Time-Domain THz Spectroscopy Reveals Coupled Protein-Hydration Dielectric Response in Solutions of Native and Fibrils of Human Lysozyme

Terahertz Transmission through a Gold Mirror or Electrode

Hundreds of nanometer-thick metal layers are used as electrical conductors in various technologies and research fields. The intensity of the radiation transmitted by such devices is a small fraction and is often neglected. Here, it is shown that intense terahertz time-domain spectroscopy can probe the absolute electro-optical properties of a 100 nm thick gold sample in transmission geometry without the need to apply electrical contacts or handle wires. The terahertz conductivity of the metal film agrees with that obtained from standard contact measurements of the static component within the error bars. This experimental approach can help to quantify the electrical properties of opaque and conductive materials such as the composite electrodes used in photovoltaic or electrochemical applications, and in the quality control of metal films.

Water determines the intramolecular dynamics of proteins. En example of bovine serum albumin

In this work, the terahertz time-domain spectroscopy method analyzed solutions of bovine serum albumin (BSA) in two high concentrations (50 and 334 mg/mL) at three pH values (2.5, 6.5, 8.5) and the same solvents without protein, at 25°C. The spectra of dry BSA were also recorded. For the first time, a method for determining the complex dielectric permittivity of protein molecules in aqueous solutions, without the dielectric contribution of the aqueous phase, is proposed. It is shown that the dielectric permittivity of dissolved and dry BSA (lyophilized, in the native conformation) differ significantly in the terahertz frequency range. These differences are small near 70 cm-1, but they increase greatly with decreasing frequency. It was found that the dielectric losses of protein molecules in solution are close to the dielectric losses of the aqueous environment, which in this frequency range are determined by intermolecular relaxation processes of water. Since dielectric losses are directly related to molecular dynamics, this fact shows that the intramolecular dynamics of the protein completely adjusts to the intermolecular dynamics of the aqueous environment. It also indicates that the native conformation does not determine all the fundamental characteristics of a protein molecule, in particular, it does not determine the dynamics of the protein, which significantly depends on the water environment.

Peculiarities of the Dynamical Hydration Shell of Native Conformation Protein Using a Bovine Serum Albumin Example

This paper describes an approach based on the method of terahertz time-domain spectroscopy, which allows the analysis of dynamical hydration shells of proteins with a thickness of 1-2 nm. Using the example of bovine serum albumin in three conformations, it is shown that the hydration shells of the protein are characterized by increased binding of water molecules in the primary hydration layers, and in more distant areas of hydration, on the contrary, the water structure is somewhat destroyed. The fraction of free or weakly bound molecules, usually observed in the structure of liquid water in hydration shells, become more numerous but its average binding is greater than in undisturbed water. The energy distribution of hydrogen bonds in hydration shells is narrowed compared to undisturbed water. All these manifestations of hydration are most pronounced for the native conformation of the protein. Also, the hydration shells of the native protein are characterized by a smaller number of hydrogen bonds and a tendency to decrease their average energy compared to non-native conformations. The fact of a pronounced peculiarity of the hydration shells of the protein in the native conformation has been noted for different proteins before. However, the methodological approach used in this work for the first time allowed this peculiarity to be described by specific parameters of the intermolecular structure and dynamics of water.

Terahertz spectroscopy as a method for investigation of hydration shells of biomolecules

The hydration of biomolecules is one of the fundamental processes underlying the construction of living matter. The formation of the native conformation of most biomolecules is possible only in an aqueous environment. At the same time, not only water affects the structure of biomolecules, but also biomolecules affect the structure of water, forming hydration shells. However, the study of the structure of biomolecules is given much more attention than their hydration shells. A real breakthrough in the study of hydration occurred with the development of the THz spectroscopy method, which showed that the hydration shell of biomolecules is not limited to 1-2 layers of strongly bound water, but also includes more distant areas of hydration with altered molecular dynamics. This review examines the fundamental features of the THz frequency range as a source of information about the structural and dynamic characteristics of water that change during hydration. The applied approaches to the study of hydration shells of biomolecules based on THz spectroscopy are described. The data on the hydration of biomolecules of all main types obtained from the beginning of the application of THz spectroscopy to the present are summarized. The emphasis is placed on the possible participation of extended hydration shells in the realization of the biological functions of biomolecules and at the same time on the insufficient knowledge of their structural and dynamic characteristics.

