HIV/AIDS antivirals, upon binding of a tight clinical inhibitor darunavir. Changes in the vibrational density of states of matching structural elements in the two monomers of the homodimeric protein are not identical, indicating asymmetric effects of darunavir on the vibrational dynamics. Three of the 11 major secondary structure elements contribute over 40% to the overall changes in the vibrational density of states upon darunavir binding. Molecular dynamics simulations informed by experiments allowed us to estimate that the altered vibrational dynamics of the protease would contribute -3.6 kcal mol^-1 at 300 K, or 25%, to the free energy of darunavir binding. As HIV-1 protease drug resistance remains a concern, our results open a new avenue to help establish a direct quantitative link between protein vibrational dynamics and drug resistance.

Functional-State Dependence of Picosecond Protein Dynamics

We examine temperature-dependent picosecond dynamics of two benchmarking proteins lysozyme and cytochrome c using temperature-dependent terahertz permittivity measurements. We find that a double Arrhenius temperature dependence with activation energies E₁ ∼ 0.1 kJ/mol and E₂ ∼ 10 kJ/mol fits the folded and ligand-free state response. The higher activation energy is consistent with the so-called protein dynamical transition associated with beta relaxations at the solvent-protein interface. The lower activation energy is consistent with correlated structural motions. When the structure is removed by denaturing, the lower-activation-energy process is no longer present. Additionally, the lower-activation-energy process is diminished with ligand binding but not for changes in the internal oxidation state. We suggest that the lower-energy activation process is associated with collective structural motions that are no longer accessible with denaturing or binding.

Low-frequency vibrational modes in G-quadruplexes reveal the mechanical properties of nucleic acids

Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition. However, understanding the vibrational basis of these mechanisms relies on theoretical models due to the lack of experimental evidence. Here we present the low-frequency vibrational spectra of G-quadruplexes (structures formed by four strands of DNA) and B-DNA characterized using femtosecond optical Kerr-effect spectroscopy. Contrary to expectation, we found that G-quadruplexes show several strongly underdamped delocalized phonon-like modes that have the potential to contribute to the biology of the DNA at the atomic level. In addition, G-quadruplexes present modes at a higher frequency than B-DNA demonstrating that changes in the stiffness of the molecule alter its gigahertz to terahertz vibrational profile.

Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA–protein recognition.

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.

Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis

Proteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but experimentally identifying the vibrations associated with specific motions has proved challenging. Spectroscopy is an ideal tool to explore these excitations, but measurements have been largely unable to identify important frequency bands. The result is at odds with some previous calculations and raises the question what methods could successfully characterize protein structural vibrations. Here we show the lack of spectral structure arises in part from the variations in protein structure as the protein samples the energy landscape. However, by averaging over the energy landscape as sampled using an aggregate 18.5 μs of all-atom molecular dynamics simulation of hen egg white lysozyme and normal-mode analyses, we find vibrations with large overlap with functional displacements are surprisingly concentrated in narrow frequency bands. These bands are not apparent in either the ensemble averaged vibrational density of states or isotropic absorption. However, in the case of the ensemble averaged anisotropic absorption, there is persistent spectral structure and overlap between this structure and the functional displacement frequency bands. We systematically lay out heuristics for calculating the spectra robustly, including the need for statistical sampling of the protein and inclusion of adequate water in the spectral calculation. The results show the congested spectrum of these complex molecules obscures important frequency bands associated with function and reveal a method to overcome this congestion by combining structurally sensitive spectroscopy with robust normal mode ensemble analysis.

Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1

Allosteric molecules provide a powerful means to modulate protein function. However, the effect of such ligands on distal orthosteric sites cannot be easily described by classical docking methods. Here, we applied machine learning (ML) approaches to expose the links between local dynamic patterns and different degrees of allosteric inhibition of the ATPase function in the molecular chaperone TRAP1. We focused on 11 novel allosteric modulators with similar affinities to the target but with inhibitory efficacy between the 26.3 and 76%. Using a set of experimentally related local descriptors, ML enabled us to connect the molecular dynamics (MD) accessible to ligand-bound (perturbed) and unbound (unperturbed) systems to the degree of ATPase allosteric inhibition. The ML analysis of the comparative perturbed ensembles revealed a redistribution of dynamic states in the inhibitor-bound versus inhibitor-free systems following allosteric binding. Linear regression models were built to quantify the percentage of experimental variance explained by the predicted inhibitor-bound TRAP1 states. Our strategy provides a comparative MD–ML framework to infer allosteric ligand functionality. Alleviating the time scale issues which prevent the routine use of MD, a combination of MD and ML represents a promising strategy to support in silico mechanistic studies and drug design.

Terahertz Spectroscopy Tracks Proteolysis by a Joint Analysis of Absorptance and Debye Model

Terahertz waves have attracted great attention in biomolecule research because of the fact that they cover the range of energy levels of weak interactions, skeleton vibrations, and dipole rotations during inter- and intramolecular interactions in biomacromolecules. In this study, we validated the feasibility of employing terahertz time-domain spectroscopy (THz-TDS) for the nondestructive and label-free monitoring of protein digestion. The acid protease, pepsin, was used at its optimal pH to hydrolyze bovine serum albumin. Correspondingly, the control group experiment was also conducted by adjusting the pH value to inactivate pepsin. The progress of these two experiments was tracked by a compact commercial THz-TDS for 1 h. On one hand, the reaction-time-dependent absorption coefficient was calculated, and a direct absorption coefficient analysis was completed. The results indicate that protein hydrolysis can be easily monitored over time by focusing on the variation tendency of the absorption coefficient from a macroscopic perspective. On the other hand, we explored the use of the Debye model to analyze the dielectric properties of the solution during protein hydrolysis. The results of the Debye analysis prove that it is possible to investigate in detail the microscopic dynamics of biomacromolecule solutions at the molecular level by THz-TDS. Our research examined the process of protein hydrolysis by a combination of absorption spectra and Debye analysis and demonstrated that terahertz spectroscopy is a powerful technology for the investigation of biomolecular reactions, with potential applications in variety of fields.

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.

Resolving Anharmonic Lattice Dynamics in Molecular Crystals with X-Ray Diffraction and Terahertz Spectroscopy

Molecular crystals are increasingly being used for advanced applications, ranging from pharmaceutics to organic electronics, with their utility dictated by a combination of their three-dimensional structures and molecular dynamics-with anharmonicity in the low-frequency vibrations crucial to numerous bulk phenomena. Through the use of temperature-dependent x-ray diffraction and terahertz time-domain spectroscopy, the structures and dynamics of a pair of isomeric molecular crystals exhibiting nearly free rotation of a CF_{3} functional group at ambient conditions are fully characterized. Using a recently developed solid-state anharmonic vibrational correction, and applying it to a molecular crystal for the first time, the temperature-dependent spatial displacements of atoms along particular terahertz modes are obtained, and are found to be in excellent agreement with the experimental observations, including the assignment of a previously unexplained absorption feature in the low-frequency spectrum of one of the solids.

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.

DROIDS 3.0-Detecting Genetic and Drug Class Variant Impact on Conserved Protein Binding Dynamics

