The influence of water on protein properties

Dimer Is Not Double: The Unexpected Behavior of Two-Floor Peptide Nanosponge

Using the framework of an investigation of the stimuli-responsive behavior of peptide assembly on a solid surface, this study on the behavior of a chemisorbed peptide on a gold surface was performed. The studied peptide is a dimeric form of the antimicrobial peptide Trichogin GAIV, which was also modified by substituting the glycine with lysine residues, while the N-terminus octanoyl group was replaced by a lipoic one that was able to bind to the gold surface. In this way, a chemically linked peptide assembly that is pH-responsive was obtained because of the protonation/deprotonation of the sidechains of the Lys residues. Information about the effect of protonation/deprotonation equilibria switching the pH from acid (pH = 3) to basic (pH = 11) conditions was obtained macroscopically by performing Quartz crystal microbalance with dissipation monitoring (QCM-D), Surface Plasmon Resonance (SPR), Nanoplasmonic Sensing (NPS), and FTIR techniques. Using molecular dynamics (MD) simulations, it is possible to explain, at the molecular level, our main experimental results: (1) pH changes induce a squeezing behavior in the system, consisting in thickness and mass variations in the peptide layer, which are mainly due to the pH-driven hydrophilic/hydrophobic character of the lysine residues, and (2) the observed hysteresis is due to small conformational rearrangements from helix to beta sheets occurring mainly on the first half of the peptide, closer to the surface, while the second half remains almost unaffected. The latter result, together with the evidence that the layer thickness is not simply double the assembly of the monomeric analog, indicates that the dimeric peptide does not behave as a double monomer, but assumes very peculiar features.

Synthesis of Fe-Doped Peroxidase Mimetic Nanozymes from Natural Hemoglobin for Colorimetric Biosensing and In Vitro Anticancer Effects

Despite their efficiency and specificity, the instability of natural enzymes in harsh conditions has inspired researchers to replace them with nanomaterials. In the present study, extracted hemoglobin from blood biowastes was hydrothermally converted to catalytically active carbon nanoparticles (BDNPs). Their application as nanozymes for the colorimetric biosensing of H₂O₂ and glucose and selective cancer cell-killing ability was demonstrated. Particles that were prepared at 100 °C (BDNP-100) showed the highest peroxidase mimetic activity, with Michaelis-Menten constants (K_m) of 11.8 mM and 0.121 mM and maximum reaction rates (V_max) of 8.56 × 10^-8 mol L^-1 s^-1 and 0.538 × 10^-8 mol L^-1 s^-1, for H₂O₂ and TMB, respectively. The cascade catalytic reactions, catalyzed by glucose oxidase and BDNP-100, served as the basis for the sensitive and selective colorimetric glucose determination. A linear range of 50-700 µM, a response time of 4 min, a limit of detection (3σ/N) of 40 µM, and a limit of quantification (10σ/N) of 134 µM was achieved. In addition, the reactive oxygen species (ROS)-generating ability of BDNP-100 was employed for evaluating its potential in cancer therapy. Human breast cancer cells (MCF-7), in the forms of monolayer cell cultures and 3D spheroids, were studied by MTT, apoptosis, and ROS assays. The in vitro cellular experiments showed dose-dependent cytotoxicity of BDNP-100 toward MCF-7 cells in the presence of 50 µM of exogenous H₂O₂. However, no obvious damage was induced to normal cells in the same experimental conditions, verifying the selective cancer cell-killing ability of BDNP-100.

Effect of artificial sweetener saccharin on lysozyme aggregation: A combined spectroscopic and in silico approach

The use of saccharin in food products attracts much attention as it involves the risk of lethal allergies and many protein aggregation diseases. However, its role in protein aggregation has not been explored to date. This study embodies the effect of artificial sweeteners on HEWL in the absence and presence of commonly available natural products such as curcumin and EGCG. Various techniques have been used to characterize the protein interaction, such as steady-state emission and time-resolved fluorescence, FTIR, gel electrophoresis, TEM, and molecular docking. Steady-state and time-resolved studies revealed the binding strength and concomitant effect of saccharin on HEWL protein. Kinetic measurements revealed that saccharin causes significant enhancement of HEWL aggregation with a considerable reduction in lag phase time i.e. from 37 hr to 08 hr. Whereas in the presence of natural products, the effect of saccharin on HEWL aggregation was significantly reduced specifically in the case of curcumin. The result obtained in the fluorescence experiment were also supported by the gel electrophoresis technique and morphological images taken by TEM. The rapid change in the secondary structure of the protein in the presence of saccharin was confirmed by the FTIR spectroscopy technique. This study is instrumental in understanding the effect of saccharin on protein aggregation and the role of commonly available natural products in curbing its effect.

