Effect of the environment on the protein dynamical transition: a neutron scattering study

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.

Dynamic Personality of Proteins and Effect of the Molecular Environment

Protein dynamics display distinct traits that are linked to their specific biological function. However, the interplay between intrinsic dynamics and the molecular environment on protein stability remains poorly understood. In this study, we investigate, by incoherent neutron scattering, the subnanosecond time scale dynamics of three model proteins: the mesophilic lysozyme, the thermophilic thermolysin, and the intrinsically disordered β-casein. Moreover, we address the influence of water, glycerol, and glucose, which create progressively more viscous matrices around the protein surface. By comparing the protein thermal fluctuations, we find that the internal dynamics of thermolysin are less affected by the environment compared to lysozyme and β-casein. We ascribe this behavior to the protein dynamic personality, i.e., to the stiffer dynamics of the thermophilic protein that contrasts the influence of the environment. Remarkably, lysozyme and thermolysin in all molecular environments reach a critical common flexibility when approaching the calorimetric melting temperature.

An experimentally representative in-silico protocol for dynamical studies of lyophilised and weakly hydrated amorphous proteins

Characterization of biopolymers in both dry and weakly hydrated amorphous states has implications for the pharmaceutical industry since it provides understanding of the effect of lyophilisation on stability and biological activity. Atomistic Molecular Dynamics (MD) simulations probe structural and dynamical features related to system functionality. However, while simulations in homogenous aqueous environments are routine, dehydrated model assemblies are a challenge with systems investigated in-silico needing careful consideration; simulated systems potentially differing markedly despite seemingly negligible changes in procedure. Here we propose an in-silico protocol to model proteins in lyophilised and weakly hydrated amorphous states that is both more experimentally representative and routinely applicable. Since the outputs from MD align directly with those accessed by neutron scattering, the efficacy of the simulation protocol proposed is shown by validating against experimental neutron data for apoferritin and insulin. This work also highlights that without cooperative experimental and simulative data, development of simulative procedures using MD alone would prove most challenging.

Direct Observation of the Mutual Coupling Effect in the Protein-Water-Glycerol Mixture by Combining Neutron Scattering and Selective Deuteration

Numerous studies have discussed the impact of cosolvents on the structure, dynamics, and stability of proteins in aqueous solutions. However, the dynamics of cosolvents in the protein-water-cosolvent ternary system is largely unexplored in experiments due to technical difficulty. Consequently, a comprehensive understanding of the interplay among proteins, water, and cosolvents is still lacking. Here, we employed selective deuteration and neutron scattering techniques to characterize the individual motions of each component in the protein/water/glycerol (GLY) mixture across various temperatures. The consistent dynamic onset temperatures and the correlation between the MSD of the protein and the viscosity of solvents revealed the mutual coupling effects among the three components. Furthermore, our experimental and simulation results showed that the hydrogen bond relaxation energy barrier in the ternary system is ∼43 kJ/mol, whereas in the protein-water binary system it is merely ∼35 kJ/mol. Therefore, we suggest that GLY can enhance hydrogen bond interactions in the ternary system through the mutual coupling effect, thereby serving as one of the protective mechanisms of protein preservation by GLY.

Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions

The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.

Nanocrystallites Modulate Intermolecular Interactions in Cryoprotected Protein Solutions

Studying protein interactions at low temperatures has important implications for optimizing cryostorage processes of biological tissue, food, and protein-based drugs. One of the major issues is related to the formation of ice nanocrystals, which can occur even in the presence of cryoprotectants and can lead to protein denaturation. The presence of ice nanocrystals in protein solutions poses several challenges since, contrary to microscopic ice crystals, they can be difficult to resolve and can complicate the interpretation of experimental data. Here, using a combination of small- and wide-angle X-ray scattering (SAXS and WAXS), we investigate the structural evolution of concentrated lysozyme solutions in a cryoprotected glycerol-water mixture from room temperature (T = 300 K) down to cryogenic temperatures (T = 195 K). Upon cooling, we observe a transition near the melting temperature of the solution (T ≈ 245 K), which manifests both in the temperature dependence of the scattering intensity peak position reflecting protein-protein length scales (SAXS) and the interatomic distances within the solvent (WAXS). Upon thermal cycling, a hysteresis is observed in the scattering intensity, which is attributed to the formation of nanocrystallites in the order of 10 nm. The experimental data are well described by the two-Yukawa model, which indicates temperature-dependent changes in the short-range attraction of the protein-protein interaction potential. Our results demonstrate that the nanocrystal growth yields effectively stronger protein-protein attraction and influences the protein pair distribution function beyond the first coordination shell.

