Water as a Biomolecule

The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research

The biophysics of water, has been debated over more than a century. Although its importance is still underestimated, significant breakthroughs occurred in recent years. The influence of protein condensation on water availability control was documented, new findings on water-transport proteins emerged, and the way water molecules rearrange to minimize free energy at interfaces was deciphered, influencing membrane thermodynamics. The state of knowledge continued to progress in the field of deep-sea marine biology, highlighting unknown effects of high hydrostatic pressure and/or temperature on interactions between proteins and ligands in extreme environments, and membrane structure adaptations. The role of osmolytes in protein stability control under stress is also discussed here in relation to fish egg hydration/buoyancy. The complexity of water movements within the cell is updated, all these findings leading to a better view of their impact on many cellular processes. The way water flow and osmotic gradients generated by ion transport work together to produce the driving force behind cell migration is also relevant to both marine biology and cancer research. Additional common points concern water dynamic changes during the neoplastic transformation of cells and tissues, or embryo development. This could improve imaging techniques, early cancer diagnosis, and understanding of the molecular and physiological basis of buoyancy for many marine species.

Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment

Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.

Linking surface tension to water polarization with a new hypothesis: The Ling-Damodaran Isotherm

Studying aqueous solutions of complex (bio)polymers is essential from both theoretical and practical perspectives. To understand the principles that govern the properties of these solutions is pivotal for the study of biological processes, considering that the most distinguished components of the cells are polymers (proteins, nucleic acids). These macromolecular aqueous systems, known as colloids, has raise the interest of scientists in recent years. It is known that several physicochemical properties deviate from ideal behaviour in this kind of solutions and that the physical state of water is different compared to its pure state. Particularly, the surface tension of such mixtures often shows a peculiar profile at semi-dilute and concentrated conditions. Here, we joined the colloidal concept of water polarization (proposed in the Association-Induction Hypothesis) with Damodaran's formalism for surface tension to theoretically derive a compelling mathematical model that explains the behaviour of polymer solutions. We measured the surface tension and osmolarity of different polyethylene oxide solutions and we used the ACDAN fluorescence probe to assess the water dipolar relaxation (polarization) in these mixtures. As a proof of concept, we also studied the influence of these polymer solutions on lipid interfaces. Our isotherm model explains the experimental observations with a unifying view that correlates with other measured properties, such as osmolarity and water dipolar relaxation. This provides a link between interfacial and bulk physicochemical properties of polymer solutions, also giving a new framework for studying the interaction of colloidal systems with lipid membranes interfaces.

Permeability enhancement of Kv1.2 potassium channel by a terahertz electromagnetic field

As biomolecules vibrate and rotate in the terahertz band, the biological effects of terahertz electromagnetic fields have drawn considerable attention from the physiological and medical communities. Ion channels are the basis of biological electrical signals, so studying the effect of terahertz electromagnetic fields on ion channels is significant. In this paper, the effect of a terahertz electromagnetic field with three different frequencies, 6, 15, and 25 THz, on the Kv1.2 potassium ion channel was investigated by molecular dynamics simulations. The results show that an electromagnetic field with a 15 THz frequency can significantly enhance the permeability of the Kv1.2 potassium ion channel, which is 1.7 times higher than without an applied electric field. By analyzing the behavior of water molecules, it is found that the electromagnetic field with the 15 THz frequency shortens the duration of frozen and relaxation processes when potassium ions pass through the channel, increases the proportion of the direct knock-on mode, and, thus, enhances the permeability of the Kv1.2 potassium ion channel.

