Trehalose prevents myoglobin collapse and preserves its internal mobility

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.

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.

Spray-dried respirable powders containing bacteriophages for the treatment of pulmonary infections

Myoviridae bacteriophages were processed into a dry powder inhalable dosage form using a low-temperature spray-drying process. The phages were incorporated into microparticles consisting of trehalose, leucine, and optionally a third excipient (either a surfactant or casein sodium salt). The particles were designed to have high dispersibility and a respirable particle size, and to preserve the phages during processing. Bacteriophages KS4- M, KS14, and cocktails of phages ΦKZ/D3 and ΦKZ/D3/KS4-M were spray-dried with a processing loss ranging from 0.4 to 0.8 log pfu. The aerosol performance of the resulting dry powders as delivered from an Aerolizer® dry powder inhaler (DPI) exceeded the performance of commercially available DPIs; the emitted mass and the in vitro total lung mass of the lead formulation were 82.7% and 69.7% of filled capsule mass, respectively. The total lung mass had a mass median aerodynamic diameter of 2.5-2.8 µm. The total in vitro lung doses of the phages, delivered from a single actuation of the inhaler, ranged from 10(7) to 10(8) pfu, levels that are expected to be efficacious in vivo. Spray drying of bacteriophages into a respirable dry powder was found to be feasible.

Mechanistic models facilitate efficient development of leucine containing microparticles for pulmonary drug delivery

Mechanistic models of the spray drying and particle formation processes were used to conduct a formulation study with minimal use of material and time. A model microparticle vehicle suitable for respiratory delivery of biological pharmaceutical actives was designed. L-leucine was chosen as one of the excipients, because of its ability to enhance aerosol dispersibility. Trehalose was the second excipient. The spray drying process parameters used to manufacture the particles were calculated a priori. The kinetics of the particle formation process were assessed using a constant evaporation rate model. The experimental work was focused on the effect of increasing L-leucine mass fraction in the formulation, specifically its effect on leucine crystallinity in the microparticles, on powder density, and on powder dispersibility. Particle, powder and aerosol properties were assessed using analytical methods with minimal sample requirement, namely linear Raman spectroscopy, scanning electron microscopy, time-of-flight aerodynamic diameter measurements, and a new technique to determine compressed bulk density of the powder. The crystallinity of leucine in the microparticles was found to be correlated with a change in particle morphology, reduction in powder density, and improvement in dispersibility. It was demonstrated that the use of mechanistic models in combination with selected analytical techniques allows rapid formulation of microparticles for respiratory drug delivery using batch sizes of less than 80 mg.

Thermal denaturation of myoglobin in water--disaccharide matrixes: relation with the glass transition of the system

Proteins embedded in glassy saccharide systems are protected against adverse environmental conditions [Crowe et al. Annu. Rev. Physiol. 1998, 60, 73-103]. To further characterize this process, we studied the relationship between the glass transition temperature of the protein-containing saccharide system (T(g)) and the temperature of thermal denaturation of the embedded protein (T(den)). To this end, we studied by differential scanning calorimetry the thermal denaturation of ferric myoglobin in water/disaccharide mixtures containing nonreducing (trehalose, sucrose) or reducing (maltose, lactose) disaccharides. All the samples studied are, at room temperature, liquid systems whose viscosity varies from very low to very large values, depending on the water content. At a high water/saccharide mole ratio, homogeneous glass formation does not occur; regions of glass form, whose T(g) does not vary by varying the saccharide content, and the disaccharide barely affects the myoglobin denaturation temperature. At a suitably low water/saccharide mole ratio, by lowering the temperature, the systems undergo transition to the glassy state whose T(g) is determined by the water content; the Gordon-Taylor relationship between T(g) and the water/disaccharide mole ratio is obeyed; and T(den) increases by decreasing the hydration regardless of the disaccharide, such effect being entropy-driven. The presence of the protein was found to lower the T(g). Furthermore, for nonreducing disaccharides, plots of T(den) vs T(g) give linear correlations, whereas for reducing disaccharides, data exhibit an erratic behavior below a critical water/disaccharide ratio. We ascribe this behavior to the likelihood that in the latter samples, proteins have undergone Maillard reaction before thermal denaturation.