Investigating the Impact of Synchrotron THz Radiation on the Corneal Hydration Using Synchrotron THz-Far Infrared Beamline

Due to increasing interest in imaging, industrial, and the development of wireless communication operating at THz frequencies, it is crucial to ascertain possible health impacts arising from exposure to THz radiation. This paper reports on the pilot study of transmittance and absorbance spectra of the porcine cornea following THz frequency irradiation at a synchrotron THz/Far-IR beamline. The exposure period was 4 hours. One cornea was exposed to the radiation, with a second cornea acting as a control. An Attenuated Total Reflection (ATR) apparatus was used, and the frequency range of 2.4 to 8 THz was selected to evaluate any changes. It was found that the synchrotron THz radiation intensities are too low to produce induced corneal injury, but may lead to subtle changes in the state of water. Our results suggest that THz spectroscopy is a promising modality for corneal tissue hydration sensing.

Detecting the First Hydration Shell Structure around Biomolecules at Interfaces

Understanding the role of water in biological processes remains a central challenge in the life sciences. Water structures in hydration shells of biomolecules are difficult to study in situ due to overwhelming background from aqueous environments. Biological interfaces introduce additional complexity because biomolecular hydration differs at interfaces compared to bulk solution. Here, we perform experimental and computational studies of chiral sum frequency generation (chiral SFG) spectroscopy to probe chirality transfer from a protein to the surrounding water molecules. This work reveals that chiral SFG probes the first hydration shell around the protein almost exclusively. We explain the selectivity to the first hydration shell in terms of the asymmetry induced by the protein structure and specific protein-water hydrogen-bonding interactions. This work establishes chiral SFG as a powerful technique for studying hydration shell structures around biomolecules at interfaces, presenting new possibilities to address grand research challenges in biology, including the molecular origins of life.

Spectroscopy of excised skin patches exposed to THz and far-IR radiation

Applications of far infrared (Far-IR) and terahertz (THz) radiation in areas such as healthcare and security are fast-growing. As a consequence, humans and the environment are becoming more exposed to mm-wave and Far-IR radiation than previously. We examined typical skin-care and sunscreen ingredients and propitiatory products with transmission FTIR, ATR-FTIR and THz-time domain spectroscopy (THz-TDS) methods using fresh and dehydrated toad and fresh human skin samples for their absorption properties in these frequency ranges. The skin hydration compounds glycerol and sorbitol have comparable absorption characteristics to physiological bulk water. Products containing these and similar hydrating compounds have significant Far-IR absorption characteristics. The sunscreen ingredients ZnO (20 micron), TiO2 (mesh 325), and graphene platelet demonstrate a generally poor Far-IR absorbance, with TiO2 displaying some frequency-specific absorption in the 3-6 THz and 12 THz regions. The Far-IR absorbance of proprietary sunscreens was, however, shown not to be significant. The absorption properties of melanin, collagen, bound water, and other constituents are significant in dehydrated skin samples but are not of the same order of importance as the hydrating agents examined.

The key role of solvent in condensation: Mapping water in liquid-liquid phase-separated FUS

Formation of biomolecular condensates through liquid-liquid phase separation (LLPS) has emerged as a pervasive principle in cell biology, allowing compartmentalization and spatiotemporal regulation of dynamic cellular processes. Proteins that form condensates under physiological conditions often contain intrinsically disordered regions with low-complexity domains. Among them, the RNA-binding proteins FUS and TDP-43 have been a focus of intense investigation because aberrant condensation and aggregation of these proteins is linked to neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal dementia. LLPS occurs when protein-rich condensates form surrounded by a dilute aqueous solution. LLPS is per se entropically unfavorable. Energetically favorable multivalent protein-protein interactions are one important aspect to offset entropic costs. Another proposed aspect is the release of entropically unfavorable preordered hydration water into the bulk. We used attenuated total reflection spectroscopy in the terahertz frequency range to characterize the changes in the hydrogen bonding network accompanying the FUS enrichment in liquid-liquid phase-separated droplets to provide experimental evidence for the key role of the solvent as a thermodynamic driving force. The FUS concentration inside LLPS droplets was determined to be increased to 2.0 mM independent of the initial protein concentration (5 or 10 μM solutions) by fluorescence measurements. With terahertz spectroscopy, we revealed a dewetting of hydrophobic side chains in phase-separated FUS. Thus, the release of entropically unfavorable water populations into the bulk goes hand in hand with enthalpically favorable protein-protein interaction. Both changes are energetically favorable, and our study shows that both contribute to the thermodynamic driving force in phase separation.

