Coupling between lysozyme and trehalose dynamics: microscopic insights from molecular-dynamics simulations

Advancing predictions of protein stability in the solid state

The β-relaxation associated with the sub-glass transition temperature (T_g,β) is attributed to fast, localised molecular motions which can occur below the primary glass transition temperature (T_g,α). Consistent with T_g,β being observed well-below storage temperatures, the β-relaxation associated motions have been hypothesised to influence protein stability in the solid state and could thus impact the quality of e.g. protein powders for inhalation or reconstitution and injection. Why then do distinct solid state protein formulations with similar aggregation profiles after drying and immediate reconstitution, display different profiles when reconstituted following prolonged storage? Is the value of T_g,β, associated with the β-relaxation process of the system, a reliable parameter for characterising the behaviour of proteins in the solid state? Bearing this in mind, in this work we further explore the different relaxation dynamics of glassy solid state monoclonal antibody formulations using terahertz time-domain spectroscopy and dynamical mechanical analysis. By conducting a 52 week stability study on a series of multi-component spray-dried formulations, an approach for characterising and analysing the solid state dynamics and how these relate to protein stability is outlined.

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".

Revisiting the conundrum of trehalose stabilization

Protein aggregation and loss of protein's biological functionality are manifestations of protein instability. Cosolvents, in particular trehalose, are widely accepted antidotes against such destabilization. Although numerous theories have been promulgated in the literature with regard to its mechanism of stabilization, the present scenario is still elusive in view of the discrepancies existing in them. To this end, we have revisited the conundrum and attempted to rationalize the mechanism by conducting thorough investigation of the effect of trehalose on the native, partially unfolded and denatured states of protein "Lysozyme" by means of molecular dynamic (MD) simulations under different temperature and concentration regimes. Two-dimensional contour plots along with principal component analysis suggest that trehalose molecules offer on-pathway stabilization unaltering the principal direction of protein's motion, although it slows down protein dynamics so that the protein gets trapped in the homogeneous ensemble of conformations closer to the native state. Free energy landscape reveals higher population of native compared to intermediate and denatured states. Delphi results and calculation of the preferential interaction parameter demonstrate that this relative stabilization of the native state can be ascribed to be the consequence of favourable interactions of trehalose with side chains of certain loci on the protein surface encompassing polar flexible residues. Stability of protein results from the observed difference in binding affinity of trehalose for native and denatured states of protein. Our findings are at variance with the common conception of relative destabilization of the denatured state. Rather, we provide evidence for relative stabilization of the native state. This stabilization is due to interplay of protein-trehalose, water-trehalose, water-water, protein-water and trehalose-trehalose interactions.

Stabilization of proteins in solid form

Immunogenicity of aggregated or otherwise degraded protein delivered from depots or other biopharmaceutical products is an increasing concern, and the ability to deliver stable, active protein is of central importance. We review characterization approaches for solid protein dosage forms with respect to metrics that are intended to be predictive of protein stability against aggregation and other degradation processes. Each of these approaches is ultimately motivated by hypothetical connections between protein stability and the material property being measured. We critically evaluate correlations between these properties and stability outcomes, and use these evaluations to revise the currently standing hypotheses. Based on this we provide simple physical principles that are necessary (and possibly sufficient) for generating solid delivery vehicles with stable protein loads. Essentially, proteins should be strongly coupled (typically through H-bonds) to the bulk regions of a phase-homogeneous matrix with suppressed β relaxation. We also provide a framework for reliable characterization of solid protein forms with respect to stability.

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.

Long-time mean-square displacements in proteins

We propose a method for obtaining the intrinsic, long-time mean square displacement (MSD) of atoms and molecules in proteins from finite-time molecular dynamics (MD) simulations. Typical data from simulations are limited to times of 1 to 10 ns, and over this time period the calculated MSD continues to increase without a clear limiting value. The proposed method consists of fitting a model to MD simulation-derived values of the incoherent intermediate neutron scattering function, I(inc)(Q,t), for finite times. The infinite-time MSD, <r(2)>, appears as a parameter in the model and is determined by fits of the model to the finite-time I(inc)(Q,t). Specifically, the <r(2)> is defined in the usual way in terms of the Debye-Waller factor as I(Q,t=∞)=exp(-Q(2)<r(2)>/3). The method is illustrated by obtaining the intrinsic MSD <r(2)> of hydrated lysozyme powder (h=0.4 g water/g protein) over a wide temperature range. The intrinsic <r(2)> obtained from data out to 1 and to 10 ns is found to be the same. The intrinsic <r(2)> is approximately twice the value of the MSD that is reached in simulations after times of 1 ns which correspond to those observed using neutron instruments that have an energy resolution width of 1 μeV.