The application of statistical methods to comparatively framed questions about the molecular dynamics (MD) of proteins can potentially enable investigations of biomolecular function beyond the current sequence and structural methods in bioinformatics. However, the chaotic behavior in single MD trajectories requires statistical inference that is derived from large ensembles of simulations representing the comparative functional states of a protein under investigation. Meaningful interpretation of such complex forms of big data poses serious challenges to users of MD. Here, we announce Detecting Relative Outlier Impacts from Molecular Dynamic Simulation (DROIDS) 3.0, a method and software package for comparative protein dynamics that includes maxDemon 1.0, a multimethod machine learning application that trains on large ensemble comparisons of concerted protein motions in opposing functional states generated by DROIDS and deploys learned classifications of these states onto newly generated MD simulations. Local canonical correlations in learning patterns generated from independent, yet identically prepared, MD validation runs are used to identify regions of functionally conserved protein dynamics. The subsequent impacts of genetic and/or drug class variants on conserved dynamics can also be analyzed by deploying the classifiers on variant MD simulations and quantifying how often these altered protein systems display opposing functional states. Here, we present several case studies of complex changes in functional protein dynamics caused by temperature, genetic mutation, and binding interactions with nucleic acids and small molecules. We demonstrate that our machine learning algorithm can properly identify regions of functionally conserved dynamics in ubiquitin and TATA-binding protein (TBP). We quantify the impact of genetic variation in TBP and drug class variation targeting the ATP-binding region of Hsp90 on conserved dynamics. We identify regions of conserved dynamics in Hsp90 that connect the ATP binding pocket to other functional regions. We also demonstrate that dynamic impacts of various Hsp90 inhibitors rank accordingly with how closely they mimic natural ATP binding.

Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties

Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments.

Near-field THz micropolarimetry

We introduce a method for rapid determination of anisotropic terahertz absorption with sub micron resolution and high spectral integrity in the terahertz range. The method is ideal for microscopic and environmentally sensitive materials such as 2-D materials and protein crystals where the anisotropic absorption is critical to understanding underlying physics. We introduce the idea of using an iso-response relationship between the THz polarization and electro optic probe polarization to enable stationary sample polarization measurements covering a full 2π polarization dependence measurement.

Stationary Sample Anisotropic THz Spectroscopy using Discretely Tunable THz Sources

We demonstrate anisotropic THz spectroscopy of sucrose using newly developed compact discretely tunable THz sources for turn-key spectroscopic systems.

Strong coupling of collective intermolecular vibrations in organic materials at terahertz frequencies

Several years ago, strong coupling between electronic molecular transitions and photonic structures was shown to modify the electronic landscape of the molecules and affect their chemical behavior. Since then, this concept has evolved into a new field known as polaritonic chemistry. An important ingredient in the progress of this field was the demonstration of strong coupling with intra-molecular vibrations, which enabled the modification of processes occurring at the electronic ground-state. Here we demonstrate strong coupling with collective, inter-molecular vibrations occurring in organic materials in the low-terahertz region (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\lesssim$$\end{document}≲10¹² Hz). Using a cavity filled with α-lactose molecules, we measure the temporal evolution and observe coherent Rabi oscillations, corresponding to a splitting of 68 GHz. These results take strong coupling into a new class of materials and processes, including skeletal polymer motions, protein dynamics, metal organic frameworks and other materials, in which collective, spatially extended degrees of freedom participate in the dynamics.

Here, the authors demonstrate strong coupling between collective, terahertz inter-molecular vibrations of organic materials and a Fabry-Pérot cavity. These results extend the applicability of polaritonic chemistry to large-scale organic systems, such as biological macromolecules and polymer chains.

Tunable compact narrow band THz sources for frequency domain THz anisotropic spectroscopy

We demonstrate frequency domain THz anisotropy signature detection for protein crystal models using newly developed compact tunable narrow band THz sources based on Orientation Patterned Gallium Phosphide for turn-key spectroscopic systems.

Protein and RNA dynamical fingerprinting

Protein structural vibrations impact biology by steering the structure to functional intermediate states; enhancing tunneling events; and optimizing energy transfer. Strong water absorption and a broad continuous vibrational density of states have prevented optical identification of these vibrations. Recently spectroscopic signatures that change with functional state were measured using anisotropic terahertz microscopy. The technique however has complex sample positioning requirements and long measurement times, limiting access for the biomolecular community. Here we demonstrate that a simplified system increases spectroscopic structure to dynamically fingerprint biomacromolecules with a factor of 6 reduction in data acquisition time. Using this technique, polarization varying anisotropy terahertz microscopy, we show sensitivity to inhibitor binding and unique vibrational spectra for several proteins and an RNA G-quadruplex. The technique’s sensitivity to anisotropic absorbance and birefringence provides rapid assessment of macromolecular dynamics that impact biology.