Nonlinear TeraHertz Transmission by Liquid Water at 1 THz

The solvation properties of liquid water originate from the transient network of hydrogen-bonded molecules. In order to probe the coupling between the different modes of this network, nonlinear terahertz (THz) spectroscopy techniques are required. Ideally, these techniques should use a minimal volume and capitalize on sensitive field-resolved detection. Here we performed open aperture z-scan transmission experiments on static liquid cells, and detect the THz fields with electro-optical techniques. We show that it is possible to quantify the nonlinear response of liquid water at ~1 THz even when large signals originate from the sample holder windows.

Solvent dynamics play a decisive role in the complex formation of biologically relevant redox proteins

Electron transfer processes between proteins are vital in many biological systems. Yet, the role of the solvent in influencing these redox reactions remains largely unknown. In this study, terahertz-time domain spectroscopy (THz-TDS) is used to probe the collective hydration dynamics of flavoenzyme ferredoxin-NADP+-reductase (FNR), electron transfer protein ferredoxin-1 (PetF), and the transient complex that results from their interaction. Results reveal changes in the sub-picosecond hydration dynamics that are dependent upon the surface electrostatic properties of the individual proteins and the transient complex. Retarded solvent dynamics of 8-9 ps are observed for FNR, PetF, and the FNR:PetF transient complex. Binding of the FNR:PetF complex to the substrate NADP+ results in bulk-like solvent dynamics of 7 ps, showing that formation of the ternary complex is entropically favored. Our THz measurements reveal that the electrostatic interaction of the protein surface with water results in charge sensitive changes in the solvent dynamics. Complex formation between the positively charged FNR:NADP+ pre-complex and the negatively charged PetF is not only entropically favored, but in addition the solvent reorganization into more bulk-like water assists the molecular recognition process. The change in hydration dynamics observed here suggests that the interaction with the solvent plays a significant role in mediating electron transfer processes between proteins.

Length-scale dependence of protein hydration-shell density

Here we present a computational approach based on molecular dynamics (MD) simulation to study the dependence of the protein hydration-shell density on the size of the protein molecule. The hydration-shell density of eighteen different proteins, differing in size, shape and function (eight of them are antifreeze proteins), is calculated. The results obtained show that an increase in the hydration-shell density, relative to that of the bulk, is observed (in the range of 4-14%) for all studied proteins and that this increment strongly correlates with the protein size. In particular, a decrease in the density increment is observed for decreasing protein size. A simple model is proposed in which the basic idea is to approximate the protein molecule as an effective ellipsoid and to partition the relevant parameters, i.e. the solvent-accessible volume and the corresponding solvent density, into two regions: inside and outside the effective protein ellipsoid. It is found that, within the model developed here, almost all of the hydration-density increase is located inside the protein ellipsoid, basically corresponding to pockets within, or at the surface of the protein molecule. The observed decrease in the density increment is caused by the protein size only and no difference is found between antifreeze and non-antifreeze proteins.

