Communication: Protein dynamical transition vs. liquid-liquid phase transition in protein hydration water

Structure and slow dynamics of protein hydration water with cryopreserving DMSO and trehalose upon cooling

We study, through molecular dynamics simulations, three aqueous solutions with one lysozyme protein and three different concentrations of trehalose and dimethyl sulfoxide (DMSO). We analyze the structural and dynamical properties of the protein hydration water upon cooling. We find that trehalose plays a major role in modifying the structure of the network of HBs between water molecules in the hydration layer of the protein. The dynamics of hydration water presents, in addition to the α-relaxation, typical of glass formers, a slower long-time relaxation process, which greatly slows down the dynamics of water, particularly in the systems with trehalose, where it becomes dominant at low temperatures. In all the solutions, we observe, from the behavior of the α-relaxation times, a shift of the Mode Coupling Theory crossover temperature and the fragile-to-strong crossover temperature toward higher values with respect to bulk water. We also observe a strong-to-strong crossover from the temperature behavior of the long-relaxation times. In the aqueous solution with only DMSO, the transition shifts to a lower temperature than in the case with only lysozyme reported in the literature. We observe that the addition of trehalose to the mixture has the opposite effect of restoring the original location of the strong-to-strong crossover. In all the solutions analyzed in this work, the observed temperature of the protein dynamical transition is slightly shifted at lower temperatures than that of the strong-to-strong crossover, but their relative order is the same, showing a correlation between the motion of the protein and that of the hydration water.

Dynamical Transition in Dehydrated Proteins

Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilized sucrose exhibited steadily increasing absorption with temperature as anharmonic excitations commenced as the system emerged from a deep minimum of the potential energy landscape where harmonic vibrations dominate. The polypeptide bacitracin and two globular proteins, lysozyme and human serum albumin, showed a more complex temperature dependence. Further analysis focused on the spectral signature below and above the boson peak. We found evidence of the onset of anharmonic motions that are characteristic for partial unfolding and molecular jamming in the dry biomolecules. The activation of modes of the protein molecules at temperatures comparable to the protein dynamical transition temperature was observed in the absence of hydration. No evidence of Fröhlich coherence, postulated to facilitate biological function, was found in our experiments.

Coherent X-ray Scattering Reveals Nanoscale Fluctuations in Hydrated Proteins

Hydrated proteins undergo a transition in the deeply supercooled regime, which is attributed to rapid changes in hydration water and protein structural dynamics. Here, we investigate the nanoscale stress-relaxation in hydrated lysozyme proteins stimulated and probed by X-ray Photon Correlation Spectroscopy (XPCS). This approach allows us to access the nanoscale dynamics in the deeply supercooled regime (T = 180 K), which is typically not accessible through equilibrium methods. The observed stimulated dynamic response is attributed to collective stress-relaxation as the system transitions from a jammed granular state to an elastically driven regime. The relaxation time constants exhibit Arrhenius temperature dependence upon cooling with a minimum in the Kohlrausch-Williams-Watts exponent at T = 227 K. The observed minimum is attributed to an increase in dynamical heterogeneity, which coincides with enhanced fluctuations observed in the two-time correlation functions and a maximum in the dynamic susceptibility quantified by the normalized variance χ_T. The amplification of fluctuations is consistent with previous studies of hydrated proteins, which indicate the key role of density and enthalpy fluctuations in hydration water. Our study provides new insights into X-ray stimulated stress-relaxation and the underlying mechanisms behind spatiotemporal fluctuations in biological granular materials.