Catalyst-free C(sp3)-H functionalization of methyl azaarenes with heteroaromatic trifluoromethyl ketone hydrates: "all-water" synthesis of α-trifluoromethyl tertiary alcohols

An efficient catalyst-free C(sp³)-H bond functionalization of methyl azaarenes with heteroaromatic trifluoromethyl ketone hydrates in neat water has been developed for the synthesis of α-trifluoromethyl tertiary alcohols bearing N-heteroaromatics. This method not only features excellent efficiency, broad substrate scope, catalyst-free conditions, and easy gram-scale preparation but also represents a new and rare example of "all-water" synthesis of trifluoromethylated molecules.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

Impact of macromolecular crowding on the mesomorphic behavior of lipid self-assemblies

Using LAURDAN fluorescence we observed that water dynamics measured at the interface of DOPC bilayers can be differentially regulated by the presence of crowded suspensions of different proteins (HSA, IgG, Gelatin) and PEG, under conditions where the polymers are not in direct molecular contact with the lipid interface. Specifically, we found that the decrease in water dipolar relaxation at the membrane interface correlates with an increased fraction of randomly oriented (or random coil) configurations in the polymers, as Gelatin > PEG > IgG > HSA. By using the same experimental strategy, we also demonstrated that structural transitions from globular to extended conformations in proteins can induce transitions between lamellar and non-lamellar phases in mixtures of DOPC and monoolein. Independent experiments using Raman spectroscopy showed that aqueous suspensions of polymers exhibiting high proportions of randomly oriented conformations display increased fractions of tetracoordinated water, a configuration that is dominant in ice. This indicates a greater capacity of this type of structure for polarizing water and consequently reducing its chemical activity. This effect is in line with one of the tenets of the Association Induction Hypothesis, which predicts a long-range dynamic structuring of water molecules via their interactions with proteins (or other polymers) showing extended conformations. Overall, our results suggest a crucial role of water in promoting couplings between structural changes in macromolecules and supramolecular arrangements of lipids. This mechanism may be of relevance to cell structure/function when the crowded nature of the intracellular milieu is considered.

Redefining the concept of hydration water near soft interfaces

Water determines the properties of biological systems. Therefore, understanding the nature of the mutual interaction between water and biosystems is of primary importance for a proper assessment of any biological activity, e.g., the efficacy of new drugs or vaccines. A convenient way to characterize the interactions between biosystems and water is to analyze their impact on water density and dynamics in the proximity of the interfaces. It is commonly accepted that water bulk density and dynamical properties are recovered at distances of the order of 1 nm away from the surface of biological systems. This notion leads to the definition of hydration or biological water as the nanoscopic layer of water covering the surface of biosystems and to the expectation that all the effects of the water-interface interaction are limited to this thin region. Here, we review some of our latest contributions, showing that phospholipid membranes affect the water dynamics, structural properties, and hydrogen bond network at a distance that is more than twice as large as the commonly evoked ∼1nm thick layer and of the order of 2.4 nm. Furthermore, we unveil that at a shorter distance ∼0.5nm from the membrane, instead, there is an additional interface between lipid-bound and unbound water. Bound water has a structural role in the stability of the membrane. Our results imply that the concept of hydration water should be revised or extended and pave the way to a deeper understanding of the mutual interactions between water and biological systems.

Hydrogen-Bond Dynamics and Energetics of Biological Water

Water molecules in the immediate vicinity of biomacromolecules and biomimetic organized assemblies often exhibit a markedly distinct behavior from that of their bulk counterparts. The overall sluggish behavior of biological water substantially affects the stability and integrity of biomolecules, as well as the successful execution of various crucial water-mediated biochemical phenomena. In this Minireview, insights are provided into the features of truncated hydrogen-bond networks that grant biological water its unique characteristics. In particular, experimental results and theoretical investigations, based on chemical kinetics, are presented that have shed light on the dynamics and energetics governing such characteristics. It is emphasized how such details help us to understand the energetics of biological water, an aspect relatively less explored than its dynamics. For instance, when biological water at hydrophilic or charged protein surfaces was explored, the free energy of H-bond breakage was found to be of the order of 0.4 kcal mol^-1 higher than that of bulk water.

Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor

The multiple-solvent crystal structure (MSCS) approach uses high concentrations of organic solvents to characterize the interactions and effects of solvents on proteins. Here, the method has been further developed and an MSCS data-handling pipeline is presented that uses the Detection of Related Solvent Positions (DRoP) program to improve data quality. DRoP is used to selectively model conserved water molecules, so that an advanced stage of structural refinement is reached quickly. This allows the placement of organic molecules more accurately and convergence on high-quality maps and structures. This pipeline was applied to the chromatin-associated protein barrier-to-autointegration factor (BAF), resulting in structural models with better than average statistics. DRoP and Phenix Structure Comparison were used to characterize the data sets and to identify a binding site that overlaps with the interaction site of BAF with emerin. The conserved water-mediated networks identified by DRoP suggested a mechanism by which water molecules are used to drive the binding of DNA. Normalized and differential B-factor analysis is shown to be a valuable tool to characterize the effects of specific solvents on defined regions of BAF. Specific solvents are identified that cause stabilization of functionally important regions of the protein. This work presents tools and a standardized approach for the analysis and comprehension of MSCS data sets.

A Novel Tool for Visualization of Water Molecular Structure and Its Changes, Expressed on the Scale of Temperature Influence

Aquaphotomics utilizes water-light interaction for in-depth exploration of water, its structure and role in aqueous and biologic systems. The aquagram, a major analytical tool of aquaphotomics, allows comparison of water molecular structures of different samples by comparing their respective absorbance spectral patterns. Temperature is the strongest perturbation of water changing almost all water species. To better interpret and understand spectral patterns, the objective of this work was to develop a novel, temperature-scaled aquagram that provides standardized information about changes in water molecular structure caused by solutes, with its effects translated to those which would have been caused by respective temperature changes. NIR spectra of Milli-Q water in the temperature range of 20–70 °C and aqueous solutions of potassium chloride in concentration range of 1 to 1000 mM were recorded to demonstrate the applicability of the proposed novel tool. The obtained results presented the influence of salt on the water molecular structure expressed as the equivalent effect of temperature in degrees of Celsius. The temperature-based aquagrams showed the well-known structure breaking and structure making effects of salts on water spectral pattern, for the first time presented in the terms of temperature influence on pure water. This new method enables comparison of spectral patterns providing a universal tool for evaluation of various bio-aqueous systems which can provide better insight into the system’s functionality.

Determining terahertz resonant peaks of biomolecules in aqueous environment

The resonant peaks of biomolecules provide information on the molecules' physical and chemical properties. Although many biomolecules have resonant peaks in the terahertz region, it is difficult to observe their specific signals in aqueous environments. Hence, this paper proposes a method for determining these peaks. We found the specific resonant peaks of a modified nucleoside, 5-methlycytidine and modified HEK293T DNA in an aqueous solution through baseline correction. We evaluated the consistency of various fitting functions used for determining the peaks with various parameters. We separated two resonance peaks of 5-methlycytidine at 1.59 and 1.97 THz and for artificially methylated HEK293T DNA at 1.64 and 2.0 THz.

Radical cyclizations of enynes/dienes with alcohols in water using a green oxidant

A simple, eco-friendly, and efficient methodology for performing radical cyclizations of enynes/dienes with alcohols in water has been established.

Optical mapping of biological water in single live cells by stimulated Raman excited fluorescence microscopy

Water is arguably the most common and yet least understood material on Earth. Indeed, the biophysical behavior of water in crowded intracellular milieu is a long-debated issue. Understanding of the spatial and compositional heterogeneity of water inside cells remains elusive, largely due to a lack of proper water-sensing tools with high sensitivity and spatial resolution. Recently, stimulated Raman excited fluorescence (SREF) microscopy was reported as the most sensitive vibrational imaging in the optical far field. Herein we develop SREF into a water-sensing tool by coupling it with vibrational solvatochromism. This technique allows us to directly visualize spatially-resolved distribution of water states inside single mammalian cells. Qualitatively, our result supports the concept of biological water and reveals intracellular water heterogeneity between nucleus and cytoplasm. Quantitatively, we unveil a compositional map of the water pool inside living cells. Hence we hope SREF will be a promising tool to study intracellular water and its relationship with cellular activities.