Effect of trehalose on protein structure

Trehalose is a ubiquitous molecule that occurs in lower and higher life forms but not in mammals. Till about 40 years ago, trehalose was visualized as a storage molecule, aiding the release of glucose for carrying out cellular functions. This perception has now changed dramatically. The role of trehalose has expanded, and this molecule has now been implicated in a variety of situations. Trehalose is synthesized as a stress-responsive factor when cells are exposed to environmental stresses like heat, cold, oxidation, desiccation, and so forth. When unicellular organisms are exposed to stress, they adapt by synthesizing huge amounts of trehalose, which helps them in retaining cellular integrity. This is thought to occur by prevention of denaturation of proteins by trehalose, which would otherwise degrade under stress. This explanation may be rational, since recently, trehalose has been shown to slow down the rate of polyglutamine-mediated protein aggregation and the resultant pathogenesis by stabilizing an aggregation-prone model protein. In recent years, trehalose has also proved useful in the cryopreservation of sperm and stem cells and in the development of a highly reliable organ preservation solution. This review aims to highlight the changing perception of the role of trehalose over the last 10 years and to propose common mechanisms that may be involved in all the myriad ways in which trehalose stabilizes protein structures. These will take into account the structure of trehalose molecule and its interactions with its environment, and the explanations will focus on the role of trehalose in preventing protein denaturation.

Long term storage of virus templated fluorescent materials for sensing applications

Wild type, mutant, and chemically modified Cowpea mosaic viruses (CPMV) were studied for long term preservation in the presence and absence of cryoprotectants. Viral complexes were reconstituted and tested via fluorescence spectroscopy and a UV/vis-based RNase assay for structural integrity. When viruses lyophilized in the absence of cryoprotectant were rehydrated and RNase treated, UV absorption increased, indicating that the capsids were damaged. The addition of trehalose during lyophilization protected capsid integrity for at least 7 weeks. Measurements of the fluorescence peak maximum of CPMV lyophilized with trehalose and reconstituted also indicate that the virus remained intact. Microarray binding assays indicated that CPMV particles chemically modified for use as a fluorescent tracer were intact and retained binding specificity after lyophilization in the presence of trehalose. Thus, we demonstrate that functionalized CPMV nanostructures can be stored for the long term, enabling their use in practical sensing applications.

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

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems.

How homogeneous are the trehalose, maltose, and sucrose water solutions? An insight from molecular dynamics simulations

The structural properties resulting from the reciprocal influence between water and three well-known homologous disaccharides, namely, trehalose, maltose, and sucrose, in aqueous solutions have been investigated in the 4-66 wt % concentration range by means of molecular dynamics computer simulations. Hydration numbers clearly show that trehalose binds to a larger number of water molecules than do maltose or sucrose, thus affecting the water structure to a deeper extent. Two-dimensional radial distribution functions of trehalose solutions definitely reveal that water is preferentially localized at the hydration sites found in the trehalose dihydrate crystal, this tendency being enhanced when increasing trehalose concentration. Over a rather wide concentration range (4-49 wt %), the fluctuations of the radius of gyration and of the glycosidic dihedral angles of trehalose indicate a higher flexibility with respect to maltose and sucrose. At sugar concentrations between 33 and 66 wt %, the mean sugar cluster size and the number of sugar-sugar hydrogen bonds formed within sugar clusters reveal that trehalose is able to form larger clusters than sucrose but smaller than maltose. These features suggest that trehalose-water mixtures would be more homogeneous than the two others, thus reducing both desiccation stresses and ice formation.

Changes in vibrational modes of water and bioprotectants in solution

Inelastic neutron scattering (INS) measurements have been performed on trehalose and sucrose/H(2)O mixtures at very low temperature as a function of concentration by using the TOSCA spectrometer at the ISIS Facility (DRAL, UK). The aim of this work is to investigate by INS the vibrational behaviour of water in presence of trehalose and sucrose in order to characterize the changes induced by these disaccharides on the H(2)O hydrogen-bonded network. In particular, we obtained information about the effects of the two disaccharides in the translational, librational and bending spectral regions of ice. The disaccharide bioprotective effectiveness can be linked by the high destructuring effect emphasised by the analysis of the librational modes region. On the other hand, the analysis of the vibrational region corresponding to the ice bending modes show a high "crystallinity" degree which can justify the cryptobiotic action of disaccharides.

Sugar-derived glasses support thermal and photo-initiated electron transfer processes over macroscopic distances

Trehalose-derived glasses are shown to support long range electron transfer reactions between spatially well separated donors and protein acceptors. The results indicate that these matrices can be used not only to greatly stabilize protein structures but also to facilitate both thermal and photo-initiated hemeprotein reduction over large macroscopic distances. To date the promise of exciting new protein-based technologies that can harness the exceptional tunability of protein functionality has been significantly thwarted by both intrinsic instability and stringent solvent/environment requirements for the expression of functional properties. The presented results raise the prospect of overcoming these limitations with respect to incorporating redox active proteins into solid state devices such as tunable batteries, switches, and solar cells. The findings also have implications for formulations intended to enhance long term storage of biomaterials, new protein-based synthetic strategies, and biophysical studies of functional intermediates trapped under nonequilibrium conditions. In addition, the study shows that certain sugars such as glucose or tagatose, when added to redox-inactive glassy matrices, can be used as a source of thermal electrons that can be harvested by suitable redox active proteins, raising the prospect of using common sugars as an electron source in solid state thermal fuel cells.