Polymorphism and Ligand Binding Modulate Fast Dynamics of Human Telomeric G-Quadruplexes

Telomeric G-quadruplexes (G4s) are promising targets in the design and development of anticancer drugs. Their actual topology depends on several factors, resulting in structural polymorphism. In this study, we investigate how the fast dynamics of the telomeric sequence AG3(TTAG3)3 (Tel22) depends on the conformation. By using Fourier transform Infrared spectroscopy, we show that, in the hydrated powder state, Tel22 adopts parallel and mixed antiparallel/parallel topologies in the presence of K+ and Na+ ions, respectively. These conformational differences are reflected in the reduced mobility of Tel22 in Na+ environment in the sub-nanosecond timescale, as probed by elastic incoherent neutron scattering. These findings are consistent with the G4 antiparallel conformation being more stable than the parallel one, possibly due to the presence of ordered hydration water networks. In addition, we study the effect of Tel22 complexation with BRACO19 ligand. Despite the quite similar conformation in the complexed and uncomplexed state, the fast dynamics of Tel22-BRACO19 is enhanced compared to that of Tel22 alone, independently of the ions. We ascribe this effect to the preferential binding of water molecules to Tel22 against the ligand. The present results suggest that the effect of polymorphism and complexation on the G4 fast dynamics is mediated by hydration water.

Effect of water activity on the mechanical glass transition and dynamical transition of bacteria

The purpose of this study was to clarify the glass-transition behavior of bacteria (Cronobacter sakazakii) as a function of water activity (aw). From the water sorption isotherm (298 K) for C. sakazakii, monolayer water content and monolayer aw were determined to be 0.0724 g/g-dry matter and 0.252, respectively. Mechanical relaxation was investigated at 298 K. In a higher aw range of over 0.529, the degree of mechanical relaxation increased with an increase in aw. From the effect of aw on the degree of mechanical relaxation, the mechanical awc (aw at which mechanical glass transition occurs at 298 K) was determined to be 0.667. Mean-square displacement of atoms in the bacteria was investigated by incoherent elastic neutron scattering. The mean-square displacement increased gradually with an increase in temperature depending on the aw of samples. From the linear fitting, two or three dynamical transition temperatures (low, middle, and high Tds) were determined at each aw. The low-Td values (142-158 K) were almost independent from aw. There was a minor effect of aw on the middle Td (214-234 K) except for the anhydrous sample (261 K). The high Td (252-322 K) largely increased with the decrease in aw. From the aw dependence of the high Td, the dynamical awc was determined to be 0.675, which was almost equivalent to the mechanical awc. The high Td was assumed to be the glass-transition temperature (Tg), and anhydrous Tg was estimated to be 409 K. In addition, molecular relaxation time (τ) of the bacteria was calculated as a function of aw. From the result, it is suggested that the progress of metabolism in the bacterial system requires a lower τ than approximately 6 × 10-5 s.

The functional role of the hemoglobin-water interface

The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from in vitro, in vivo, and computational experiments (molecular dynamics simulations) are summarized and put into perspective. One of the main findings from the computations is that the stability of the deoxy, ligand-free T-state (T₀) can be stabilized relative to the deoxy R-state (R₀) only in sufficiently large simulation boxes for the hydrophobic effect to manifest itself. This effect directly influences protein stability and is operative also under physiological conditions. Furthermore, molecular simulations provide a dynamical interpretation of the Perutz model for Hb function. Results from experiments using higher protein concentrations and realistic cellular environments are also discussed. One of the next great challenges for computational studies, which as we show is likely to be taken up in the near future, is to provide a molecular-level understanding of the dynamics of proteins in such crowded environments.

Specific Interactions and Environment Flexibility Tune Protein Stability under Extreme Crowding

Macromolecular crowding influences protein mobility and stability in vivo. A precise description of the crowding effect on protein thermal stability requires the estimate of the combined effects of excluded volume, specific protein-environment interactions, as well as the thermal response of the crowders. Here, we explore an ideal model system, the lysozyme protein in powder state, to dissect the factors controlling the melting of the protein under extreme crowding. By deploying state-of-the art molecular simulations, supported by calorimetric experiments, we assess the role of the environment flexibility and of intermolecular electrostatic interactions. In particular, we show that the temperature-dependent flexibility of the macromolecular crowders, along with specific interactions, significantly alleviates the stabilizing contributions of the static volume effect.