Aquaphotomics-From Innovative Knowledge to Integrative Platform in Science and Technology

Aquaphotomics is a young scientific discipline based on innovative knowledge of water molecular network, which as an intrinsic part of every aqueous system is being shaped by all of its components and the properties of the environment. With a high capacity for hydrogen bonding, water molecules are extremely sensitive to any changes the system undergoes. In highly aqueous systems-especially biological-water is the most abundant molecule. Minute changes in system elements or surroundings affect multitude of water molecules, causing rearrangements of water molecular network. Using light of various frequencies as a probe, the specifics of water structure can be extracted from the water spectrum, indirectly providing information about all the internal and external elements influencing the system. The water spectral pattern hence becomes an integrative descriptor of the system state. Aquaphotomics and the new knowledge of water originated from the field of near infrared spectroscopy. This technique resulted in significant findings about water structure-function relationships in various systems contributing to a better understanding of basic life phenomena. From this foundation, aquaphotomics started integration with other disciplines into systematized science from which a variety of applications ensued. This review will present the basics of this emerging science and its technological potential.

The medical application of terahertz technology in non-invasive detection of cells and tissues: opportunities and challenges

Terahertz (THz = 1012 Hz) spectroscopy has shown great potential in biomedical research due to its unique features, such as the non-invasive and label-free identification of living cells and medical imaging. In this review, we summarized the advantages and progresses achieved in THz spectroscopy technology for blood cell detection, cancer cell characterization, bacterial identification and biological tissue discrimination, further introducing THz imaging systems and its progress in tissue imaging. We also highlighted the biological effects of THz radiation during its biological applications and the existing challenges and strategies to accelerate future clinical applications. The future prospects for THz spectroscopy will focus on developing rapid, label-free, and convenient biosensors for point-of-care tests and THz in vivo imaging.

Comparative Study of the Effects of Temperature and Pressure on the Water-Mediated Interactions between Apolar Nanoscale Solutes

We perform molecular dynamics simulations to study the effects of temperature and pressure on the water-mediated interaction (WMI) between two nanoscale (apolar) graphene plates at 240 ≤ T ≤ 400 K and -100 ≤ P ≤ 1200 MPa. These are thermodynamic conditions relevant to, for example, cooling-, heating-, compression-, and decompression-induced protein denaturation. We find that at all ( T, P) studied, the potential of mean force between the graphene plates, as a function of plate separation r, exhibits local minima at specific plate separations r = r _n that can accommodate n water layers ( n = 0,1,2,3). In particular, our results show that isobaric cooling and isothermal compression have a similar effect on WMI between the plates; both processes tend to suppress the attraction and ultimate collapse of the graphene plates by kinetically trapping the plates at the metastable states with r = r _n ( n > 0). In addition, isobaric heating and isothermal decompression also have a similar effect; both processes tend to reduce the range and strength of the interactions between the graphene plates. Interestingly, at low temperatures, the WMI between the plates is affected by crystallization. However, crystallization depends deeply on the water model considered, SPC/E and TIP4P/2005 water models, with the crystallization occurring at different ( T, P) conditions, into different forms of ice.

Temperature Effects on Water-Mediated Interactions at the Nanoscale

We perform molecular dynamics simulations to study the effects of temperature on the water-mediated interactions between nanoscale apolar solutes. Specifically, we calculate the potential of mean force (PMF) between two graphene plates immersed in water at 240 ≤ T ≤ 400 K and P = 0.1 MPa. These are thermodynamic conditions relevant to cooling- and heating-induced protein denaturation. It is found that both cooling and heating tend to suppress the attraction, and ultimate collapse, of the graphene plates. However, the underlying role played by water upon heating and cooling is different. Isobaric heating reduces the strength and range of the interactions between the plates. Instead, isobaric cooling stabilizes the plates separations that can accommodate an integer number of water layers between the graphene plates. In particular, the energy barriers separating these plate separations increase linearly with 1/ T. We also explore the sensitivity of the plates PMF to the water model employed. In the case of the TIP4P/2005 model, water confined between the plates crystallizes into a defective bilayer ice at low temperatures, whereas in the case of the SPC/E model, water remains in the liquid state at same thermodynamic conditions. The effects of varying water-graphene interactions on the plates PMF are also studied.