The Hydrophobic Effect Studied by Using Interacting Colloidal Suspensions

Interactions between nanoparticles (NPs) determine their self-organization and dynamic processes. In these systems, a quantitative description of the interparticle forces is complicated by the presence of the hydrophobic effect (HE), treatable only qualitatively, and due to the competition between the hydrophobic and hydrophilic forces. Recently, instead, a sort of crossover of HE from hydrophilic to hydrophobic has been experimentally observed on a local scale, by increasing the temperature, in pure confined water and studying the occurrence of this crossover in different water-methanol solutions. Starting from these results, we then considered the idea of studying this process in different nanoparticle solutions. By using photon correlation spectroscopy (PCS) experiments on dendrimer with OH terminal groups (dissolved in water and methanol, respectively), we show the existence of this hydrophobic-hydrophilic crossover with a well defined temperature and nanoparticle volume fraction dependence. In this frame, we have used the mode coupling theory extended model to evaluate the measured time-dependent density correlation functions (ISFs). In this context we will, therefore, show how the measured spectra are strongly dependent on the specificity of the interactions between the particles in solution. The observed transition demonstrates that just the HE, depending sensitively on the system thermodynamics, determines the hydrophobic and hydrophilic interaction properties of the studied nanostructures surface.

Electronic Structure and Solvation Effects from Core and Valence Photoelectron Spectroscopy of Serum Albumin

X-ray photoelectron spectroscopy of bovine serum albumin (BSA) in a liquid jet is used to investigate the electronic structure of a solvated protein, yielding insight into charge transfer mechanisms in biological systems in their natural environment. No structural damage was observed in BSA following X-ray photoelectron spectroscopy in a liquid jet sample environment. Carbon and nitrogen atoms in different chemical environments were resolved in the X-ray photoelectron spectra of both solid and solvated BSA. The calculations of charge distributions demonstrate the difficulty of assigning chemical contributions in complex systems in an aqueous environment. The high-resolution X-ray core electron spectra recorded are unchanged upon solvation. A comparison of the valence bands of BSA in both phases is also presented. These bands display a higher sensitivity to solvation effects. The ionization energy of the solvated BSA is determined at 5.7 ± 0.3 eV. Experimental results are compared with theoretical calculations to distinguish the contributions of various molecular components to the electronic structure. This comparison points towards the role of water in hole delocalization in proteins.

Direct observation of reversible liquid-liquid transition in a trehalose aqueous solution

Recent studies on liquid water suggest that the two liquid waters exist in the supercooled temperature region and that their existence relates to the anomalous behavior of low-temperature liquid water such as the maximum density at 4 °C. However, the experimental investigation of two liquid waters is difficult because of the rapid crystallization. In this study, a reversible liquid–liquid transition in a trehalose aqueous solution by the change in pressure was observed directly. This result suggests strongly that two liquid waters exist in the aqueous solution. This study has implications for wide fields related to liquid water, such as solution chemistry, cryobiology, meteorology, and food engineering.

Water forms two glassy waters, low-density and high-density amorphs, which undergo a reversible polyamorphic transition with the change in pressure. The two glassy waters transform into the different liquids, low-density liquid (LDL) and high-density liquid (HDL), at high temperatures. It is predicted that the two liquid waters also undergo a liquid–liquid transition (LLT). However, the reversible LLT, particularly the LDL-to-HDL transition, has not been observed directly due to rapid crystallization. Here, I prepared a glassy dilute trehalose aqueous solution (0.020 molar fraction) without segregation and measured the isothermal volume change at 0.01 to 1.00 GPa below 160 K. The polyamorphic transition and the glass-to-liquid transition for the high-density and low-density solutions were examined, and the liquid region where both LDL and HDL existed was determined. The results show that the reversible polyamorphic transition induced by the pressure change above 140 K is the LLT. That is, the transition from LDL to HDL is observed. Moreover, the pressure hysteresis of LLT suggests strongly that the LLT has a first-order nature. The direct observation of the reversible LLT in the trehalose aqueous solution has implications for understanding not only the liquid–liquid critical point hypothesis of pure water but also the relation between aqueous solution and water polyamorphism.