Put a cork in it: Plugging the M2 viral ion channel to sink influenza

The ongoing threat of seasonal and pandemic influenza to human health requires antivirals that can effectively supplement existing vaccination strategies. The M2 protein of influenza A virus (IAV) is a proton-gated, proton-selective ion channel that is required for virus replication and is an established antiviral target. While licensed adamantane-based M2 antivirals have been historically used, M2 mutations that confer major adamantane resistance are now so prevalent in circulating virus strains that these drugs are no longer recommended. Here we review the current understanding of IAV M2 structure and function, mechanisms of inhibition, the rise of drug resistance mutations, and ongoing efforts to develop new antivirals that target resistant forms of M2.

Temperature Induced Dynamical Transition of Biomolecules in Polarizable and Nonpolarizable TIP3P Water

Temperature induced dynamical transition (DT), associated with a sharp rise in molecular flexibility, is well-known to be exhibited between 270 and 280 K in glycerol to 200-230 K in hydrated biomolecules and is controlled by diffusivity (viscosity) of the solvation layer. In the molecular dynamics (MD) community, especially for water as a solvent, this has been an intense area of research despite decades of investigations. However, in general, water in these studies is described by empirical nonpolarizable force fields in which electronic polarizability is treated implicitly with effective charges and related parameters. This might have led to the present trait of discovery that DTs of biomolecules, irrespective of the potential functions for water models used, occur within a narrow band of temperature variation (30-40 K). Whereas a water molecule in a biomolecular surface and one in bulk are polarized differently, therefore explicit treatment of water polarizability would be a powerful approach toward the treatment of hydration water, believed to cause the DT manifestation. Using MD simulations, we investigated the effects of polarizable water on the DT of biomolecules and the dynamic properties of hydration water. We chose two types of solutes: globular protein (lysozyme) and more open and flexible RNAs (a hairpin and a riboswitch) with different natures of hydrophilic sites than proteins in general. We found that the characteristic temperature of DT ( T_DT) for the solutes in polarizable water is always higher than that in its nonpolarizable counterpart. In particular, for RNAs, the variations are found to be ∼45 K between the two water models, whereas for the more compact lysozyme, it is only ∼4 K. The results are discussed in light of the enormous increase in relaxation times of a liquid upon cooling in the paradigm of dynamic switchover in hydration water with liquid-liquid phase transition, derived from the existence of the second critical point. Our result supports the idea that structures of biomolecules and their interactions with the hydration water determines T_DT and provides evidence for the decisive role of polarizable water on the onset of DT, which has been hitherto ignored.

FTIR Spectroscopic Study of the Secondary Structure of Globular Proteins in Aqueous Protic Ionic Liquids

Protein misfolding is a detrimental effect which can lead to the inactivation of enzymes, aggregation, and the formation of insoluble protein fibrils called Amyloids. Consequently, it is important to understand the mechanism of protein folding, and under which conditions it can be avoided or mitigated. Ionic liquids (ILs) have previously been shown as capable of increasing or decreasing protein stability, depending on the specific IL, IL concentration and which protein. However, a greater range of IL-proteins need to be systematically explored to enable the development of structure-property relationships. In this work, the secondary structure of four proteins, lysozyme, trypsin, β-lactoglobulin and α-amylase, were studied in aqueous solutions of 10 protic ionic liquids (PILs) with 0-50 mol% PIL present. The PILs consisted of ethyl-, ethanol-, diethanol- and triethanolammonium cations paired with nitrate, formate, acetate or glycolate anions. The secondary structure was obtained using ATR-FTIR spectroscopy. It was found that lysozyme and trypsin retained its secondary structure, consistent with a native folded state, for many of the aqueous IL solutions which contained a formate or nitrate anion at the most dilute concentrations. In contrast, α-amylase and β-lactoglobulin generally had poor stability and solubility in the IL solutions. This may be due to the isoelectric point of α-amylase and β-lactoglobulin being closer to the pH of the solvents. All four proteins were insoluble in ethyl-, ethanol- and diethanolammonium acetate, though α-amylase and trypsin retained their secondary structure in up to 20 and 30 mol% of triethanolammonium acetate, respectively. It was evident that the protein stability varied substantially depending on the protein-IL combination, and the IL concentration in water. Overall, the findings indicated that some ions and some ILs were in general better for protein solubility and stability than others, such as acetate leading to poor solubility, and EAN and EAF generally leading to better protein stability than the other PILs. This study of four proteins in 10 aqueous PILs clearly showed that there are many complexities in their interactions and no clear general trend, despite the similarities between the PIL structures. This highlights the need for more and larger studies to enable the selection and optimization of PIL solvents used with biomolecules.