A Long Journey into the Investigation of the Structure–Dynamics–Function Paradigm in Proteins through the Activities of the Palermo Biophysics Group

An overview of the biophysics activity at the Department of Physics and Chemistry Emilio Segrè of the University of Palermo is given. For forty years, the focus of the research has been on the protein structure–dynamics–function paradigm, with the aim of understanding the molecular basis of the relevant mechanisms and the key role of solvent. At least three research lines are identified; the main results obtained in collaboration with other groups in Italy and abroad are presented. This review is dedicated to the memory of Professors Massimo Ugo Palma, Maria Beatrice Palma Vittorelli, and Lorenzo Cordone, which were the founders of the Palermo School of Biophysics. We all have been, directly or indirectly, their pupils; we miss their enthusiasm for scientific research, their deep physical insights, their suggestions, their strict but always constructive criticisms, and, most of all, their friendship. This paper is dedicated also to the memory of Prof. Hans Frauenfelder, whose pioneering works on nonexponential rebinding kinetics, protein substates, and energy landscape have inspired a large part of our work in the field of protein dynamics.

On the existence of soliton-like collective modes in liquid water at the viscoelastic crossover

The problem of large-density variations in supercooled and ambient water has been widely discussed in the past years. Recent studies have indicated the possibility of nanometer-sized density variations on the subpicosecond and picosecond time scales. The nature of fluctuating density heterogeneities remains a highly debated issue. In the present work, we address the problem of possible association of such density variations with the dynamics of terahertz longitudinal acoustic-like modes in liquid water. Our study is based on the fact that the subpicosecond dynamics of liquid water are essentially governed by the structural relaxation. Using a mode coupling theory approach, we found that for typical values of parameters of liquid water, the dynamic mechanism coming from the combination of the structural relaxation process and the finiteness of the amplitude of terahertz longitudinal acoustic-like mode gives rise to a soliton-like collective mode on a temperature-dependent nanometer length scale. The characteristics of this mode are consistent with the estimates of the amplitudes and temperature-dependent correlation lengths of density fluctuations in liquid water obtained in experiments and simulations. Thus, the fully dynamic mechanism could contribute to the formation and dynamics of fluctuating density heterogeneities. The soliton-like collective excitations suggested by our analysis may be relevant to different phenomena connected with supercooled water and can be expected to be associated with some ultrafast biological processes.

Diffusivelike Motions in a Solvent-Free Protein-Polymer Hybrid

The interaction between proteins and hydration water stabilizes protein structure and promotes functional dynamics, with water translational motions enabling protein flexibility. Engineered solvent-free protein-polymer hybrids have been shown to preserve protein structure, function, and dynamics. Here, we used neutron scattering, protein and polymer perdeuteration, and molecular dynamics simulations to explore how a polymer dynamically replaces water. Even though relaxation rates and vibrational properties are strongly modified in polymer coated compared to hydrated proteins, liquidlike polymer dynamics appear to plasticize the conjugated protein in a qualitatively similar way as do hydration-water translational motions.

Probing the dynamics of biological matter by elastic, quasi-elastic, and inelastic neutron scattering

The so-called function-structure-dynamics paradigm established that a close relationship links the way biological molecules work (function), their 3-dimensional organization (structure) and the changes of this organization in time (dynamics), which characterize biomolecules as highly dynamic objects. A typical example of protein dynamics is provided by protein reactions with substrates: equilibrium thermal fluctuations of protein structure are necessary to allow the access of substrates to the active site, where the functional reaction occurs. Neutron scattering is a powerful technique to study equilibrium protein structural dynamics. The incoherent structure factor, which is dominant in neutron scattering from biological matter, is related to the time-position self correlation function of protein/solvent nuclei. Here the basic theory of neutron scattering and the principles of the technologies used to measure it are described. Some selected applications of neutron scattering for investigating the structural dynamics of biological molecules are also reviewed.

Role of hydration water in the onset of protein structural dynamics

Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.

Dynamical aspects of supercooled TIP3P-water in the grooves of DNA

We investigate by molecular dynamics simulations the mobility of the water located at the DNA minor and major grooves. We employ the TIP3P water model, and our system is analyzed for a range of temperatures 190-300 K. For high temperatures, the water at the grooves shows an Arrhenius behavior similar to that observed in the bulk water. At lower temperatures, a departure from the bulk behavior is observed. This slowing down in the dynamics is compared with the dynamics of the hydrogen of the DNA at the grooves and with the autocorrelation functions of the water hydrogen bonds. Our results indicate that the hydrogen bonds of the water at the minor grooves are highly correlated, which suggests that this is the mechanism for the slow dynamics at this high confinement.