The Comparative Study of the State of Conservation of Two Medieval Documents on Parchment from Different Historical Periods

The paper explores the potentiality of an experimental multianalytic protocol with appropriate methodology for determining the chemical and morphostructural characteristics of two old documents on parchment support. Such a protocol can authenticate and assess the state of conservation under the influence of environmental factors during storage and archival documentation, thus advancing preventive and prophylactic measures in “treasure” deposits such as the National Archives of Romania, where these documents are kept. The work methodology consisted of three stages. The first stage consists of visual observation for identifying deteriorations and degradations, alongside the selection of representatives’ areas from where micro-samples were collected. The second stage involves Scanning Electron Microscopy coupled by Energy Dispersive X-ray Spectrometry (SEM-EDX) analysis, for highlighting the morphology and determining the elemental composition; lastly, the Fourier-transform infrared (FTIR) analysis and correlation of results establish the chemical and morphostructural changes. The use of this gradual system of analyses allowed determining the differences between these two documents in terms of the materials used for producing them, their manufacturing technologies, the writing and ornamentation, and the overall state of conservation. The results provided the first accurate picture of the chemical nature and manufacturing of the two parchment documents by determining the main characteristics of the collagen and of the finishing, writing, and decoration materials, in view of the natural aging through the oxidative and gelatinization processes of the collagen. The SEM-EDX results revealed the morphological changes of the parchment that occurred at various levels in the collagen fibrous mesh and established the state of conservation of the support, writing, and decorations.

A compact device for simultaneous dielectric spectroscopy and microgravimetric analysis under controlled humidity

Water plays a key role in the functioning of natural and synthetic molecular systems. Despite several hydration studies, different techniques are employed individually for monitoring different physical features such as kinetics, dynamics, and absorption. This study describes a compact hydration cell that enables simultaneous dielectric relaxation spectroscopy (DRS) and mass loss/uptake measurements in thin organic layers under controlled humidity conditions and in a wide temperature range. This approach enabled us to correlate the physical quantities obtained during the same experiment by complementary techniques. To demonstrate the performance of this device, a 200 nm thick poly(methyl methacrylate) (PMMA) layer was measured at various relative humidity levels (0%-75%), temperatures (25-75 °C), and frequencies (DRS: 0.1 Hz-1 MHz) to study how hydration and dehydration processes affect its molecular dynamics. The results show the capability of this setup to study the changes in the PMMA film regarding the kinetics and molecular dynamics upon variation of the water content.

Glass polymorphism and liquid-liquid phase transition in aqueous solutions: experiments and computer simulations

One of the most intriguing anomalies of water is its ability to exist as distinct amorphous ice forms (glass polymorphism or polyamorphism). This resonates well with the possible first-order liquid-liquid phase transition (LLPT) in the supercooled state, where ice is the stable phase. In this Perspective, we review experiments and computer simulations that search for LLPT and polyamorphism in aqueous solutions containing salts and alcohols. Most studies on ionic solutes are devoted to NaCl and LiCl; studies on alcohols have mainly focused on glycerol. Less attention has been paid to protein solutions and hydrophobic solutes, even though they reveal promising avenues. While all solutions show polyamorphism and an LLPT only in dilute, sub-eutectic mixtures, there are differences regarding the nature of the transition. Isocompositional transitions for varying mole fractions are observed in alcohol but not in ionic solutions. This is because water can surround alcohol molecules either in a low- or high-density configuration whereas for ionic solutes, the water ion hydration shell is forced into high-density structures. Consequently, the polyamorphic transition and the LLPT are prevented near the ions, but take place in patches of water within the solutions. We highlight discrepancies and different interpretations within the experimental community as well as the key challenges that need consideration when comparing experiments and simulations. We point out where reinterpretation of past studies helps to draw a unified, consistent picture. In addition to the literature review, we provide original experimental results. A list of eleven open questions that need further consideration is identified.

Hysteresis in the temperature dependence of the IR bending vibration of deeply cooled confined water

Using Fourier Transform Infrared (FTIR) spectroscopy, we investigate the temperature dependence of the bending vibrations of water confined in the pores of a silica hydrogel in the temperature interval of 270-180 K. We also investigate the presence of thermal hysteresis by cooling and reheating temperature scans. The results clearly show the presence, at about 230 K, of a crossover in the temperature dependence of the IR spectra; moreover, the presence of hysteresis is clearly demonstrated. By comparing FTIR data with neutron diffraction data and previous calorimetric data on the same samples, we conclude that the crossover and the hysteretical behavior do not involve a water glass transition or crystallization but are related to a first-order-like liquid-liquid transition.