Hydrophobic Distal Pocket Affects NO−Heme Geminate Recombination Dynamics in Dehaloperoxidase and H64V Myoglobin

The recombination dynamics of NO with dehaloperoxidase (DHP) from Amphitrite ornata following photolysis were measured by femtosecond time-resolved absorption spectroscopy. Singular value decomposition (SVD) analysis reveals two important basis spectra. The first SVD basis spectrum reports on the population of photolyzed NO molecules and has the appearance of the equilibrium difference spectrum between the deoxy and NO forms of DHP. The first basis time course has two kinetic components with time constants of tau(11) approximately 9 ps and tau(12) approximately 50 ps that correspond to geminate recombination. The fast geminate process tau(11) arises from a contact pair with the heme iron in a bound state with S = 3/2 spin. The slow geminate process tau(12) corresponds to the recombination from a more remote docking site >3 A from the heme iron with the greater barrier corresponding to a S = 5/2 spin state. The second SVD basis spectrum represents a time-dependent Soret band shift indicative of heme photophysical processes and protein relaxation with time constants of tau(21) approximately 3 ps and tau(22) approximately 17 ps, respectively. A comparison between the more rapid rate constant of the slow geminate phase in DHP-NO and horse heart myoglobin (HHMbNO) or sperm whale myoglobin (SWMbNO) suggests that protein interactions with photolyzed NO are weaker in DHP than in the wild-type MbNOs, consistent with the hydrophobic distal pocket of DHP. The slower protein relaxation rate tau(22) in DHP-NO relative to HHMbNO implies less effective trapping in the docking site of the distal pocket and is consistent with a greater yield for the fast geminate process. The trends observed for DHP-NO also hold for the H64V mutant of SWMb (H64V MbNO), consistent with a more hydrophobic distal pocket for that protein as well. We examine the influence of solution viscosity on NO recombination by varying the glycerol content in the range from 0% to 90% (v/v). The dominant effect of increasing viscosity is the increase of the rate of the slow geminate process, tau(12), coupled with a population decrease of the slow geminate component. Both phenomena are similar to the effect of viscosity on wild-type Mb due to slowing of protein relaxation resulting from an increased solution viscosity and protein surface dehydration.

WATER MEDIATION IN PROTEIN FOLDING AND MOLECULAR RECOGNITION

Water is essential for life in many ways, and without it biomolecules might no longer truly be biomolecules. In particular, water is important to the structure, stability, dynamics, and function of biological macromolecules. In protein folding, water mediates the collapse of the chain and the search for the native topology through a funneled energy landscape. Water actively participates in molecular recognition by mediating the interactions between binding partners and contributes to either enthalpic or entropic stabilization. Accordingly, water must be included in recognition and structure prediction codes to capture specificity. Thus water should not be treated as an inert environment, but rather as an integral and active component of biomolecular systems, where it has both dynamic and structural roles. Focusing on water sheds light on the physics and function of biological machinery and self-assembly and may advance our understanding of the natural design of proteins and nucleic acids.

Role of solvent on protein-matrix coupling in MbCO embedded in water-saccharide systems: a Fourier transform infrared spectroscopy study

Embedding protein in sugar systems of low water content enables one to investigate the protein dynamic-structure function in matrixes whose rigidity is modulated by varying the content of residual water. Accordingly, studying the dynamics and structure thermal evolution of a protein in sugar systems of different hydration constitutes a tool for disentangling solvent rigidity from temperature effects. Furthermore, studies performed using different sugars may give information on how the detailed composition of the surrounding solvent affects the internal protein dynamics and structural evolution. In this work, we compare Fourier transform infrared spectroscopy measurements (300-20 K) on MbCO embedded in trehalose, sucrose, maltose, raffinose, and glucose matrixes of different water content. At all the water contents investigated, the protein-solvent coupling was tighter in trehalose than in the other sugars, thus suggesting a molecular basis for the trehalose peculiarity. These results are in line with the observation that protein-matrix phase separation takes place in lysozyme-lactose, whereas it is absent in lysozyme-trehalose systems; indeed, these behaviors may respectively be due to the lack or presence of suitable water-mediated hydrogen-bond networks, which match the protein surface to the surroundings. The above processes might be at the basis of pattern recognition in crowded living systems; indeed, hydration shells structural and dynamic matching is first needed for successful come together of interacting biomolecules.

Desiccation kinetics of biopreservation solutions in microchannels

A microfluidic device was utilized to measure the viscosity gradients formed in carbohydrate solutions of biological significance during desiccation and skin formation. A complementary numerical model employed the free volume theory to predict the concentration-dependent diffusion coefficients and viscosity gradients in concentrated solutions. It was established that the glassy skin formation at the gas-liquid interface played a key role in water entrapment and the formation and persistence of very steep concentration and viscosity gradients in the desiccating solutions. The results of this study highlighted an important phenomenon that should be accounted for during isothermal drying of glass-forming solutions: solutions with high glass transition temperatures, inevitably, dry heterogeneously. In the final product, there are significant spatial variations in water and solute content affecting the storage stability.