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.

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.

Slow Dynamics around a Protein and Its Coupling to Solvent

Solvent is essential for protein dynamics and function, but its role in regulating the dynamics remains debated. Here, we employ saturation transfer electron spin resonance (ST-ESR) to explore the issue and characterize the dynamics on a longer (from μs to s) time scale than has been extensively studied. We first demonstrate the reliability of ST-ESR by showing that the dynamical changeovers revealed in the spectra agree to liquid-liquid transition (LLT) in the state diagram of the glycerol/water system. Then, we utilize ST-ESR with four different probes to systematically map out the variation in local (site-specific) dynamics around a protein surface at subfreezing temperatures (180-240 K) in 10 mol % glycerol/water mixtures. At highly exposed sites, protein and solvent dynamics are coupled, whereas they deviate from each other when temperature is greater than LLT temperature (∼190 K) of the solvent. At less exposed sites, protein however exhibits a dynamic, which is distinct from the bulk solvent, throughout the temperature range studied. Dominant dynamic components are thus revealed, showing that (from low to high temperatures) the overall structural fluctuation, rotamer dynamics, and internal side-chain dynamics, in turn, dominate the temperature dependence of spin-label motions. The structural fluctuation component is relatively slow, collective, and independent of protein structural segments, which is thus inferred to a fundamental dynamic component intrinsic to protein. This study corroborates that bulk solvent plasticizes protein and facilitates rather than slaves protein dynamics.

The effects of pressure on the energy landscape of proteins

Protein dynamics is characterized by fluctuations among different conformational substates, i.e. the different minima of their energy landscape. At temperatures above ~200 K, these fluctuations lead to a steep increase in the thermal dependence of all dynamical properties, phenomenon known as Protein Dynamical Transition. In spite of the intense studies, little is known about the effects of pressure on these processes, investigated mostly near room temperature. We studied by neutron scattering the dynamics of myoglobin in a wide temperature and pressure range. Our results show that high pressure reduces protein motions, but does not affect the onset temperature for the Protein Dynamical Transition, indicating that the energy differences and barriers among conformational substates do not change with pressure. Instead, high pressure values strongly reduce the average structural differences between the accessible conformational substates, thus increasing the roughness of the free energy landscape of the system.

Dynamical and orientational structural crossovers in low-temperature glycerol

Mean-square displacements of hydrogen atoms in glass-forming materials and proteins, as reported by incoherent elastic neutron scattering, show kinks in their temperature dependence. This crossover, known as the dynamical transition, connects two approximately linear regimes. It is often assigned to the dynamical freezing of subsets of molecular modes at the point of equality between their corresponding relaxation times and the instrumental observation window. The origin of the dynamical transition in glass-forming glycerol is studied here by extensive molecular dynamics simulations. We find the dynamical transition to occur for both the center-of-mass translations and the molecular rotations at the same temperature, insensitive to changes of the observation window. Both the translational and rotational dynamics of glycerol show a dynamic crossover from the structural to a secondary relaxation at the temperature of the dynamical transition. A significant and discontinuous increase in the orientational Kirkwood factor and in the dielectric constant is observed in the same range of temperatures. No indication is found of a true thermodynamic transition to an ordered low-temperature phase. We therefore suggest that all observed crossovers are dynamic in character. The increase in the dielectric constant is related to the dynamic freezing of dipolar domains on the time scale of simulations.