Evidence of a low-temperature dynamical transition in concentrated microgels

A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a "protein-like" dynamical transition in nonbiological aqueous environments. To this aim, we exploit the popular colloidal system of poly-N-isopropylacrylamide (PNIPAM) microgels, extending their investigation to unprecedentedly high concentrations. Owing to the heterogeneous architecture of the microgels, water crystallization is avoided in concentrated samples, allowing us to monitor atomic dynamics at low temperatures. By elastic incoherent neutron scattering and molecular dynamics simulations, we find that a dynamical transition occurs at a temperature T _d ~ 250 K, independently from PNIPAM mass fraction. However, the transition is smeared out on approaching dry conditions. The quantitative agreement between experiments and simulations provides evidence that the transition occurs simultaneously for PNIPAM and water dynamics. The similarity of these results with hydrated protein powders suggests that the dynamical transition is a generic feature in complex macromolecular systems, independently from their biological function.

Determination of Dynamical Heterogeneity from Dynamic Neutron Scattering of Proteins

Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scattering methods. These displacements can also be calculated numerically using data from molecular dynamics simulations. An enormous amount of data on the average mean-square motional displacement (MSD) of H as a function of protein temperature, hydration, and other conditions has been collected. H resides in a wide spectrum of sites in a protein. Some H are tightly bound to molecular chains, and the H motion is dictated by that of the chain. Other H are quite independent. As a result, there is a distribution of motions and MSDs of H within a protein that is denoted dynamical heterogeneity. The goal of this paper is to incorporate a distribution of MSDs into models of the H incoherent intermediate scattering function, I(Q,t), that is calculated and observed. The aim is to contribute information on the distribution as well as on the average MSD from comparison of the models with simulations and experiment. For example, we find that simulations of I(Q,t) in lysozyme are well reproduced if the distribution of MSDs is bimodal with two broad peaks rather than a single broad peak.

Temperature Dependence of Tryptophan Fluorescence Lifetime in Aqueous Glycerol and Trehalose Solutions

The temperature dependences of tryptophan fluorescence decay kinetics in aqueous glycerol and 1 M trehalose solutions were examined. The fluorescence decay kinetics were recorded in the spectral region of 292.5-417.5 nm with nanosecond time resolution. The kinetics curves were approximated by the sum of three exponential terms, and the spectral distribution (DAS) of these components was determined. An antisymbatic course of fluorescence decay times of two (fast and medium) components in the temperature range from -60 to +10°C was observed. The third (slow) component showed only slight temperature dependence. The antisymbatic behavior of fluorescence lifetimes of the fast and medium components was explained on the assumption that some of the excited tryptophan molecules are transferred from a short-wavelength B-form with short fluorescence lifetime to a long-wavelength R-form with an intermediate fluorescence lifetime. This transfer occurred in the indicated temperature range.

Ergodicity breaking of iron displacement in heme proteins

We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.

Molecular Packing, Hydrogen Bonding, and Fast Dynamics in Lysozyme/Trehalose/Glycerol and Trehalose/Glycerol Glasses at Low Hydration

Water and glycerol are well-known to facilitate the structural relaxation of amorphous protein matrices. However, several studies evidenced that they may also limit fast (∼picosecond-nanosecond, ps-ns) and small-amplitude (∼Å) motions of proteins, which govern their stability in freeze-dried sugar mixtures. To determine how they interact with proteins and sugars in glassy matrices and, thereby, modulate their fast dynamics, we performed molecular dynamics (MD) simulations of lysozyme/trehalose/glycerol (LTG) and trehalose/glycerol (TG) mixtures at low glycerol and water concentrations. Upon addition of glycerol and/or water, the glass transition temperature, T_g, of LTG and TG mixtures decreases, the molecular packing of glasses is improved, and the mean-square displacements (MSDs) of lysozyme and trehalose either decrease or increase, depending on the time scale and on the temperature considered. A detailed analysis of the hydrogen bonds (HBs) formed between species reveals that water and glycerol may antiplasticize the fast dynamics of lysozyme and trehalose by increasing the total number and/or the strength of the HBs they form in glassy matrices.

Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion

Internal subnanosecond timescale motions are key for the function of proteins, and are coupled to the surrounding solvent environment. These fast fluctuations guide protein conformational changes, yet their role for protein stability, and for unfolding, remains elusive. Here, in analogy with the Lindemann criterion for the melting of solids, we demonstrate a common scaling of structural fluctuations of lysozyme protein embedded in different environments as the thermal unfolding transition is approached. By combining elastic incoherent neutron scattering and advanced molecular simulations, we show that, although different solvents modify the protein melting temperature, a unique dynamical regime is attained in proximity of thermal unfolding in all solvents that we tested. This solvation shell-independent dynamical regime arises from an equivalent sampling of the energy landscape at the respective melting temperatures. Thus, we propose that a threshold for the conformational entropy provided by structural fluctuations of proteins exists, beyond which thermal unfolding is triggered.

Moving in the Right Direction: Protein Vibrations Steering Function

Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for possible new therapies; however, the control mechanisms are under debate. Calculations have indicated protein vibrations enable structural change. However, previous measurements found these vibrations only weakly depend on the functional state. By using the novel technique of anisotropic terahertz microscopy, we find that there is a dramatic change to the vibrational directionality with inhibitor binding to lysozyme, whereas the vibrational energy distribution, as measured by neutron inelastic scattering, is only slightly altered. The anisotropic terahertz measurements provide unique access to the directionality of the intramolecular vibrations, and immediately resolve the inconsistency between calculations and previous measurements, which were only sensitive to the energy distribution. The biological importance of the vibrational directions versus the energy distribution is revealed by our calculations comparing wild-type lysozyme with a higher catalytic rate double deletion mutant. The vibrational energy distribution is identical, but the more efficient mutant shows an obvious reorientation of motions. These results show that it is essential to characterize the directionality of motion to understand and control protein dynamics to optimize or inhibit function.

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles

Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to 'surface-melted' inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a 'glassy' state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations ('colored' or 'pink' noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the dynamics of ubiquitin to be even more like a polycrystalline material in which the α-helix and β-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the α-helix and β-sheet domains.

Communication: Contrasting effects of glycerol and DMSO on lipid membrane surface hydration dynamics and forces

Glycerol and dimethyl sulfoxide (DMSO) are commonly used cryoprotectants in cellular systems, but due to the challenges of measuring the properties of surface-bound solvent, fundamental questions remain regarding the concentration, interactions, and conformation of these solutes at lipid membrane surfaces. We measured the surface water diffusivity at gel-phase dipalmitoylphosphatidylcholine (DPPC) bilayer surfaces in aqueous solutions containing ≤7.5 mol. % of DMSO or glycerol using Overhauser dynamic nuclear polarization. We found that glycerol similarly affects the diffusivity of water near the bilayer surface and that in the bulk solution (within 20%), while DMSO substantially increases the diffusivity of surface water relative to bulk water. We compare these measurements of water dynamics with those of equilibrium forces between DPPC bilayers in the same solvent mixtures. DMSO greatly decreases the range and magnitude of the repulsive forces between the bilayers, whereas glycerol increases it. We propose that the differences in hydrogen bonding capability of the two solutes leads DMSO to dehydrate the lipid head groups, while glycerol affects surface hydration only as much as it affects the bulk water properties. The results suggest that the mechanism of the two most common cryoprotectants must be fundamentally different: in the case of DMSO by decoupling the solvent from the lipid surface, and in the case of glycerol by altering the hydrogen bond structure and intermolecular cohesion of the global solvent, as manifested by increased solvent viscosity.

Proteins in binary solvents

Proteins in living organisms exist in complex aqueous solutions or embedded in membranes. In solution, proteins are surrounded by a tightly bound hydration layer, which is more ordered and less mobile than bulk water. As a consequence, water plays a major role in controlling protein structure stability, conformational flexibility, dynamics, and functionality, but it also appears that protein surface regulates the structuring of the surrounding water. The presence of cosolvents can modify the hydration layer characteristics and then the whole protein structural and dynamical properties. Because cytoplasm or biological liquids are complex solutions, the knowledge of the solvation shell characteristics in mixed solvents should be considered as a crucial step in describing biological processes at molecular level. This review reports on recent studies on the structural and thermodynamic properties of model proteins dissolved in binary solvent mixtures by small-angle neutron scattering (SANS) and differential scanning microcalorimetry (DSC) techniques. We will show that contrast variation SANS experiments allow to acquire a direct knowledge of both protein structure and protein solvation shell (in terms of low-resolution shape and solvent/cosolvent composition), while DSC experiments provide information on all the relevant thermodynamic properties. We will focus on two main points. First, an extended description of the thermodynamic model used to define the equilibria between water and cosolvent molecules in the protein solvation shell will be presented. Second, the determination of the peculiar characteristics of the protein solvation layer, which will be illustrated by considering different systems. As a conclusion, we will show that the investigation of structure and thermodynamics of proteins in binary aqueous mixtures is an important way to understand the role of hydration in protein stability and activity.