The Position 68(E11) Side Chain in Myoglobin Regulates Ligand Capture, Bond Formation with Heme Iron, and Internal Movement into the Xenon Cavities

After photodissociation, ligand rebinding to myoglobin exhibits complex kinetic patterns associated with multiple first-order geminate recombination processes occurring within the protein and a simpler bimolecular phase representing second-order ligand rebinding from the solvent. A smooth transition from cryogenic-like to solution phase properties can be obtained by using a combination of sol-gel encapsulation, addition of glycerol as a bathing medium, and temperature tuning (-15 --> 65 degrees C). This approach was applied to a series of double mutants, myoglobin CO (H64L/V68X, where X = Ala, Val, Leu, Asn, and Phe), which were designed to examine the contributions of the position 68(E11) side chain to the appearance and disappearance of internal rebinding phases in the absence of steric and polar interactions with the distal histidine. Based on the effects of viscosity, temperature, and the stereochemistry of the E11 side chain, the three major phases, B --> A, C --> A, and D --> A, can be assigned, respectively, to ligand rebinding from the following: (i) the distal heme pocket, (ii) the xenon cavities prior to large amplitude side chain conformational relaxation, and (iii) the xenon cavities after significant conformational relaxation of the position 68(E11) side chain. The relative amplitudes of the B --> A and C --> A phases depend markedly on the size and shape of the E11 side chain, which regulates sterically both ligand return to the heme iron atom and ligand migration to the xenon cavities. The internal xenon cavities provide a transient docking site that allows side chain relaxations and the entry of water into the vacated distal pocket, which in turn slows ligand recombination markedly.

Determination of the Fe−CO Bond Energy in Myoglobin Using Heterodyne-Detected Transient Thermal Phase Grating Spectroscopy

The bond energies at active sites of proteins are intimately coupled to the structure-function relationship in biological systems. Due to the unknown nature of the protein relaxation along a reaction coordinate, it has not been possible to directly determine bond energies relevant to protein function. By embedding proteins in trehalose glasses, it is possible to freeze out protein relaxation on short time scales and determine the bond energies of photolabile ligands using photothermal spectroscopies. As a prototypical example, the photodissociation dynamics and energetics of carboxy-myoglobin (MbCO) in a trehalose glass matrix at room temperature were studied by transient absorption (or pump-probe) and transient thermal phase grating spectroscopy to determine the CO recombination dynamics and associated energetics, respectively. Both the initial energetics of the bond breaking and the energy released upon bond reformation could be used, on a time scale faster than significant protein relaxation, to determine the Fe-CO bond energy as 34 +/- 4 kcal/mol. This bond energy is significantly larger than that typically cited (25 kcal/mol) on the basis of indirect measurements but is in good agreement with recent theoretical predictions (35 kcal/mol) (Rovira, C.; Parrinello, M. Int. J. Quantum Chem. 2000, 80, 1172). This result in combination with the theoretical study suggests that protein structure plays a significant role in the bond energies at active sites which in turn provides a tuning element of the effective barrier heights independent to the transition state region.

Thermodynamic and dynamic factors involved in the stability of native protein structure in amorphous solids in relation to levels of hydration

The internal, dynamical fluctuations of protein molecules exhibit many of the features typical of polymeric and bulk small molecule glass forming systems. The response of a protein's internal molecular mobility to temperature changes is similar to that of other amorphous systems, in that different types of motions freeze out at different temperatures, suggesting they exhibit the alpha-beta-modes of motion typical of polymeric glass formers. These modes of motion are attributed to the dynamic regimes that afford proteins the flexibility for function but that also develop into the large-scale collective motions that lead to unfolding. The protein dynamical transition, T(d), which has the same meaning as the T(g) value of other amorphous systems, is attributed to the temperature where protein activity is lost and the unfolding process is inhibited. This review describes how modulation of T(d) by hydration and lyoprotectants can determine the stability of protein molecules that have been processed as bulk, amorphous materials. It also examines the thermodynamic, dynamic, and molecular factors involved in stabilizing folded proteins, and the effects typical pharmaceutical processes can have on native protein structure in going from the solution state to the solid state.

Local compressibilities of proteins: comparison of optical experiments and simulations for horse heart cytochrome-c

Spectroscopy with probe molecules yields local information on the environment of the probe. In this article we compare local compressibilities of cytochrome-c as obtained from molecular dynamics simulations with experimental results as obtained from spectroscopic measurements. The simulations show that the protein-core around the heme is much less compressible in a glycerol/water solvent than in pure water. The pocket is also much less compressible than the protein as a whole, although the compressibility of the water inside the rather incompressible protein-core is almost liquidlike. We show that the local compressibility values capture the collective correlations of local volume fluctuations with volume fluctuations in the surrounding protein-solvent system. The decoupling of the volume fluctuations of the core from the solvent shell explains the reduction of the heme-core-compressibility in glycerol/water solvent. This decoupling could be traced back to the suppression of the exchange between pocket-water and hydration-shell-water upon addition of glycerol as co-solvent.