Microscopic mechanism of protein cryopreservation in an aqueous solution with trehalose

In order to investigate the cryoprotective mechanism of trehalose on proteins, we use molecular dynamics computer simulations to study the microscopic dynamics of water upon cooling in an aqueous solution of lysozyme and trehalose. We find that the presence of trehalose causes global retardation of the dynamics of water. Comparing aqueous solutions of lysozyme with/without trehalose, we observe that the dynamics of water in the hydration layers close to the protein is dramatically slower when trehalose is present in the system. We also analyze the structure of water and trehalose around the lysozyme and find that the trehalose molecules form a cage surrounding the protein that contains very slow water molecules. We conclude that the transient cage of trehalose molecules that entraps and slows the water molecules prevents the crystallisation of protein hydration water upon cooling.

The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures

We present a Molecular Dynamics simulation study of the effect of trehalose concentration on the structure and dynamics of individual proteins immersed in trehalose/water mixtures. Hen egg-white Lysozyme is used in this study and trehalose concentrations of 0%, 10%, 20%, 30% and 100% by weight are explored. Surprisingly, we have found that changes in trehalose concentration do not change the global structural characteristics of the protein as measured by standard quantities like the mean square deviation, radius of gyration, solvent accessible surface area, inertia tensor and asphericity. Only in the limit of pure trehalose these metrics change significantly. Specifically, we found that the protein is compressed by 2% when immersed in pure trehalose. At the amino acid level there is noticeable rearrangement of the surface residues due to the change in polarity of the surrounding environment with the addition of trehalose. From a dynamic perspective, our computation of the Incoherent Intermediate Scattering Function shows that the protein slows down with increasing trehalose concentration; however, this slowdown is not monotonic. Finally, we also report in-depth results for the hydration layer around the protein including its structure, hydrogen-bonding characteristics and dynamic behavior at different length scales.

Fragility and cooperative motion in a glass-forming polymer-nanoparticle composite

Polymer-nanoparticle composites play a vital role in ongoing materials development. The behavior of the glass transition of these materials is important for their processing and applications, and also represents a problem of fundamental physical interest. Changes of the polymer glass transition temperature Tg due to nanoparticles have been fairly well catalogued, but the breadth of the transition and how rapidly transport properties vary with temperature T - termed the fragility m of glass-formation - is comparatively poorly understood. In the present work, we calculate both Tg and m of a model polymer nanocomposite by molecular dynamics simulations. We systematically consider how Tg and m vary both for the material as a whole, as well as locally, for a range of nanoparticle (NP) concentrations and two polymer-NP interactions. We find large positive and negative changes in Tg and m that can be interpreted in terms of the Adam-Gibbs model of glass-formation, where the scale of the cooperative motion is identified with the scale of string-like cooperative motion. This provides a molecular perpective of fragility changes due to the addition of NPs and for glass formation more generally. We also contrast the behavior along isobaric and isochoric approaches to Tg , since these differing paths can be important to compare experiments (isobaric) and simulations (very often isochoric). Our findings have practical implications for understanding the properties of nanocomposites and fundamental significance for understanding the properties glass-forming materials more broadly.

How strongly does trehalose interact with lysozyme in the solid state? Insights from molecular dynamics simulation and inelastic neutron scattering

Therapeutic proteins are usually conserved in glassy matrixes composed of stabilizing excipients and a small amount of water, which both control their long-term stability, and thus their potential use in medical treatments. To shed some light on the protein-matrix interactions in such systems, we performed molecular dynamics (MD) simulations on matrixes of (i) the model globular protein lysozyme (L), (ii) the well-known bioprotectant trehalose (T), and (iii) the 1:1 (in weight) lysozyme/trehalose mixture (LT), at hydration levels h of 0.0, 0.075, and 0.15 (in g of water/g of protein or sugar). We also supplemented these simulations with complementary inelastic neutron scattering (INS) experiments on the L, T, and LT lyophilized (freeze-dried) samples. The densities and free volume distributions indicate that trehalose improves the molecular packing of the LT glass with respect to the L one. Accordingly, the low-frequency vibrational densities of states (VDOS) and the mean square displacements (MSDs) of lysozyme reveal that it is less flexible-and thus less likely to unfold-in the presence of trehalose. Furthermore, at low contents (h = 0.075), water systematically stiffens the vibrational motions of lysozyme and trehalose, whereas it increases their MSDs on the nanosecond (ns) time scale. This stems from the hydrogen bonds (HBs) that lysozyme and trehalose form with water, which, interestingly, are stronger than the ones they form with each other but which, nonetheless, relax faster on the ns time scale, given the larger mobility of water. Moreover, lysozyme interacts preferentially with water in the hydrated LT mixtures, and trehalose appears to slow down significantly the relaxation of lysozyme-water HBs. Overall, our results suggest that the stabilizing efficiency of trehalose arises from its ability to (i) increase the number of HBs formed by proteins in the dry state and (ii) make the HBs formed by water with proteins stable on long (>ns) time scales.