Reentrant condensation of lysozyme: Implications for studying dynamics of lysozyme in aqueous solutions of lithium chloride

Recent studies have outlined the use of eutectic solutions of lithium chloride in water to study microscopic dynamics of lysozyme in an aqueous solvent that is remarkably similar to pure water in many respects, yet allows experiments over a wide temperature range without solvent crystallization. The eutectic point in a (H2O)R(LiCl) system corresponds to R ≈ 7.3, and it is of interest to investigate whether less-concentrated aqueous solutions of LiCl could be used in low-temperature studies of a solvated protein. We have investigated a range of concentrations of lysozyme and LiCl in aqueous solutions to identify systems that do not show phase separation and avoid solvent crystallization on cooling down. Compared to the lysozyme concentration in solution, the concentration of LiCl in the aqueous solvent plays the major role in determining systems suitable for low-temperature studies. We have observed interesting and rich phase behavior reminiscent of reentrant condensation of proteins.

Computational investigation of dynamical transitions in Trp-cage miniprotein powders

We investigate computationally the dynamical transitions in Trp-cage miniprotein powders, at three levels of hydration: 0.04, 0.26 and 0.4 g water/g protein. We identify two distinct temperatures where transitions in protein dynamics occur. Thermal motions are harmonic and independent of hydration level below T_low ≈ 160 K, above which all powders exhibit harmonic behavior but with a different and enhanced temperature dependence. The second onset, which is often referred to as the protein dynamical transition, occurs at a higher temperature T_D that decreases as the hydration level increases, and at the lowest hydration level investigated here (0.04 g/g) is absent in the temperature range we studied in this work (T ≤ 300 K). Protein motions become anharmonic at T_D, and their amplitude increases with hydration level. Upon heating above T_D, hydrophilic residues experience a pronounced enhancement in the amplitude of their characteristic motions in hydrated powders, whereas it is the hydrophobic residues that experience the more pronounced enhancement in the least hydrated system. The dynamical transition in Trp-cage is a collective phenomenon, with every residue experiencing a transition to anharmonic behavior at the same temperature.

Atomistic details of protein dynamics and the role of hydration water

BACKGROUND

The importance of protein dynamics for their biological activity is now well recognized. Different experimental and computational techniques have been employed to study protein dynamics, hierarchy of different processes and the coupling between protein and hydration water dynamics. Yet, understanding the atomistic details of protein dynamics and the role of hydration water remains rather limited.

SCOOP OF REVIEW

Based on overview of neutron scattering, molecular dynamic simulations, NMR and dielectric spectroscopy results we present a general picture of protein dynamics covering time scales from faster than ps to microseconds and the influence of hydration water on different relaxation processes.

MAJOR CONCLUSIONS

Internal protein dynamics spread over a wide time range from faster than picosecond to longer than microseconds. We suggest that the structural relaxation in hydrated proteins appears on the microsecond time scale, while faster processes present mostly motion of side groups and some domains. Hydration water plays a crucial role in protein dynamics on all time scales. It controls the coupled protein-hydration water relaxation on 10-100ps time scale. This process defines the friction for slower protein dynamics. Analysis suggests that changes in amount of hydration water affect not only general friction, but also influence significantly the protein's energy landscape.

GENERAL SIGNIFICANCE

The proposed atomistic picture of protein dynamics provides deeper understanding of various relaxation processes and their hierarchy, similarity and differences between various biological macromolecules, including proteins, DNA and RNA. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".

Microscopic relaxations in a protein sustained down to 160K in a non-glass forming organic solvent

BACKGROUND

We have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160K.

METHODS

We have utilized quasielastic neutron scattering.

RESULTS

A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamical transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature.

CONCLUSIONS

Our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics.

GENERAL SIGNIFICANCE

We hypothesize that, if the long debated idea regarding the direct link between the microscopic relaxations and the biological activity in proteins is correct, then not only the microscopic relaxations, but also the activity, could be sustained in proteins all the way down to the freezing temperature of a non-glass forming solvent with a weak temperature dependence of its viscosity. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.