A hierarchy of functionally important relaxations within myoglobin based on solvent effects, mutations and kinetic model

Geminate CO rebinding in myoglobin is studied for two viscous solvents, trehalose and sol-gel (bathed in 100% glycerol) at several temperatures. Mutations in key distal hemepocket residues are used to eliminate or enhance specific relaxation modes. The time-resolved data are analyzed with a modified Agmon-Hopfield model which is capable of providing excellent fits in cases where a single relaxation mode is dominant. Using this approach, we determine the relaxation rate constants of specific functionally important modes, obtaining also their Arrhenius activation energies. We find a hierarchy of distal pocket modes controlling the rebinding kinetics. The "heme access mode" (HAM) is responsible for the major slow-down in rebinding. It is a solvent-coupled cooperative mode which restricts ligand return from the xenon cavities. Bulky side-chains, like those His64 and Trp29 (in the L29W mutant), operate like overdamped pendulums which move over and block the binding site. They may be either unslaved (His64) or moderately slaved (Trp29) to the solvent. Small side-chain relaxations, most notably of leucines, are revealed in some mutants (V68L, V68A). They are conjectured to facilitate inter-cavity ligand motion. When all relaxations are arrested (H64L in trehalose), we observe pure inhomogeneous kinetics with no temperature dependence, suggesting that proximal relaxation is not a factor on the investigated timescale.

Temperature excursion infrared (TEIR) spectroscopy used to study hydrogen bonding between water and biomolecules

Water is a highly polar molecule that is capable of making four H-bonding linkages. Stability and specificity of folding of water-soluble protein macromolecules are determined by the interplay between water and functional groups of the protein. Yet, under some conditions, water can be replaced with sugar or other polar protic molecules with retention of protein structure. Infrared (IR) spectroscopy allows one to probe groups on the protein that interact with solvent, whether the solvent is water, sugar or glycerol. The basis of the measurement is that IR spectral lines of functional groups involved in H-bonding show characteristic spectral shifts with temperature excursion, reflecting the dipolar nature of the group and its ability to H-bond. For groups involved in H-bonding to water, the stretching mode absorption bands shift to lower frequency, whereas bending mode absorption bands shift to higher frequency as temperature decreases. The results indicate increasing H-bonding and decreasing entropy occurring as a function of temperature, even at cryogenic temperatures. The frequencies of the amide group modes are temperature dependent, showing that as temperature decreases, the amide group H-bonds to water strengthen. These results are relevant to protein stability as a function of temperature. The influence of solvent relaxation is demonstrated for tryptophan fluorescence over the same temperature range where the solvent was examined by infrared spectroscopy.

Nonlinear optical studies of heme protein dynamics: Implications for proteins as hybrid states of matter

Protein structure is fundamentally related to function. However, static structures alone are insufficient to understand how a protein works. Dynamics play an equally important role. Given that proteins are highly associated aperiodic systems, it may be expected that protein dynamics would follow glass-like dynamics. However, protein functions occur on time scales orders of magnitude faster than the time scales typically associated with glassy systems. It is becoming clear that the reaction forces driving functions do not sample entirely the large number of configurations available to a protein but are highly directed along an optimized pathway. Could there be any correlation between specific topological features in protein structures and dynamics that leads to strongly correlated atomic displacements in the dynamical response to a perturbation? This review will try to provide an answer by focusing upon recent nonlinear optical studies with the aim of directly observing functionally important protein motions over the entire dynamic range of the protein response function. The specific system chosen is photoinduced dynamics of ligand dissociation at the active site in heme proteins, with myoglobin serving as the simplest model system. The energetics and nuclear motions from the very earliest events involved in bond breaking on the femtosecond time scale all the way out to ligand escape and bimolecular rebinding on the microsecond and millisecond time scale have been mapped out. The picture that is emerging is that the system consists of strongly coupled motions from the very instant the bond breaks at the active site that cascade into low frequency collective modes specific to the protein structure. It is this coupling that imparts the ability of a protein to function on time scales more commensurate with liquids while simultaneously conserving structural integrity akin to solids.

Coupling of protein relaxation to ligand binding and migration in myoglobin

Protein relaxation, ligand binding, and ligand migration into a hydrophobic cavity in myoglobin are unified by a bounded diffusion model which produces an accurate fit to complex ligand rebinding data over eight decades in time and a 160 K temperature range, in qualitative agreement with time-resolved x-ray crystallography. Protein relaxation operates in a cyclic manner to move the ligand away from the binding site.

