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

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 of thick and diluted water solutions

While bright terahertz sources are used to perform nonlinear experiments, they can be advantageous for high-precision linear measurements of opaque samples. By placing the sample away from the focus, nonlinearities can be suppressed, and sizeable amounts of transmitted radiation detected. Here, this approach is demonstrated for a 0.5 mm thick layer of liquid water in a static sample holder. Variations of the index of refraction as small as (7 ± 2) · 10-4 were detected at 0.58 THz for an aqueous salt solution containing ten millimoles of sodium chloride. To my knowledge, this precision is unprecedented in time-domain spectroscopy studies of diluted aqueous systems or other optically thick and opaque materials.

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.

Importance of Hydrogen Bonding in Crowded Environments: A Physical Chemistry Perspective

Cells are heterogeneous on every length and time scale; cytosol contains thousands of proteins, lipids, nucleic acids, and small molecules, and molecular interactions within this crowded environment determine the structure, dynamics, and stability of biomolecules. For decades, the effects of crowding at the atomistic scale have been overlooked in favor of more tractable models largely based on thermodynamics. Crowding can affect the conformations and stability of biomolecules by modulating water structure and dynamics within the cell, and these effects are nonlocal and environment dependent. Thus, characterizing water's hydrogen-bond (H-bond) networks is a critical step toward a complete microscopic crowding model. This perspective provides an overview of molecular crowding and describes recent time-resolved spectroscopy approaches investigating H-bond networks and dynamics in crowded or otherwise complex aqueous environments. Ultrafast spectroscopy combined with atomistic simulations has emerged as a powerful combination for studying H-bond structure and dynamics in heterogeneous multicomponent systems. We discuss the ongoing challenges toward developing a complete atomistic description of macromolecular crowding from an experimental as well as a theoretical perspective.

Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction

Although it is well-known that limited local mutations of enzymes, such as matrix metalloproteinases (MMPs), may change enzyme activity by orders of magnitude as well as its stability, the completely rational design of proteins is still challenging. These local changes alter the electrostatic potential and thus local electrostatic fields, which impacts the dynamics of water molecules close the protein surface. Here we show by a combined computational design, experimental, and molecular dynamics (MD) study that local mutations have not only a local but also a global effect on the solvent: In the specific case of the matrix metalloprotease MMP14, we found that the nature of local mutations, coupled with surface morphology, have the ability to influence large patches of the water hydrogen-bonding network at the protein surface, which is correlated with stability. The solvent contribution can be experimentally probed via terahertz (THz) spectroscopy, thus opening the door to the exciting perspective of rational protein design in which a systematic tuning of hydration water properties allows manipulation of protein stability and enzymatic activity.

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.

Nanofabrication Techniques in Large-Area Molecular Electronic Devices

The societal impact of the electronics industry is enormous—not to mention how this industry impinges on the global economy. The foreseen limits of the current technology—technical, economic, and sustainability issues—open the door to the search for successor technologies. In this context, molecular electronics has emerged as a promising candidate that, at least in the short-term, will not likely replace our silicon-based electronics, but improve its performance through a nascent hybrid technology. Such technology will take advantage of both the small dimensions of the molecules and new functionalities resulting from the quantum effects that govern the properties at the molecular scale. An optimization of interface engineering and integration of molecules to form densely integrated individually addressable arrays of molecules are two crucial aspects in the molecular electronics field. These challenges should be met to establish the bridge between organic functional materials and hard electronics required for the incorporation of such hybrid technology in the market. In this review, the most advanced methods for fabricating large-area molecular electronic devices are presented, highlighting their advantages and limitations. Special emphasis is focused on bottom-up methodologies for the fabrication of well-ordered and tightly-packed monolayers onto the bottom electrode, followed by a description of the top-contact deposition methods so far used.

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.