Protein dynamics: from rattling in a cage to structural relaxation

We present an overview of protein dynamics based mostly on results of neutron scattering, dielectric relaxation spectroscopy and molecular dynamics simulations. We identify several major classes of protein motions on the time scale from faster than picoseconds to several microseconds, and discuss the coupling of these processes to solvent dynamics. Our analysis suggests that the microsecond backbone relaxation process might be the main structural relaxation of the protein that defines its glass transition temperature, while faster processes present some localized secondary relaxations. Based on the overview, we formulate a general picture of protein dynamics and discuss the challenges in this field.

Local minimum in fragility for trehalose/glycerol mixtures: implications for biopharmaceutical stabilization

Approximately a decade ago it was observed that adding a small amount (5 wt %) of glycerol to trehalose could substantially improve the stability of enzymes stored in these glasses even though the final glass transition temperature (Tg) was reduced by ∼20 K. This finding inspired great interest in the fast dynamics of dehydrated trehalose/glycerol mixtures, leading to the observation that suppression of fast dynamics was optimal in the presence of ∼5 wt % of glycerol. It was also recognized that the fast dynamics should, in theory, be related to the fragility of these glass formers, but experimental confirmation of this hypothesis has been lacking for trehalose/glycerol mixtures or any other mixtures of this nature. In the present study a dynamic mechanical analyzer (DMA) was used to determine both the Tg and the kinetic fragility index (m) of trehalose/glycerol mixtures within the mass fraction range of 80-100 wt % of trehalose. It was found that the fragility index correlated with the mass fraction of trehalose in a nonmonotonic manner, with a local minimum between 87.5 and 95 wt % of trehalose, whereas the composition dependence of Tg was found to follow a Gordon-Taylor-like relationship, with no local minimum. The composition of 5-12.5 wt % glycerol in trehalose thus yielded a matrix that maximized the strong glass-forming contribution of glycerol, while minimizing its Tg lowering effect. This quantitative evidence supports speculation about the fragility characteristics of these mixtures that has been ongoing for the past decade. The DMA-based Tg and fragility determination method developed in this study represents a new approach for identifying optimal compositions for preservation of biologics.

Motional displacements in proteins: The origin of wave-vector-dependent values

The average mean-square displacement, 〈r(2)〉, of H atoms in a protein is frequently determined using incoherent neutron-scattering experiments. 〈r(2)〉 is obtained from the observed elastic incoherent dynamic structure factor, S(i)(Q,ω=0), assuming the form S(i)(Q,ω=0) =exp(-Q(2)〈r(2)〉/3). This is often referred to as the Gaussian approximation (GA) to S(i)(Q,ω=0). 〈r(2)〉 obtained in this way depends on the value of the wave vector, Q considered. Equivalently, the observed S(i)(Q,ω=0) deviates from the GA. We investigate the origin of the Q dependence of 〈r(2)〉 by evaluating the scattering functions in different approximations using molecular dynamics (MD) simulation of the protein lysozyme. We find that keeping only the Gaussian term in a cumulant expansion of S(Q,ω) is an accurate approximation and is not the origin of the Q dependence of 〈r(2)〉. This is demonstrated by showing that the term beyond the Gaussian is negligible and that the GA is valid for an individual atom in the protein. Rather, the Q dependence (deviation from the GA) arises from the dynamical heterogeneity of the H in the protein. Specifically it arises from representing, in the analysis of data, this diverse dynamics by a single average scattering center that has a single, average 〈r(2)〉. The observed Q dependence of 〈r(2)〉 can be used to provide information on the dynamical heterogeneity in proteins.

Thermal fluctuations in chemically cross-linked polymers of cyclodextrins

The extent and nature of thermal fluctuations in the innovative class of cross-linked polymers called cyclodextrin nanosponges (CDNS) are investigated, on the picosecond time scale, through elastic and quasielastic neutron scattering experiments. Nanosponges are complex 3D polymer networks where covalent bonds connecting different cyclodextrin (CD) units and intra- and inter-molecular hydrogen-bond interactions cooperate to define the molecular architecture and fast dynamics of the polymer. The study presented here aims to clarify the nature of the conformational rearrangements activated by increasing temperature in the nanosponge polymer, and the constraints imposed by intra- and inter-molecular hydrogen-bond patterns on the internal dynamics of the macromolecule. The results suggest a picture, in which conformational rearrangements involving the torsion of the OH groups around the C-O bonds dominate the internal dynamics of the polymer over the picosecond time scale. Moreover, the estimated values of mean square displacements reveal that the motions of the hydrogen atoms in the nanosponges are progressively hampered as the cross-linking degree of the polymer is increased. Finally, the study of the molecular relaxations suggests a dynamical rearrangement of the hydrogen-bond networks, which is characterized by a jump diffusion motion of the more mobile hydrogen atoms belonging to the OH groups of the CD units. All these findings add further contribution to the rational comprehensive view of the dynamics of these macromolecules, which may be particularly beneficial in designing new drug-delivery systems with tuneable inclusion/release properties.