Water Structure and Properties at Hydrophilic and Hydrophobic Surfaces

The properties of water on both molecular and macroscopic surfaces critically influence a wide range of physical behaviors, with applications spanning from membrane science to catalysis to protein engineering. Yet, our current understanding of water interfacing molecular and material surfaces is incomplete, in part because measurement of water structure and molecular-scale properties challenges even the most advanced experimental characterization techniques and computational approaches. This review highlights progress in the ongoing development of tools working to answer fundamental questions on the principles that govern the interactions between water and surfaces. One outstanding and critical question is what universal molecular signatures capture the hydrophobicity of different surfaces in an operationally meaningful way, since traditional macroscopic hydrophobicity measures like contact angles fail to capture even basic properties of molecular or extended surfaces with any heterogeneity at the nanometer length scale. Resolving this grand challenge will require close interactions between state-of-the-art experiments, simulations, and theory, spanning research groups and using agreed-upon model systems, to synthesize an integrated knowledge of solvation water structure, dynamics, and thermodynamics.

Towards Intense THz Spectroscopy on Water: Characterization of Optical Rectification by GaP, OH1, and DSTMS at OPA Wavelengths

Water is the most prominent solvent. The unique properties of water are rooted in the dynamical hydrogen-bonded network. While TeraHertz (THz) radiation can probe directly the collective molecular network, several open issues remain about the interpretation of these highly anharmonic, coupled bands. In order to address this problem, we need intense THz radiation able to drive the liquid into the nonlinear response regime. Firstly, in this study, we summarize the available brilliant THz sources and compare their emission properties. Secondly, we characterize the THz emission by Gallium Phosphide (GaP), 2-{3-(4-hydroxystyryl)-5,5-dimethylcyclohex-2-enylidene}malononitrile (OH1), and 4-N,N-dimethylamino-4'-N'-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS) crystals pumped by an amplified near-infrared (NIR) laser with tunable wavelength. We found that both OH1 as well as DSTMS could convert NIR laser radiation between 1200 and 2500 nm into THz radiation with high efficiency (> 2 × 10-4), resulting in THz peak fields exceeding 0.1 MV/cm for modest pump excitation (~ mJ/cm2). DSTMS emits the broadest spectrum, covering the entire bandwidth of our detector from ca. 0.5 to ~7 THz, also at a laser wavelength of 2100 nm. Future improvements will require handling the photothermal damage of these delicate organic crystals, and increasing the THz frequency.

The Hydration Shell of Monomeric and Dimeric Insulin Studied by Terahertz Time-Domain Spectroscopy

Protein aggregation is believed to be a significant biological mechanism related to neurodegenerative disease, which makes the early-stage detection of aggregates a major concern. We demonstrated the use of terahertz (THz) time-domain spectroscopy to study protein-water interaction of monomeric and dimeric bovine insulin in aqueous samples. Regulated by changing pH and verified by size-exclusion chromatography and dynamic light scattering, we then measured their concentration-dependent changes in THz absorption between 0.5 and 3.0 THz and quantitatively deduced the extended hydration shell thickness by cubic distribution model and random distribution model. Under a random distribution assumption, the extended hydration thickness is 15.4 ± 0.4 Å for monomeric insulin and 17.5 ± 0.5 Å for dimeric insulin, with the hydration number of 6700 and 11,000, respectively. The hydration number of dimeric insulin is not twice but 1.64 times that of monomeric insulin, further supported by the ratio of solvent-accessible surface area. This "1.64-times" relation probably originates from the structural and conformational changes accompanied with dimerization. Combined with the investigations on insulin samples with different single amino acid mutations, residue B24 is believed to play an important role in the dimerization process. It is demonstrated that THz time-domain spectroscopy is a useful tool and has the sensitivity to provide the hydration information of different protein aggregates at an early stage.