In Aqua Veritas: The Indispensable yet Mostly Ignored Role of Water in Phase Separation and Membrane-less Organelles

Despite the common practice of presenting structures of biological molecules on an empty background and the assumption that interactions between biological macromolecules take place within the inert solvent, water represents an active component of various biological processes. This Perspective addresses indispensable, yet mostly ignored, roles of water in biological liquid-liquid phase transitions and in the biogenesis of various proteinaceous membrane-less organelles. We point out that changes in the structure of water reflected in the changes in its abilities to donate and/or accept hydrogen bonds and participate in dipole-dipole and dipole-induced dipole interactions in the presence of various solutes (ranging from small molecules to synthetic polymers and biological macromolecules) might represent a driving force for the liquid-liquid phase separation, define partitioning of various solutes in formed phases, and define the exceptional ability of intrinsically disordered proteins to be engaged in the formation of proteinaceous membrane-less organelles.

Methodologies for the Examination of Water in GPCRs

The following chapter examines some of the current "state-of-the-art" tools for predicting, scoring, and examining explicit water molecules in proteins and protein/ligand complexes, highlighting some of the ways information can be readily examined in a manner that is useful in a drug discovery process.

Picosecond orientational dynamics of water in living cells

Cells are extremely crowded, and a central question in biology is how this affects the intracellular water. Here, we use ultrafast vibrational spectroscopy and dielectric-relaxation spectroscopy to observe the random orientational motion of water molecules inside living cells of three prototypical organisms: Escherichia coli, Saccharomyces cerevisiae (yeast), and spores of Bacillus subtilis. In all three organisms, most of the intracellular water exhibits the same random orientational motion as neat water (characteristic time constants ~9 and ~2 ps for the first-order and second-order orientational correlation functions), whereas a smaller fraction exhibits slower orientational dynamics. The fraction of slow intracellular water varies between organisms, ranging from ~20% in E. coli to ~45% in B. subtilis spores. Comparison with the water dynamics observed in solutions mimicking the chemical composition of (parts of) the cytosol shows that the slow water is bound mostly to proteins, and to a lesser extent to other biomolecules and ions.

The cytoplasm’s crowdedness leads one to expect that cell water is different from bulk water. By measuring the rotational motion of water molecules in living cells, Tros et al. find that apart from a small fraction of water solvating biomolecules, cell water has the same dynamics as bulk water.

Water is an active matrix of life for cell and molecular biology

Szent-Győrgi called water the "matrix of life" and claimed that there was no life without it. This statement is true, as far as we know, on our planet, but it is not clear whether it must hold throughout the cosmos. To evaluate that question requires a close consideration of the many varied and subtle roles that water plays in living cells-a consideration that must be free of both an assumed essentialism that gives water an almost mystical life-giving agency and a traditional tendency to see it as a merely passive solvent. Water is a participant in the "life of the cell," and here I describe some of the features of that active agency. Water's value for molecular biology comes from both the structural and dynamic characteristics of its status as a complex, structured liquid as well as its nature as a polar, protic, and amphoteric reagent. Any discussion of water as life's matrix must, however, begin with an acknowledgment that our understanding of it as both a liquid and a solvent is still incomplete.

How water mediates the long-range interactions between remote protein molecules

A mechanism of the influence of the presence of one protein molecule on the internal dynamics of another is proposed.

Structural influence of proteins upon adsorption to MoS2 nanomaterials: comparison of MoS2 force field parameters

Molybdenum disulfide (MoS₂) has recently emerged as a promising nanomaterial in a wide range of applications due to its unique and impressive properties.