Fast dynamics and stabilization of proteins: binary glasses of trehalose and glycerol

We present elastic and inelastic incoherent neutron scattering data from a series of trehalose glasses diluted with glycerol. A strong correlation with recently published protein stability data in the same series of glasses illustrates that the dynamics at Q >or= 0.71 A(-1) and omega > 200 MHz are important to stabilization of horseradish peroxidase and yeast alcohol dehydrogenase in these glasses. To the best of our knowledge, this is the first direct evidence that enzyme stability in a room temperature glass depends upon suppressing these short-length scale, high-frequency dynamics within the glass. We briefly discuss the coupling of protein motions to the local dynamics of the glass. Also, we show that T(g) alone is not a good indicator for the protein stability in this series of glasses; the glass that confers the maximum room-temperature stability does not have the highest T(g).

Protein and solvent dynamics: How strongly are they coupled?

Analysis of Raman and neutron scattering spectra of lysozyme demonstrates that the protein dynamics follow the dynamics of the solvents glycerol and trehalose over the entire temperature range measured 100-350 K. The protein's fast conformational fluctuations and low-frequency vibrations and their temperature variations are very sensitive to behavior of the solvents. Our results give insight into previous counterintuitive observations that protein relaxation is stronger in solid trehalose than in liquid glycerol. They also provide insight into the effectiveness of glycerol as a biological cryopreservant.

Spectroscopically and kinetically distinct conformational populations of sol-gel-encapsulated carbonmonoxy myoglobin. A comparison with hemoglobin

We have used sol-gel encapsulation protocols to trap kinetically and spectroscopically distinct conformational populations of native horse carbonmonoxy myoglobin. The method allows for direct comparison of functional and spectroscopic properties of equilibrium and non-equilibrium populations under the same temperature and viscosity conditions. The results implicate tertiary structure changes that include the proximal heme environment in the mechanism for population-specific differences in the observed rebinding kinetics. Differences in the resonance Raman frequency of nu(Fe-His), the iron-proximal histidine stretching mode, are attributed to differences in the positioning of the F helix. For myoglobin, the degree of separation between the F helix and the heme is assigned as the conformational coordinate that modulates both this frequency and the innermost barrier controlling CO rebinding. A comparison with the behavior of encapsulated derivatives of human adult hemoglobin indicates that these CO binding-induced conformational changes are qualitatively similar to the tertiary changes that occur within both the R and T quaternary states. Protein-specific differences in the time scale for the proposed F helix relaxation are attributed to variations in the intra-helical hydrogen bonding patterns that help stabilize the position of the F helix.

Hydration, slaving and protein function

Protein dynamics is crucial for protein function. Proteins in living systems are not isolated, but operate in networks and in a carefully regulated environment. Understanding the external control of protein dynamics is consequently important. Hydration and solvent viscosity are among the salient properties of the environment. Dehydrated proteins and proteins in a rigid environment do not function properly. It is consequently important to understand the effect of hydration and solvent viscosity in detail. We discuss experiments that separate the two effects. These experiments have predominantly been performed with wild-type horse and sperm whale myoglobin, using the binding of carbon monoxide over a broad range of temperatures as a tool. The experiments demonstrate that data taken only in the physiological temperature range are not sufficient to understand the effect of hydration and solvent on protein relaxation and function. While the actual data come from myoglobin, it is expected that the results apply to most or all globular proteins.

Optical and IR absorption as probe of dynamics of heme proteins

The spectroscopy of horseradish peroxidase with and without the substrate analogue benzohydroxamic acid (BHA) was monitored in different solvents as a function of the temperature in the interval from 10 to 300 K. Thermal broadening of the Q(0,0) optical absorption band arises mainly from interaction of the electronic pi --> pi transition with the heme vibrations. In contrast, the width of the IR absorption band of CO bound to heme is controlled by the coupling of the CO transition moment to the electric field of the protein matrix. The IR bandwidth of the substrate free enzyme in the glycerol/H2O solvent hardly changes in the glassy matrix and strongly increases upon heating above the glass transition. Heating of the same enzyme in the trehalose/H2O glass considerably broadens the band. The binding of the substrate strongly diminishes the temperature broadening of the CO band. This result is consistent with the view that the BHA strongly reduces the amplitude of vibrations of the heme pocket environment. Unusually strong thermal broadening of the CO band above the glass transition is interpreted to be caused by thermal population of a very flexible excited conformational substate. The thermal broadening of the same band in the trehalose glass is caused by an increase of the protein vibrational amplitude in each of the conformational substates, their population being independent of the temperature in the glassy matrix.