Surface Topography Effects of Globular Biomolecules on Hydration Water

Hydration water serves as a microscopic manifestation of structural stability and functions of biomolecules. To develop bio-nanomaterials in applications, it is important to study how the surface topography and heterogeneity of biomolecules result in their diversity of the hydration dynamics and energetics. We here performed molecular dynamics simulations combined with the steered molecular dynamics and umbrella sampling to investigate the dynamics and escape process associated with the free energy change of water molecules close to a globular biomolecule, i.e., hemoglobin (Hb) and G-quadruplex DNA (GDNA). The residence time, power of long-time tail, and dipole relaxation time were found to display drastic changes within the averaged hydration shell of 3.0-5.0 Å. Compared with bulk water, in the inner hydration shell, the water dipole moment displays a slower relaxation process and is more oriented toward GDNA than toward Hb, forming a hedgehog-like structure when it surrounds GDNA. In particular, a spine water structure is observed in the GDNA narrow groove. The water isotope effect not only prolongs the dynamic time scales of libration motion in the inner hydration shell and the dipole relaxation processes in the bulk but also strengthens the DNA spine water structure. The potential of the mean force profile reflects the integrity of the hydration shell structure and enables us to obtain detailed insights into the structures formed by water, such as the caged H-bond network and the edge bridge structures; it also reveals that local hydration shell free energy (LHSFE) depends on H-bond rupture processes and ranges from 0.2 to 4.2 kcal/mol. Our results demonstrate that the surface topography of a biomolecule influences the integrity of the hydration shell structure and LHSFE. Our studies are able to identify various further applications in the areas of microfluid devices and nano-dewetting on bioinspired surfaces.

A Biophysical Perspective on Enzyme Catalysis

Even after a century of investigation, our understanding of how enzymes work remains far from complete. In particular, several factors that enable enzymes to achieve high catalytic efficiencies remain only poorly understood. A number of theories have been developed, which propose or reaffirm that enzymes work as structural scaffolds, serving to bring together and properly orient the participants so that the reaction can proceed; therefore, leading to enzymes being viewed as only passive participants in the catalyzed reaction. A growing body of evidence shows that enzymes are not rigid structures but are constantly undergoing a wide range of internal motions and conformational fluctuations. In this Perspective, on the basis of studies from our group, we discuss the emerging biophysical model of enzyme catalysis that provides a detailed understanding of the interconnection among internal protein motions, conformational substates, enzyme mechanisms, and the catalytic efficiency of enzymes. For a number of enzymes, networks of conserved residues that extend from the surface of the enzyme all the way to the active site have been discovered. These networks are hypothesized to serve as pathways of energy transfer that enables thermodynamical coupling of the surrounding solvent with enzyme catalysis and play a role in promoting enzyme function. Additionally, the role of enzyme structure and electrostatic effects has been well acknowledged for quite some time. Collectively, the recent knowledge gained about enzyme mechanisms suggests that the conventional paradigm of enzyme structure encoding function is incomplete and needs to be extended to structure encodes dynamics, and together these enzyme features encode function including catalytic rate acceleration.

Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions

In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B₂₂, and the diffusion interaction coefficient, k_D. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.

The spatial range of protein hydration

Proteins interact with their aqueous surroundings, thereby modifying the physical properties of the solvent. The extent of this perturbation has been investigated by numerous methods in the past half-century, but a consensus has still not emerged regarding the spatial range of the perturbation. To a large extent, the disparate views found in the current literature can be traced to the lack of a rigorous definition of the perturbation range. Stating that a particular solvent property differs from its bulk value at a certain distance from the protein is not particularly helpful since such findings depend on the sensitivity and precision of the technique used to probe the system. What is needed is a well-defined decay length, an intrinsic property of the protein in a dilute aqueous solution, that specifies the length scale on which a given physical property approaches its bulk-water value. Based on molecular dynamics simulations of four small globular proteins, we present such an analysis of the structural and dynamic properties of the hydrogen-bonded solvent network. The results demonstrate unequivocally that the solvent perturbation is short-ranged, with all investigated properties having exponential decay lengths of less than one hydration shell. The short range of the perturbation is a consequence of the high energy density of bulk water, rendering this solvent highly resistant to structural perturbations. The electric field from the protein, which under certain conditions can be long-ranged, induces a weak alignment of water dipoles, which, however, is merely the linear dielectric response of bulk water and, therefore, should not be thought of as a structural perturbation. By decomposing the first hydration shell into polarity-based subsets, we find that the hydration structure of the nonpolar parts of the protein surface is similar to that of small nonpolar solutes. For all four examined proteins, the mean number of water-water hydrogen bonds in the nonpolar subset is within 1% of the value in bulk water, suggesting that the fragmentation and topography of the nonpolar protein-water interface has evolved to minimize the propensity for protein aggregation by reducing the unfavorable free energy of hydrophobic hydration.