Molecular Sponge: pH-Driven Reversible Squeezing of Stimuli-Sensitive Peptide Monolayers

The cyclic change of structure, thickness, and density, with pH switching from acidic (pH = 3) to basic (pH = 11) condition, has been revealed for chemisorbed monolayers of the peptide Lipo-Aib-Lys-Leu-Aib-Lys-Lys-Leu-Aib-Lys-Ile-Lol, a trichogin GA IV-analogue carrying Lys residues instead of Gly ones at positions 2, 5, 6, and 9, while a homologous peptide not containing Lys residues does not show any response to pH changes. Experimental and theoretical results, obtained by means of quartz crystal microbalance with dissipation monitoring, surface plasmon resonance, nanoplasmonic sensing technique, Fourier transform infrared-reflection attenuated spectroscopy and dynamic force spectroscopy, and molecular dynamics simulations provide detailed information on the overall monolayer structure changes with pH, including the analysis of the intra- and interchain peptide dynamics, the structure of the peptide layer/water/solid interface, as well as the position and role of solvation and nonsolvation water. The observed stimuli-responsive behavior of L1 peptide monolayers is accounted in terms of the occurrence of a pH-induced wetting/dewetting process, due to the pH-induced switching of the hydrophilic character of charged lysine groups to hydrophobic one of the same uncharged groups, along the peptide chain. This behavior in turn promotes the collective change of the aggregation state of the peptide chains. The present results may pave the way to critically reexamine the mechanism of stimuli-responsive systems.

The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results

The biological activity of proteins depends on their three-dimensional structure, known as the native state. The main force driving the correct folding mechanism is the hydrophobic effect and when this folding kinetics is altered, aggregation phenomena intervene causing the occurrence of illnesses such as Alzheimer and Parkinson’s diseases. The other important effect is performed by water molecules and by their ability to form a complex network of hydrogen bonds whose dynamics influence the mobility of protein amino acids. In this work, we review the recent results obtained by means of spectroscopic techniques, such as Fourier Transform Infrared (FTIR) and Nuclear Magnetic Resonance (NMR) spectroscopies, on hydrated lysozyme. In particular, we explore the Energy Landscape from the thermal region of configurational stability up to that of the irreversible denaturation. The importance of the coupling between the solute and the solvent will be highlighted as well as the different behaviors of hydrophilic and hydrophobic moieties of protein amino acid residues.

The role of water in the degradation process of paper using 1H HR-MAS NMR spectroscopy

The thermodynamic properties of water are essential for determining the corresponding properties of every biosystem it interacts with. Indeed, the comprehension of hydration mechanisms is fundamental for the understanding and the control of paper degradation pathways induced by natural or artificial aging. In fact, the interactions between water and cellulose at the accessible sites within the fibres' complex structure are responsible for the rupture of hydrogen bonds and the consequent swelling of the cellulose fibres and consumption of the amorphous regions. In this paper we study the hydration process of cellulose in naturally and artificially aged paper samples by measuring the proton spin-lattice (T₁) and spin-spin (T₂) relaxation times of the macroscopic magnetization through nuclear magnetic resonance (NMR) experiments. The observed behaviour of T₁ and T₂ is quite complex and strictly dependent on the water content of paper samples. This has been interpreted as due to the occurrence of different mechanisms regulating the water-cellulose interaction within the fibres. Furthermore, we have measured T₁ as a function of the artificial aging time comparing the results with those measured on three paper samples dated back to the 15th century. We found that the evolution of T₁ in model papers artificially aged is correlated with that of ancient paper, providing therefore a way for estimating the degradation of cellulosic materials in terms of an equivalent time of artificial aging. These results provide fundamental information for industrial applications and for the preservation and restoration of cultural heritage materials based on cellulose such as ancient paper or textiles.

Effect of solute nature on the polyamorphic transition in glassy polyol aqueous solutions

I examined the polyamorphic behavior of glassy dilute aqueous solutions of polyols (ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol) under pressure at low temperatures. Although the volume change of the glassy aqueous solution varied continuously against pressure, the rate of the volume change appeared to vary discontinuously at the onset pressure of the gradual polyamorphic transition. It is thought that low-density liquid-like solvent water and high-density liquid-like solvent water coexist during the transition. Moreover, the existence of a solute induces the shift of polyamorphic transition to the lower-pressure side. The effect of a solute on the polyamorphic transition becomes larger in the order ethylene glycol, glycerol, meso-erythritol, xylitol, and D-sorbitol. Therefore, the solute can become a variable controlling the polyamorphic state of liquid water. This experimental result suggests that the metastable-equilibrium phase boundary between the low-density and the high-density amorphs for pure water is likely to be located at 0.22-0.23 GPa at about 150 K, which is slightly larger than the previously estimated pressure. Moreover, the solute-nature dependence on the polyamorphic transition seems to connect to that on the homogeneous nucleation temperature of polyol aqueous solution at ambient pressure. The region in which a low-density liquid appears coincides with the region in which the nucleus of ice Ih appears, suggesting that the formation of a low-density liquid is a precursory phenomenon of the nucleation of ice Ih.