Protein dynamics tunes excited state positions in light-harvesting complex II

Light harvesting and excitation energy transfer in photosynthesis are relatively well understood at cryogenic temperatures up to ∼100 K, where crystal structures of several photosynthetic complexes including the major antenna complex of green plants (LHC II) are available at nearly atomic resolution. The situation is much more complex at higher or even physiological temperatures, because the spectroscopic properties of antenna complexes typically undergo drastic changes above ∼100 K. We have addressed this problem using a combination of quasielastic neutron scattering (QENS) and optical spectroscopy on native LHC II and mutant samples lacking the Chl 2/Chl a 612 pigment molecule. Absorption difference spectra of the Chl 2/Chl a 612 mutant of LHC II reveal pronounced changes of spectral position and their widths above temperatures as low as ∼80 K. The complementary QENS data indicate an onset of conformational protein motions at about the same temperature. This finding suggests that excited state positions in LHC II are affected by protein dynamics on the picosecond time scale. In more detail, this means that at cryogenic temperatures the antenna complex is trapped in certain protein conformations. At higher temperature, however, a variety of conformational substates with different spectral position may be thermally accessible. At the same time, an analysis of the widths of the absorption difference spectra of Chl 2/Chl a 612 reveals three different reorganization energies or Huang-Rhys factors in different temperature ranges, respectively. These findings imply that (dynamic) pigment-protein interactions fine-tune electronic energy levels and electron-phonon coupling of LHC II for efficient excitation energy transfer at physiological temperatures.

Hydration-dependent dynamic crossover phenomenon in protein hydration water

The characteristic relaxation time τ of protein hydration water exhibits a strong hydration level h dependence. The dynamic crossover is observed when h is higher than the monolayer hydration level hc=0.2-0.25 and becomes more visible as h increases. When h is lower than hc, τ only exhibits Arrhenius behavior in the measured temperature range. The activation energy of the Arrhenius behavior is insensitive to h, indicating a local-like motion. Moreover, the h dependence of the crossover temperature shows that the protein dynamic transition is not directly or solely induced by the dynamic crossover in the hydration water.

Temperature-dependent dynamics of dry and hydrated β-casein studied by quasielastic neutron scattering

β-Casein is a component of casein micelle with amphillic nature and is recognized as a "natively disordered" protein that lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of β-casein are explored by quasielastic neutron scattering (QENS). An upturn in the mean square displacement (MSD) of hydrated β-casein indicates an increase of protein flexibility at a temperature of ~225 K. Another increase in MSD at ~100 K, observed in both dry and hydrated β-casein, is ascribed to the methyl group rotations, which are not sensitive to hydration. QENS analysis in the energy domain reveals that the fraction of hydrogen atoms participating in motion in a sphere of diffusion is highly hydration dependent and increases with temperature. In the time domain analysis, a logarithmic-like decay is observed in the range of picosecond to nanosecond (β-relaxation time) in the dynamics of hydrated β-casein. This dynamical behavior has been observed in hydrated globular and oligomeric proteins. Our temperature-dependent QENS experiments provide evidence that lack of a secondary structure in β-casein results in higher flexibility in its dynamics and easier reversible thermal unfolding compared to other rigid biomolecules.

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.

Does a dry protein undergo a glass transition?

Bovine serum albumin (BSA) with extremely low hydration level 0.04, which is usually defined as dry, has been investigated in the temperature range between 200 and 340 K by incoherent inelastic neutron scattering using the neutron time-of-flight spectrometer FOCUS (PSI, Switzerland). Anomalous temperature behavior has been revealed for relaxational and low-frequency vibrational dynamics of BSA in the vicinity of 250 K. The mean-square atomic displacement has been shown to exhibit a change in the slope of temperature dependence near the same temperature. The presented results point out that the glass-like transition occurs in the dry protein.