Cell viability and hydration assay based on metamaterial-enhanced terahertz spectroscopy

We analyze cell viability and hydration state of tumor cells in a label-free manner based on metamaterial-enhanced terahertz spectroscopy.

Evidence of Coupling between the Motions of Water and Peptides

Studies of protein dynamics at low temperatures are generally performed on hydrated powders and not in biologically realistic solutions of water because of water crystallization. However, here we avoid the problem of crystallization by reducing the size of the biomolecules. We have studied oligomers of the amino acid l-lysine, fully dissolved in water, and our dielectric relaxation data show that the glass transition-related dynamics of the oligomers is determined by the water dynamics, in a way similar to that previously observed for solvated proteins. This implies that the crucial role of water for protein dynamics can be extended to other types of macromolecular systems, where water is also able to determine their conformational fluctuations. Using the energy landscape picture of macromolecules, the thermodynamic criterion for such solvent-slaved macromolecular motions may be that the macromolecules need the entropy contribution from the solvent to overcome the enthalpy barriers between different conformational substates.

Hydration of proteins and nucleic acids: Advances in experiment and theory. A review

BACKGROUND

Most biological processes involve water, and the interactions of biomolecules with water affect their structure, function and dynamics.

SCOPE OF REVIEW

This review summarizes the current knowledge of protein and nucleic acid interactions with water, with a special focus on the biomolecular hydration layer. Recent developments in both experimental and computational methods that can be applied to the study of hydration structure and dynamics are reviewed, including software tools for the prediction and characterization of hydration layer properties.

MAJOR CONCLUSIONS

In the last decade, important advances have been made in our understanding of the factors that determine how biomolecules and their aqueous environment influence each other. Both experimental and computational methods contributed to the gradually emerging consensus picture of biomolecular hydration.

GENERAL SIGNIFICANCE

An improved knowledge of the structural and thermodynamic properties of the hydration layer will enable a detailed understanding of the various biological processes in which it is involved, with implications for a wide range of applications, including protein-structure prediction and structure-based drug design.

What did Erwin mean? The physics of information from the materials genomics of aperiodic crystals and water to molecular information catalysts and life

Erwin Schrödinger famously and presciently ascribed the vehicle transmitting the hereditary information underlying life to an 'aperiodic crystal'. We compare and contrast this, only later discovered to be stored in the linear biomolecule DNA, with the information-bearing, layered quasi-one-dimensional materials investigated by the emerging field of chaotic crystallography. Despite differences in functionality, the same information measures capture structure and novelty in both, suggesting an intimate coherence between the information character of biotic and abiotic matter-a broadly applicable physics of information. We review layered solids and consider three examples of how information- and computation-theoretic techniques are being applied to understand their structure. In particular, (i) we review recent efforts to apply new kinds of information measures to quantify disordered crystals; (ii) we discuss the structure of ice I in information-theoretic terms; and (iii) we recount recent investigations into the structure of tris(bicyclo[2.1.1]hexeno)benzene, showing how an information-theoretic analysis yields additional insight into its structure. We then illustrate a new Second Law of Thermodynamics that describes information processing in active low-dimensional materials, reviewing Maxwell's Demon and a new class of molecular devices that act as information catalysts. Lastly, we conclude by speculating on how these ideas from informational materials science may impact biology.