Broadband Dielectric Spectroscopy on Lysozyme in the Sub-Gigahertz to Terahertz Frequency Regions: Effects of Hydration and Thermal Excitation

We have performed dielectric spectral measurements of lysozyme in a solid state to understand the effects of hydration and thermal excitation on the low-frequency dynamics of protein. Dielectric measurements were performed under changing hydration conditions at room temperature in the frequency region of 0.5 GHz to 1.8 THz. We also studied the temperature dependence (83 to 293 K) of the complex dielectric spectra in the THz frequency region (0.3 THz to 1.8 THz). Spectral analyses were performed using model functions for the complex dielectric constant. To reproduce the spectra, we found that two relaxational modes and two underdamped modes are necessary together with an ionic conductivity term in the model function. At room temperature, the two relaxational modes have relaxation times of ∼20 ps and ∼100 ps. The faster component has a major spectral intensity and is suggested to be due to coupled water-protein motion. The two underdamped modes are necessary to reproduce the temperature dependence of the spectra in the THz region satisfactorily. The protein dynamical transition is a well-known behavior in the neutron-scattering experiment for proteins, where the atomic mean-square displacement shows a sudden change in the temperature dependence at approximately 200 K, when the samples are hydrated. A similar behavior has also been observed in the temperature dependence of the absorption spectra of protein in the THz frequency region. From our broadband dielectric spectroscopic measurements, we conclude that the increase in the spectral intensities in the THz region at approximately 200 K is due to a spectral blue-shift of the fast relaxational mode.

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.

Protein electron transfer: is biology (thermo)dynamic?

Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life's ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein's elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic activated kinetics, which extends the transition-state theory to dynamically dispersive media. Releasing the grip of thermodynamics in kinetic calculations through nonergodicity provides the mechanism for an efficient optimization between reaction rates and the spectrum of relaxation times of the protein-water thermal bath. Bath dynamics, it appears, play as important role as the free energy in optimizing biology's performance.

Liquid Polyamorphous Transition and Self-Organization in Aqueous Solutions of Ionic Surfactants

Polyamorphous transitions in supercooled water, porous substances, solutions of polyols, and proteins are studied intensively. They accompany the self-organization of hydrocarbons and surfactants. In this study, the methods of polyamorphous transition identification are proposed, and their dependence on hydrocarbons and surfactant concentration and sizes is investigated. The place of polyamorphous transitions in the general theory of phase separation is determined, and their bistability, self-oscillations, hysteresis, fluctuations, cooperative effect, enthalpy, and entropy are described. Surface, volume, and diffusion instabilities of polyamorphous transitions are analyzed. Technologies based on the properties of polyamorphous transitions are proposed.

Dipolar Nanodomains in Protein Hydration Shells

The network of hydrogen bonds characteristic of bulk water is significantly disturbed at the protein-water interface, where local fields induce mutually frustrated dipolar domains with potentially novel structure and dynamics. Here the dipolar susceptibility of hydration shells of lysozyme is studied by molecular dynamics simulations in a broad range of temperatures, 140-300 K. The real part of the susceptibility passes through a broad maximum as a function of temperature. The maximum shifts to higher temperatures with increasing frequency of the dielectric experiment. This phenomenology is consistent with that reported for bulk relaxor ferroelectrics, where it is related to the formation of dipolar nanodomains. Nanodomains in the hydration shell extend 12-15 Å from the protein surface into the bulk. Their dynamics are significantly slower than the dynamics of bulk water. The domains dynamically freeze into a ferroelectric glass below 160 K, at which point the Arrhenius plot of the dipolar relaxation time becomes significantly steeper.

Experimental evidence for a liquid-liquid crossover in deeply cooled confined water

In this work we investigate, by means of elastic neutron scattering, the pressure dependence of mean square displacements (MSD) of hydrogen atoms of deeply cooled water confined in the pores of a three-dimensional disordered SiO2 xerogel; experiments have been performed at 250 and 210 K from atmospheric pressure to 1200 bar. The "pressure anomaly" of supercooled water (i.e., a mean square displacement increase with increasing pressure) is observed in our sample at both temperatures; however, contrary to previous simulation results and to the experimental trend observed in bulk water, the pressure effect is smaller at lower (210 K) than at higher (250 K) temperature. Elastic neutron scattering results are complemented by differential scanning calorimetry data that put in evidence, besides the glass transition at about 170 K, a first-order-like endothermic transition occurring at about 230 K that, in view of the neutron scattering results, can be attributed to a liquid-liquid crossover. Our results give experimental evidence for the presence, in deeply cooled confined water, of a crossover occurring at about 230 K (at ambient pressure) from a liquid phase predominant at 210 K to another liquid phase predominant at 250 K; therefore, they are fully consistent with the liquid-liquid transition hypothesis.