Self-assembly of trehalose molecules on a lysozyme surface: the broken glass hypothesis

To help understand how sugar interactions with proteins stabilise biomolecular structures, we compare the three main hypotheses for the phenomenon with the results of long molecular dynamics simulations on lysozyme in aqueous trehalose solution (0.75 M). We show that the water replacement and water entrapment hypotheses need not be mutually exclusive, because the trehalose molecules assemble in distinctive clusters on the surface of the protein. The flexibility of the protein backbone is reduced under the sugar patches supporting earlier findings that link reduced flexibility of the protein with its higher stability. The results explain the apparent contradiction between different experimental and theoretical results for trehalose effects on proteins.

Study of solvent-protein coupling effects by neutron scattering

The present work aims to characterize the dynamical behavior of proteins immersed in bio-preserving liquids and glasses. For this purpose, the protein dUTPase was chosen, while the selected solvents were glycerol, a triol, and some homologous disaccharides, i.e., trehalose, maltose, and sucrose, which are known to be very effective bio-preserving agents. The results highlight that the disaccharides show a slowing down effect on the water dynamics, which is stronger for trehalose than in the case of the other disaccharides. Furthermore, a characterization of the medium which hosts the protein is performed by using an operative definition of fragility based on the mean square displacement extracted by elastic incoherent neutron scattering, which is directly connected to Angell's kinetic fragility based on the viscosity. Finally, a study of the dynamics of the protein sequestered within the solvents is performed. The result shows that the protein dynamics is coupled with that of the surrounding matrix.

Thermostabilization mechanism of bovine serum albumin by trehalose

Thermal denaturation of bovine serum albumin (BSA) is analyzed from differential scanning calorimetry (DSC) and Raman spectroscopy investigations. DSC curves exhibit a marked dependence on protein concentration. BSA thermal denaturation becomes broader and bimodal, and the temperature of denaturation increases with increasing protein concentration. Raman scattering investigations simultaneously carried out in the low-frequency range (10-350 cm(-1)) and in the amide I band region (1500-1800 cm(-1)) indicate that the denaturation process is described as a biphasic process independent of protein concentration. The dependence of the protein stability upon the protein concentration can be interpreted from the coupling of protein and solvent dynamics. The confrontation of previous results obtained from Raman investigations on lysozyme (LYS) and the present study of BSA brings out significant information on protein dynamics and the coupling of protein and hydration-water dynamics in relation with the solvent accessible surface area. Contrary to LYS, the modification of the dynamics of hydration water by the protein is clearly observed on BSA. The influence of trehalose on the protein dynamics was analyzed. We found that trehalose reduces the dynamic fluctuations of polar side chains at the protein-solvent interface. The mechanism of thermostabilization by trehalose is related to the reduction of the exposure of hydrophobic groups of BSA to the water molecules, and to a strengthening of intermolecular O-H interactions in the hydrogen-bond network of water, leading to the stabilization of the tertiary structure.

Universal features of water dynamics in solutions of hydrophilic polymers, biopolymers, and small glass-forming materials

A systematic investigation by dielectric spectroscopy of 18 different water-rich mixtures with very different hydrophilic substances shows universal features for the water dynamics. The temperature dependence of the relaxation times exhibits a crossover from non-Arrhenius to Arrhenius behavior at the T(g) range of the mixtures. Furthermore, the temperature dependence of the relaxation times presents a universal behavior both above and below the crossover temperature. We also show that these features suggest that the observed crossover is associated with the emergence of confinement effects.