Geminate rebinding in trehalose-glass embedded myoglobins reveals residue-specific control of intramolecular trajectories

It is becoming increasingly apparent that hydrophobic cavities (also referred to as xenon cavities) within proteins have significant functional implications. The potential functional role of these cavities in modulating the internal dynamics of carbon monoxide in myoglobin (Mb) is explored in the present study by using glassy matrices derived from trehalose to limit protein dynamics and to eliminate ligand exchange between the solvent and the protein. By varying the temperature (-15 to 65 degrees C) and humidity for samples of carbonmonoxy myoglobin embedded in trehalose-glass, it is possible to observe a hierarchy of distinct geminate recombination phases that extend from nanosecond to almost seconds that can be directly associated with rebinding from specific hydrophobic cavities. The use of mutant forms of Mb reveals the role of key residues in modulating ligand access between these cavities and the distal hemepocket.

Effect of trehalose in low concentration on the binding and transport of porphyrins in liposome-human serum albumin system

The influence of trehalose on the interaction of liposomes with porphyrins and with human serum albumin (HSA) was studied. Small unilamellar liposomes were prepared from 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) and from DMPC/1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol (DMPG) 19:1 w/w% and incorporated with mesoporphyrin IX (MP) or magnesium mesoporphyrin (MgMP). The fluorescence intensity and anisotropy of porphyrins were measured within the temperature range of 15-33 degrees C, in the presence and in the absence of 3x10(-2) M trehalose, to study the location of the porphyrins inside the liposomes and their partition between the liposomes and HSA. Based on the presented data and our earlier results (I. Bárdos-Nagy, R. Galántai, A.D. Kaposi, J. Fidy, Int. J. Pharm. 175 (1998) 255-267) we conclude that trehalose - even at this relatively low concentration - interacts with the head groups of the liposomes and that the presence of DMPG enhances the effect. This effect seems to hinder the binding of HSA to the liposome surface and influences the location of MgMP within the liposomes. In the case of MP, the porphyrin partition between the liposomes and HSA was affected by trehalose, while for MgMP, trehalose changed the structural conditions of porphyrin binding to the liposomes. The amount of trehalose used did not have a general trend to modify the association constants of porphyrin derivatives either to liposomes or to HSA.

Trehalose effect on low temperature protein dynamics: fluctuation and relaxation phenomena

We performed spectral diffusion experiments in trehalose-enriched glycerol/buffer-glass on horseradish peroxidase where the heme was replaced by metal-free mesoporphyrin IX, and compared them with the respective behavior in a pure glycerol/buffer-glass (Schlichter et al., J. Chem. Phys. 2000, 112:3045-3050). Trehalose has a significant influence: spectral diffusion broadening speeds up compared to the trehalose-free glass. This speeding up is attributed to a shortening of the correlation time of the frequency fluctuations most probably by preventing water molecules from leaving the protein interior. Superimposed to the frequency fluctuation dynamics is a relaxation dynamics that manifests itself as an aging process in the spectral diffusion broadening. Although the trehalose environment speeds up the fluctuations, it does not have any influence on the relaxation. Both relaxation and fluctuations are governed by power laws in time. The respective exponents do not seem to change with the protein environment. From the spectral dynamics, the mean square displacement in conformation space can be determined. It is governed by anomalous diffusion. The associated frequency correlation time is incredibly long, demonstrating that proteins at low temperatures are truly nonergodic systems.

Time-resolved hole-burning study on myoglobin: fluctuation of restricted water within distal pocket

We have studied the equilibrium fluctuation dynamics of Zn-substituted myoglobin and its His64-->Leu (H64L) mutant in the pH range from 5 to 9 by using time-resolved transient-hole-burning (TRTHB) spectroscopy. In the H64L mutant, we have observed a largely reduced width of the absorption spectrum and only a slight temporal shift of the hole-burning spectrum. These observations both reflect the suppressed conformational fluctuation in the mutant. On the other hand, the pH-dependent change in the absorption spectrum could not be solely explained by the change in the protonation state of His64 induced by the pH change. These results suggest that although the fluctuation dynamics observed by the TRTHB experiment of the native sample mainly reflects the conformational motion around His64, the interconversion process of His64 between its protonated and unprotonated states has a minor contribution. Instead, we have proposed a tentative interpretation that the motion of the water molecule around His64 is the main source of the observed dynamics in the TRTHB technique.

Molecular dynamics simulation of carboxy-myoglobin embedded in a trehalose-water matrix

We report on a molecular dynamics (MD) simulation of carboxy-myoglobin (MbCO) embedded in a water-trehalose system. The mean square fluctuations of protein atoms, calculated at different temperatures in the 100-300 K range, are compared with those from a previous MD simulation on an H2O-solvated MbCO and with experimental data from Mössbauer spectroscopy and incoherent elastic neutron scattering on trehalose-coated MbCO. The results show that, for almost all the atomic classes, the amplitude of the nonharmonic motions stemming from the interconversion among the protein's conformational substates is reduced with respect to the H2O-solvated system, and their onset is shifted toward higher temperature. Moreover, our simulation shows that, at 300 K, the heme performs confined diffusive motions as a whole, leaving the underlying harmonic vibrations unaltered.