The importance of individual protein molecule dynamics in developing and assessing solid state protein preparations

Processing protein solutions into the solid state is a common approach for generating stable amorphous protein mixtures that are suitable for long-term storage. Great care is typically given to protecting the protein native structure during the various drying steps that render it into the amorphous solid state. However, many studies illustrate that chemical and physical degradations still occur in spite of this amorphous material having good glassy properties and it being stored at temperatures below its glass transition temperature (Tg). Because of these persistent issues and recent biophysical studies that have refined the debate ascribing meaning to the molecular dynamical transition temperature and Tg of protein molecules, we provide an updated discussion on the impact of assessing and managing localized, individual protein molecule nondiffusive motions in the context of proteins being prepared into bulk amorphous mixtures. Our aim is to bridge the pharmaceutical studies addressing bulk amorphous preparations and their glassy behavior, with the biophysical studies historically focused on the nondiffusive internal protein dynamics and a protein's activity, along with their combined efforts in assessing the impact of solvent hydrogen-bonding networks on local stability. We also provide recommendations for future research efforts in solid-state formulation approaches.

Distributions of single-molecule properties as tools for the study of dynamical heterogeneities in nanoconfined water

The explicit trend of the distribution functions of single-molecule rotational relaxation constants and atomic mean-square displacement are used to study the dynamical heterogeneities in nanoconfined water. The trend of the single-molecule properties distributions is related to the dynamic heterogeneities, and to the dynamic crossovers found in water clusters of different shapes and sizes and confined in a variety of zeolites. This was true in all the cases that were considered, in spite of the various shapes and sizes of the clusters. It is confirmed that the high temperature dynamical crossover occurring in the temperature range 200-230 K can be interpreted at a molecular level as the formation of almost translationally rigid clusters, characterized by some rotational freedom, hydrogen bond exchange and translational jumps as cage-to-cage processes. We also suggest a mechanism for the low temperature dynamical crossover (LTDC), falling in the temperature range 150-185 K, through which the adsorbed water clusters are made of nearly rigid sub-clusters, slightly mismatched, and thus permitting a relatively free librational motion at their borders. It appears that the condition required for LTDC to occur is the presence of highly heterogeneous environments for the adsorbed molecules, with some dangling hydrogen bonds or weaker than water-water hydrogen bonds. Under these conditions some dynamics are permitted at very low temperature, although most rotational motion is frozen. Therefore, it is unlikely, though not entirely excluded, that LTDC will be found in supercooled bulk water where no heterogeneous interface is present.

Hydration dependence of myoglobin dynamics studied with elastic neutron scattering, differential scanning calorimetry and broadband dielectric spectroscopy

In this work we present a thorough investigation of the hydration dependence of myoglobin dynamics. The study is performed on D2O-hydrated protein powders in the hydration range 0<h<0.5 (h≡gr[D2O]/gr[protein]) and in the temperature range 20-300K. The protein equilibrium fluctuations are investigated with Elastic Neutron Scattering using the spectrometer IN13 at ILL (Grenoble), while the relaxations of the protein+hydration water system are investigated with Broadband Dielectric Spectroscopy; finally, Differential Scanning Calorimetry is used to obtain a thermodynamic description of the system. The effect of increasing hydration is to speed up the relaxations of the myoglobin+hydration water system and, thermodynamically, to decrease the glass transition temperature; these effects tend to saturate at h values greater than ~0.3. Moreover, the calorimetric scans put in evidence the occurrence of an endothermic peak whose onset temperature is located at ~230K independent of hydration. From the point of view of the protein equilibrium fluctuations, while the amplitude of anharmonic mean square displacements is found to increase with hydration, their onset temperature (i.e. the onset temperature of the well known "protein dynamical transition") is hydration independent. On the basis of the above results, the relevance of protein+hydration water relaxations and of the thermodynamic state of hydration water to the onset of the protein dynamical transition is discussed.