Water-mediated influence of a crowded environment on internal vibrations of a protein molecule

The influence of crowding on the protein inner dynamics is examined by putting a single protein molecule close to one or two neighboring protein molecules. The presence of additional molecules influences the amplitudes of protein fluctuations. Also, a weak dynamical coupling of collective velocities of surface atoms of proteins separated by a layer of water is detected. The possible mechanisms of these phenomena are described. The cross-correlation function of the collective velocities of surface atoms of two proteins was decomposed into the Fourier series. The amplitude spectrum displays a peak at low frequencies. Also, the results of principal component analysis suggest that the close presence of an additional protein molecule influences the high-amplitude, low-frequency modes in the most prominent way. This part of the spectrum covers biologically important protein motions. The neighbor-induced changes in the inner dynamics of the protein may be connected with the changes in the velocity power spectrum of interfacial water. The additional protein molecule changes the properties of solvation water and in this way it can influence the dynamics of the second protein. It is suggested that this phenomenon may be described, at first approximation, by a damped oscillator driven by an external random force. This model was successfully applied to conformationally rigid Choristoneura fumiferana antifreeze protein molecules.

Protein Stabilization and Enzyme Activation in Ionic Liquids: Specific Ion Effects

There are still debates on whether the hydration of ions perturbs the water structure, and what is the degree of such disturbance; therefore, the origin of Hofmeister effect on protein stabilization continues being questioned. For this reason, it is suggested to use the 'specific ion effect' instead of other misleading terms such as Hofmeister effect, Hofmeister series, lyotropic effect, and lyotropic series. In this review, we firstly discuss the controversial aspect of inorganic ion effects on water structures, and several possible contributors to the specific ion effect of protein stability. Due to recent overwhelming attraction of ionic liquids (ILs) as benign solvents in many enzymatic reactions, we further evaluate the structural properties and molecular-level interactions in neat ILs and their aqueous solutions. Next, we systematically compare the specific ion effects of ILs on enzyme stability and activity, and conclude that (a) the specificity of many enzymatic systems in diluted aqueous IL solutions is roughly in line with the traditional Hofmeister series albeit some exceptions; (b) however, the specificity follows a different track in concentrated or neat ILs because other factors (such as hydrogen-bond basicity, nucelophilicity, and hydrophobicity, etc) are playing leading roles. In addition, we demonstrate some examples of biocatalytic reactions in IL systems that are guided by the empirical specificity rule.

New terahertz dielectric spectroscopy for the study of aqueous solutions

We present the development of a high precision, tunable far-infrared (terahertz) frequency-domain dielectric spectrometer for studying the dynamics of biomolecules in aqueous solutions in the gigahertz-to-terahertz frequency. As an important benchmark system, we report on the measurements of the absorption and refractive index for liquid water in the frequency range from 5 GHz to 1.12 THz (0.17-37.36 cm(-1) or 0.268-60 mm). The system provides a coherent radiation source with power up to 20 mW in the gigahertz-to-terahertz region. The dynamic range of our instrument reaches 10(12) and the system achieves a spectral resolution of less than 100 Hz. The temperature of samples can be controlled precisely with error bars of ±0.02 °C from 0 °C to 90 °C. Given these attributes, our spectrometer provides unique capabilities for the accurate measurement of even very strongly absorbing materials such as aqueous solutions.

Solvent Properties of Water in Aqueous Solutions of Elastin-Like Polypeptide

The phase-transition temperatures of an elastin-like polypeptide (ELP) with the (GVGVP)₄₀ sequence and solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity in its aqueous solutions were quantified in the absence and presence of different salts (Na₂SO₄, NaCl, NaClO₄, and NaSCN) and various osmolytes (sucrose, sorbitol, trehalose, and trimethylamine N-oxide (TMAO)). All osmolytes decreased the ELP phase-transition temperature, whereas NaCl and Na₂SO₄ decreased, and NaSCN and NaClO₄ increased it. The determined phase-transition temperatures may be described as a linear combination of the solvent’s dipolarity/polarizability and hydrogen-bond donor acidity. The linear relationship established for the phase-transition temperature in the presence of salts differs quantitatively from that in the presence of osmolytes, in agreement with different (direct and indirect) mechanisms of the influence of salts and osmolytes on the ELP phase-transition temperature.