Effect of water polyamorphism on the molecular vibrations of glycerol in its glassy aqueous solutions

A glassy dilute glycerol-water solution undergoes a mutual polyamorphic transition relating to the transition between high- and low-density amorphous ices of solvent water. The polyamorphic transition behavior depends on the glycerol concentration, indicating that the glycerol affects the water polyamorphism. Here, we used the glassy dilute glycerol-water solution of the solute molar fraction of 0.07 and examined the effect of the polyamorphic change in solvent water on the molecular vibrations of glycerol via Raman spectroscopy. It is found that the molecular vibration of glycerol in high-density liquid like solvent water is different from that in the low-density liquid like solvent water and that the change in the molecular vibration of glycerol is synchronized with the polyamorphic transition of solvent water. The dynamical change of the solute molecule relates to the polyamorphic state of solvent water. This result suggests that the polyamorphic fluctuation of water structure emanated from the presumed liquid-liquid critical point plays an important role for the function of aqueous solution under an ambient condition such as the conformational stability of solute, the functional expression of solute, and so on.

Water Determines the Structure and Dynamics of Proteins

Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.

Energy landscape in protein folding and unfolding

We use (1)H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295 < T < 365 K and following different trajectories along the protein energy surface, we observe that the hydrophilic (the amide NH) and hydrophobic (methyl CH3 and methine CH) peptide groups evolve and exhibit different behaviors. We also discuss the role of water and hydrogen bonding in the protein configurational stability.

Confined Water as Model of Supercooled Water

Water in confined geometries has obvious relevance in biology, geology, and other areas where the material properties are strongly dependent on the amount and behavior of water in these types of materials. Another reason to restrict the size of water domains by different types of geometrical confinements has been the possibility to study the structural and dynamical behavior of water in the deeply supercooled regime (e.g., 150-230 K at ambient pressure), where bulk water immediately crystallizes to ice. In this paper we give a short review of studies with this particular goal. However, from these studies it is also clear that the interpretations of the experimental data are far from evident. Therefore, we present three main interpretations to explain the experimental data, and we discuss their advantages and disadvantages. Unfortunately, none of the proposed scenarios is able to predict all the observations for supercooled and glassy bulk water, indicating that either the structural and dynamical alterations of confined water are too severe to make predictions for bulk water or the differences in how the studied water has been prepared (applied cooling rate, resulting density of the water, etc.) are too large for direct and quantitative comparisons.

Long-range orientation correlation in water

Strong short-range intermolecular interactions result in position and orientation correlations between nearest neighbour molecules in isotropic liquids, but it is generally assumed that such correlations extend at most a few molecular diameters. Results from second-harmonic light scattering experiments presented here reveal long-range molecular orientation correlations in liquid water, where the molecular dipole orientation distribution has the form of a nearly pure transverse vector field. Spatial scales in the range 200-2000 nm are probed by the angle-dependent measurements and the observed correlations are thought to result from rotation-translation coupling in acoustic phonons in the liquid.

The role of water in protein's behavior: The two dynamical crossovers studied by NMR and FTIR techniques

The role the solvent plays in determining the biological activity of proteins is of primary importance. Water is the solvent of life and proteins need at least a water monolayer covering their surface in order to become biologically active. We study how the properties of water and the effect of its coupling with the hydrophilic moieties of proteins govern the regime of protein activity. In particular we follow, by means of Fourier Transform Infrared spectroscopy, the thermal evolution of the amide vibrational modes of hydrated lysozyme in the temperature interval 180 K < T < 350 K. In such a way we are able to observe the thermal limit of biological activity characterizing hydrated lysozyme. Finally we focus on the region of lysozyme thermal denaturation by following the evolution of the proton Nuclear Magnetic Resonance (NMR) spectra for 298 K < T < 366 K with the High-Resolution Magic Angle Spinning probe. Our data suggest that the hydrogen bond coupling between hydration water and protein hydrophilic groups is crucial in triggering the main mechanisms that define the enzymatic activity of proteins.