Lyophilization and development of solid protein pharmaceuticals

Developing recombinant protein pharmaceuticals has proved to be very challenging because of both the complexity of protein production and purification, and the limited physical and chemical stability of proteins. To overcome the instability barrier, proteins often have to be made into solid forms to achieve an acceptable shelf life as pharmaceutical products. The most commonly used method for preparing solid protein pharmaceuticals is lyophilization (freeze-drying). Unfortunately, the lyophilization process generates both freezing and drying stresses, which can denature proteins to various degrees. Even after successful lyophilization with a protein stabilizer(s), proteins in solid state may still have limited long-term storage stability. In the past two decades, numerous studies have been conducted in the area of protein lyophilization technology, and instability/stabilization during lyophilization and long-term storage. Many critical issues have been identified. To have an up-to-date perspective of the lyophilization process and more importantly, its application in formulating solid protein pharmaceuticals, this article reviews the recent investigations and achievements in these exciting areas, especially in the past 10 years. Four interrelated topics are discussed: lyophilization and its denaturation stresses, cryo- and lyo-protection of proteins by excipients, design of a robust lyophilization cycle, and with emphasis, instability, stabilization, and formulation of solid protein pharmaceuticals.

Dehydration and crystallization of trehalose and sucrose glasses containing carbonmonoxy-myoglobin

We report a study wherein we contemporarily measured 1) the dehydration process of trehalose or sucrose glasses embedding carbonmonoxy-myoglobin (MbCO) and 2) the evolution of the A substates in saccharide-coated MbCO. Our results indicate that microcrystallization processes, sizeably different in the two saccharides, take place during dehydration; moreover, the microcrystalline structure is maintained unless the dry samples are equilibrated with a humidity >/=75% (>/=60%) at 25 degrees C for the trehalose (sucrose) sample. The evolution of the parameters that characterize the A substates of MbCO indicates that 1) the effects of water withdrawal are analogous in samples dried in the presence or in the absence of sugars, although much larger effects are observed in the samples without sugar; 2) the distribution of A substates is determined by the overall matrix structure and not only by the sample water content; and 3) the population of A0 substate (i. e., the substate currently put in relation with MbCO molecules having the distal histidine out of the heme pocket) is largely enhanced during the dehydration process. However, after rehumidification its population is largely decreased with respect to the values obtained, at similar water content, during the first dehydration run.

Heme-solvent coupling: a Mössbauer study of myoglobin in sucrose

The Mössbauer effect of 57Fe-enriched samples was used to investigate the coupling of 80% sucrose/water, a protein-stabilizing solvent, to vibrational and diffusive modes of the heme iron of CO-myoglobin. For comparison we also determined the Mössbauer spectra of K4 57Fe (CN)6 (potassium ferrocyanide, PFC), where the iron is fully exposed in the same solvent. The temperature dependence of the Mössbauer parameters derived for the two samples proved to be remarkably similar, indicative of a strong coupling of the main heme displacements to the viscoelastic relaxation of the solvent. We show that CO escape out of the heme pocket couples to the same type of fluctuations, whereas intramolecular bond formation involves solvent-decoupled heme deformation modes that are less prominent in the Mössbauer spectrum. With respect to other solvents, however, sucrose shows a reduced viscosity effect on heme displacements and the kinetics of ligand binding due to preferential hydration of the protein. This result confirms thermodynamic predictions of the stabilizing action of sucrose by a dynamic method.

Protein inactivation in amorphous sucrose and trehalose matrices: effects of phase separation and crystallization

Trehalose is the most effective carbohydrate in preserving the structure and function of biological systems during dehydration and subsequent storage. We have studied the kinetics of protein inactivation in amorphous glucose/sucrose (1:10, w/w) and glucose/trehalose (1:10, w/w) systems, and examined the relationship between protein preservation, phase separation and crystallization during dry storage. The glucose/trehalose system preserved glucose-6-phosphate dehydrogenase better than did the glucose/sucrose system with the same glass transition temperature (Tg). The Williams-Landel-Ferry kinetic analysis indicated that the superiority of the glucose/trehalose system over the glucose/sucrose system was possibly associated with a low free volume and a low free volume expansion at temperatures above the Tg. Phase separation and crystallization during storage were studied using differential scanning calorimetry, and three separate domains were identified in stored samples (i.e., sugar crystals, glucose-rich and disaccharide-rich amorphous domains). Phase separation and crystallization were significantly retarded in the glucose/trehalose system. Our data suggest that the superior stability of the trehalose system is associated with several properties of the trehalose glass, including low free volume, restricted molecular mobility and the ability to resist phase separation and crystallization during storage.