Relevance of glycosylation of S-layer proteins for cell surface properties

Elucidating the building principles and intrinsic features modulating certain water-associated processes (e.g., surface roughness in the nanometer scale, surface hydration and accompanied antifouling property, etc.) of surface structures from (micro)organisms is nowadays a highly challenging task in fields like microbiology, biomimetic engineering and (bio)material sciences. Here, we show for the first time the recrystallization of the wild-type S-layer glycoprotein wtSgsE from Geobacillus stearothermophilus NRS 2004/3a and its recombinantly produced non-glycosylated form, rSgsE, on gold sensor surfaces. Whereas the proteinaceous lattice of the S-layer proteins is forming a rigid layer on the sensor surface, the glycan chains are developing an overall soft, highly dissipative film. Interestingly, to the wtSgsE lattice almost twice the amount of water is bound and/or coupled in comparison with the non-glycosylated rSgsE with the preferred region being the extending glycan residues. The present results are discussed in terms of the effect of the glycan residues on the recrystallization, the adjoining hydration layer, and the nanoscale roughness and fluidic behavior. The latter features may turn out to be one of the most general ones among bacterial and archaeal S-layer lattices.

Quantitative characterization of hydration state and destructuring effect of monosaccharides and disaccharides on water hydrogen bond network

Terahertz time-domain attenuated total reflection measurements of monosaccharide (glucose and fructose) and disaccharide (sucrose and trehalose) solutions from 0.146 M to 1.462 M were performed to evaluate (1) the hydration state and (2) the destructuring effect of saccharide solutes on the hydrogen bond (HB) network. Firstly, the extent of hydration water was determined by the decreased amount of bulk water with picosecond relaxation time that was replaced by that with much longer orientational relaxation time. As a result, we found glucose and trehalose exhibits stronger hydration capacity than fructose and sucrose, respectively, despite of the same number of the hydroxyl groups. For each saccharide, the hydration number tended to decrease with solute concentration. Secondly, the destructuring effect of these saccharide solutes on the HB network of the surrounding bulk water was discussed from the perspective of the fraction of non-hydrogen-bonded (NHB) water isolated from the HB network. We found the fraction of NHB water molecules that are not engaged in the HB network monotonously increased with saccharide concentration, indicating saccharide solutes promote the disruption of the water HB network. However, no noticeable differences were confirmed in the fraction of NHB water between glucose and fructose or between sucrose and trehalose. In contrast to hydration number, the number of NHB water produced by a single saccharide solute was less dependent on solute concentration, and three monosaccharide/disaccharide solutes were found to produce one/two NHB water molecules.

Long-Range Lipid-Water Interaction as Observed by ATR-FTIR Spectroscopy

It is commonly assumed that the structure of water at a lipid-water interface is influenced mostly in the first hydration layer. However, recent results from different experimental methods show that perturbation extends through several hydration layers. Due to its low light penetration depth, attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy is specifically suited to study interlamellar water structure in multibilayers. Results obtained by this technique confirm the long-range water structure disturbance. Consequently, in confined membrane environments nearly all water molecules can be perturbed. It is important to note that the behavior of confined water molecules differs significantly in samples prepared in excess water and in partially hydrated samples. We show in what manner the interlamellar water perturbation is influenced by the hydration level and how it is sequentially modified with a step-by-step dehydration of samples either by water evaporation or by osmotic pressure. Our results also indicate that besides different levels of hydration the lipid-water interaction is modulated by different lipid headgroups and different lipid phases as well. Therefore, modification of interlamellar water properties may clarify the role of water-mediated effects in biological processes.

Synthesis of functionalized isoxazole–oxindole hybrids via on water, catalyst free vinylogous Henry and 1,6-Michael addition reactions

Various isoxazole–oxindole hybrids were synthesized via vinylogous Henry reaction of 3,5-dimethyl-4-nitroisoxazole and isatin under catalyst free conditions in water. The products obtained were functionalized using 1,6-Michael addition reaction.

Slow-to-fast transition of hydrogen bond dynamics in acetamide hydration shell formation

The acetamide hydration shell dynamics speeds up in a remarkable way upon increasing the water amount.