Solid State Chemistry of Proteins: I. Glass Transition Behavior in Freeze Dried Disaccharide Formulations of Human Growth Hormone (HGH)

Although freeze dried formulations are commonly characterized using differential scanning calorimetry (DSC), a protein-rich system behaves as a "strong glass", and the glass transition temperature, T(g), cannot be directly determined by DSC. A strong glass means a small heat capacity change at T(g), triangle upC(p), and a very broad glass transition region, or a large triangle upT(g). However, direct experimental evidence for a small triangle upC(p) and a large triangle upT(g) have been lacking. Here, we utilize extrapolation of thermal analysis data in protein:disaccharide mixtures to evaluate T(g), triangle upT(g), and triangle upC(p) for "pure" human growth hormone (hGH) from low to moderate residual water. We find that triangle upT(g) is indeed large and triangle upC(p) is very small. Also, the T(g) for pure hGH decreases from a value of about 136 degrees C when dry to around 25 degrees C at 12% water. This glass transition is not the onset of mobility within the protein molecule but rather signals onset of whole molecule rotation and translation. We also observe complex pre-T(g) thermal events in the DSC data, which are interpreted as consequences of relaxation events, largely due to the disaccharide, and are characteristic of freeze dried systems having a broad distribution of relaxing substates.

How a vicinal layer of solvent modulates the dynamics of proteins

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein. The model further explains the increase in the flexibility of the protein once the transition takes place and the differences in the flexibility under the different solvent environments. Coupling between the vicinal layer and the protein fluctuations is necessary to interpret these observations. The vicinal layer is postulated to form once a threshold for the volumetric fluctuations in the protein to accommodate solvents of different sizes is reached. Compensation of entropic-energetic contributions from the protein-coupled vicinal layer quantifies the scaling of the dynamical transition temperatures in various solvents. The protein adapts different conformational routes for organizing the required coupling to a specific solvent, which is achieved by adjusting the amount of conformational jumps in the surface-group dihedrals.

How Do Trehalose, Maltose, and Sucrose Influence Some Structural and Dynamical Properties of Lysozyme? Insight from Molecular Dynamics Simulations

The influence of three well-known disaccharides, namely, trehalose, maltose, and sucrose, on some structural and dynamical properties of lysozyme has been investigated by means of molecular dynamics computer simulations in the 37-60 wt % concentration range. The effects of sugars on the protein conformation are found to be relatively weak, in agreement with the preferential hydration of lysozyme. Conversely, sugars seem to increase significantly the relaxation times of the protein. These effects are shown to be correlated to the fractional solvent accessibilities of lysozyme residues and further support the slaving of protein dynamics. Moreover, a significant increase in the relaxation times of lysozyme, sugars, and water molecules is observed within the studied concentration range and may result from the percolation of the hydrogen-bond network of sugar molecules. This percolation appears to be of primary importance to explain the influence of sugars on the dynamical properties of lysozyme and water.

Inertial Suppression of Protein Dynamics in a Binary Glycerol−Trehalose Glass

The traditional approach used to predict the ability of a glassy matrix to maximally preserve the activity of a protein solute is the glass transition temperature (T(g)) of the glass. Recently it has been shown that the addition of a low T(g) diluent (glycerol) can rigidify the structure of a high T(g) glassy matrix in binary glycerol-trehalose glasses. The optimal density of glycerol in trehalose minimizes the average mean square displacements of non-exchangeable protons in the glass samples. The amount of glycerol added to a trehalose glass coincides with the maximal recovery of biological activity in a separate study using similar binary glass samples. In this study, we use molecular dynamics (MD) simulations to investigate the dynamics of a hydrated protein encased in glycerol, unary trehalose and binary glycerol-trehalose glasses. We have found that we are able to reproduce the rigidification of the glycerol-trehalose glassy matrix and that there is a direct correlation between bulk glass dynamics and the extent of atomic fluctuation of protein atoms. The detailed microscopic picture that emerges is that protein dynamics are suppressed mainly by inertia of the bulk glass and to a lesser extent specific interactions at the protein-solvent interface. Thus, the inertia of the glassy matrix may be an influential factor in the determination of pharmaceutically relevant formulations.

Influence of hydration on the dynamics of lysozyme

Quasielastic neutron and light-scattering techniques along with molecular dynamics simulations were employed to study the influence of hydration on the internal dynamics of lysozyme. We identified three major relaxation processes that contribute to the observed dynamics in the picosecond to nanosecond time range: 1), fluctuations of methyl groups; 2), fast picosecond relaxation; and 3), a slow relaxation process. A low-temperature onset of anharmonicity at T approximately 100 K is ascribed to methyl-group dynamics that is not sensitive to hydration level. The increase of hydration level seems to first increase the fast relaxation process and then activate the slow relaxation process at h approximately 0.2. The quasielastic scattering intensity associated with the slow process increases sharply with an increase of hydration to above h approximately 0.2. Activation of the slow process is responsible for the dynamical transition at T approximately 200 K. The dependence of the slow process on hydration correlates with the hydration dependence of the enzymatic activity of lysozyme, whereas the dependence of the fast process seems to correlate with the hydration dependence of hydrogen exchange of lysozyme.