The characterization of biomacromolecule structural vibrations has been impeded by a broad continuous vibrational density of states obscuring molecule specific vibrations. A terahertz microscopy system using polarization control produces signatures to dynamically fingerprint proteins and a RNA G-quadruplex.

Molecular Dynamics Simulations of Macromolecular Crystals

The structures of biological macromolecules would not be known to their present extent without X-ray crystallography. Most simulations of globular proteins in solution begin by surrounding the crystal structure of the monomer in a bath of water molecules, but the standard simulation employing periodic boundary conditions is already close to a crystal lattice environment. With simple protocols, the same software and molecular models can perform simulations of the crystal lattice, including all asymmetric units and solvent to fill the box. Throughout the history of molecular dynamics, studies of crystal lattices have served to investigate the quality of the underlying force fields, correlate the simulated ensembles to experimental structure factors, and extrapolate the behavior in lattices to behavior in solution. Powerful new computers are enabling molecular simulations with greater realism and statistical convergence. Meanwhile, the advent of exciting new methods in crystallography, including femtosecond free-electron lasers and image reconstruction for time-resolved crystallography on slurries of small crystals, is expanding the range of structures accessible to X-ray diffraction. We review past fusions of simulations and crystallography, then look ahead to the ways that simulations of crystal structures will enhance structural biology in the future.

THz Anisotropy Identification using Tunable Compact Narrow Band THz Sources

We demonstrate THz anisotropy signature determination of a protein crystal model using newly developed compact tunable narrow band THz sources for turn-key spectroscopic systems for the bio molecular community.

Role of Terahertz (THz) Fluctuations in the Allosteric Properties of the PDZ Domains

With the aim of investigating the relationship between the fast fluctuations of proteins and their allosteric behavior, we perform molecular dynamics simulations of two model PDZ domains with differential allosteric responses. We focus on protein dynamics in the THz regime (0.1–3 THz) as opposed to lower frequencies. By characterizing the dynamic modulation of the protein backbone induced by ligand binding in terms of single residue and pairwise distance fluctuations, we identify a response nucleus modulated by the ligand that is visible only at THz frequencies. The residues of this nucleus undergo a significant stiffening and an increase in mutual coordination upon binding. Additionally, we find that the dynamic modulation is significantly more intense for the side chains, where it is also redistributed to distal regions not immediately in contact with the ligand allowing us to better define the response nucleus at THz frequencies. The overlap between the known allosterically responding residues of the investigated PDZ domains and the modulated region highlighted here suggests that fast THz dynamics could play a role in allosteric mechanisms.

Stress Propagation through Biological Lipid Bilayers in Silico

Membrane tension plays various critical roles in the cell. We here asked how fast and how far localized pulses of mechanical stress dynamically propagate through biological lipid bilayers. In both coarse-grained and all-atom molecular dynamics simulations of a dipalmitoylphosphatidylcholine lipid bilayer, we observed nanometer-wide stress pulses, propagating very efficiently longitudinally at a velocity of approximately 1.4 ± 0.5 nm/ps (km/s), in close agreement with the expected speed of sound from experiments. Remarkably, the predicted characteristic attenuation time of the pulses was in the order of tens of picoseconds, implying longitudinal stress propagation over length scales up to several tens of nanometers before damping. Furthermore, the computed dispersion relation leading to such damping was consistent with proposed continuum viscoelastic models of propagation. We suggest this mode of stress propagation as a potential ultrafast mechanism of signaling that may quickly couple mechanosensitive elements in crowded biological membranes.