Vibrational frequency shifts as a probe of hydrogen bonds: thermal expansion and glass transition of myoglobin in mixed solvents

Reactivity Tracking of an Enzyme Progress Coordinate

The reactivity of individual solvent-coupled protein configurations is used to track and resolve the progress coordinate for the core reaction sequence of substrate radical rearrangement and hydrogen atom transfer in the ethanolamine ammonia-lyase (EAL) enzyme from Salmonella enterica. The first-order decay of the substrate radical intermediate is the monitored reaction. Heterogeneous confinement from sucrose hydrates in the mesophase solvent surrounding the cryotrapped protein introduces distributed kinetics in the non-native decay of the substrate radical pair capture substate, which arise from an ensemble of configurational microstates. Reaction rates increase by >103-fold across the distribution to approach that for the native enabled substate for radical rearrangement, which reacts with monotonic kinetics. The native progress coordinate thus involves a collapse of the configuration space to generate optimized reactivity. Reactivity tracking reveals fundamental features of solvent-protein-reaction configurational coupling and leads to a model that refines the ensemble paradigm of enzyme catalysis for strongly adiabatic chemical steps.

Plant-protein-enabled biodegradable triboelectric nanogenerator for sustainable agriculture

As the use of triboelectric nanogenerators (TENGs) increases, the generation of related electronic waste has been a major challenge. Therefore, the development of environmentally friendly, biodegradable, and low-cost TENGs must be prioritized. Having discovered that plant proteins, by-products of grain processing, possess excellent triboelectric properties, we explore these properties by evaluating the protein structure. The proteins are recycled to fabricate triboelectric layers, and the triboelectric series according to electrical properties is determined for the first time. Using a special structure design, we construct a plant-protein-enabled biodegradable TENG by integrating a polylactic acid film, which is used as a new type of mulch film to construct a growth-promoting system that generates space electric fields for agriculture. Thus, from the plant protein to the crop, a sustainable recycling loop is implemented. Using bean seedlings as a model to confirm the feasibility of the mulch film, we further use it in the cultivation of greenhouse vegetables. Experimental results demonstrate the applicability of the proposed plant-protein-enabled biodegradable TENG in sustainable agriculture.

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.

Investigating Membrane‐Mediated Antimicrobial Peptide Interactions with Synchrotron Radiation Far‐Infrared Spectroscopy

Synchrotron radiation‐based Fourier transform infrared spectroscopy enables access to vibrational information from mid over far infrared to even terahertz domains. This information may prove critical for the elucidation of fundamental bio‐molecular phenomena including folding‐mediated innate host defence mechanisms. Antimicrobial peptides (AMPs) represent one of such phenomena. These are major effector molecules of the innate immune system, which favour attack on microbial membranes. AMPs recognise and bind to the membranes whereupon they assemble into pores or channels destabilising the membranes leading to cell death. However, specific molecular interactions responsible for antimicrobial activities have yet to be fully understood. Herein we probe such interactions by assessing molecular specific variations in the near‐THz 400–40 cm⁻¹ range for defined helical AMP templates in reconstituted phospholipid membranes. In particular, we show that a temperature‐dependent spectroscopic analysis, supported by 2D correlative tools, provides direct evidence for the membrane‐induced and folding‐mediated activity of AMPs. The far‐FTIR study offers a direct and information‐rich probe of membrane‐related antimicrobial interactions.

Effects of glass transition and hydration on the biological stability of dry yeast

The purpose of this study was to determine the effects of glass transition and hydration on the storage stability of baker's dry yeast (Saccharomyces cerevisiae). The glass transition temperature (T_g ) of the yeast decreased with increase in water activity (a_w ), and a_w at which glass transition occurs at 25 °C was determined as the critical a_w (a_wc ). From mechanical relaxation measurements at 25 °C, the yeast exhibited a large mechanical relaxation above the a_wc , and the degree of mechanical relaxation increased gradually with increasing a_w . This behavior corresponded to a gradual increase in molecular mobility with increasing a_w in the rubbery liquid state. Freezable water was observed from a_w ≥0.810, and the proportion of freezable water increased with increasing a_w . Examination of the effect of a_w on the residual biological activity of yeast samples stored at 25 °C for 30 days revealed maximum residual biological activity at a_w  = 0.225 to 0.432. In the lower a_w range, the residual biological activity decreased because of oxidation of lipids. In the higher a_w range, the residual biological activity decreased gradually with increasing a_w . The yeast samples maintained a relatively high residual biological activity, because they could maintain relatively low molecular mobility even in the rubbery liquid state, as suggested by their mechanical relaxation behavior. At a_w ≥0.809, residual activity decreased to a negligible value. This could be explained by the appearance of secondary hydrate water (freezable water). Hydrate water protects yeast cells from lipid oxidation but reduces the T_g . As a result, the yeast cells are stabilized maximally only at the a_wc . PRACTICAL APPLICATION: Although the growth rate of yeast cells becomes negligible below a certain a_w , the biological activity of dry yeast decreases gradually during storage. The fact that dry yeast can be maximally stabilized at the a_wc is practically useful as a criterion for controlling storage stability. In addition, it was found that a remarkable reduction in the molecular mobility, which is otherwise ordinarily increased due to the glass-to-rubber transition, is prevented in yeast. It is possible that the crystallization of amorphous sugar can be prevented by yeast extract. The suggested effect is expected to result in enhanced quality of carbohydrate-based foods.

Temperature-Induced Collapse of Elastin-like Peptides Studied by 2DIR Spectroscopy

Elastin-like peptides are hydrophobic biopolymers that exhibit a reversible coacervation transition when the temperature is raised above a critical point. Here, we use a combination of linear infrared spectroscopy, two-dimensional infrared spectroscopy, and molecular dynamics simulations to study the structural dynamics of two elastin-like peptides. Specifically, we investigate the effect of the solvent environment and temperature on the structural dynamics of a short (5-residue) elastin-like peptide and of a long (450-residue) elastin-like peptide. We identify two vibrational energy transfer processes that take place within the amide I' band of both peptides. We observe that the rate constant of one of the exchange processes is strongly dependent on the solvent environment and argue that the coacervation transition is accompanied by a desolvation of the peptide backbone where up to 75% of the water molecules are displaced. We also study the spectral diffusion dynamics of the valine(1) residue that is present in both peptides. We find that these dynamics are relatively slow and indicative of an amide group that is shielded from the solvent. We conclude that the coacervation transition of elastin-like peptides is probably not associated with a conformational change involving this residue.

The Role of Backbone Hydration of Poly(N-isopropyl acrylamide) Across the Volume Phase Transition Compared to its Monomer

Thermo-responsive polymers undergo a reversible coil-to-globule transition in water after which the chains collapse and aggregate into bigger globules when passing to above its lower critical solution temperature (LCST). The hydrogen bonding with the amide groups in the side chains has to be contrasted with the hydration interaction of the hydrophobic main-chain hydrocarbons. In the present investigation we study molecular changes in the polymer poly(N-isopropyl acrylamide) (PNIPAM) and in its monomer N-isopropyl acrylamide (NIPAM) in solution across the LCST transition. Employing Fourier-transform infrared spectroscopy we probe changes in conformation and hydrogen bonding. We observe a nearly discontinuous shift of the peak frequencies and areas of vibrational bands across the LCST transition for PNIPAM whereas NIPAM exhibits a continuous linear change with temperature. This supports the crucial role of the polymer backbone with respect to hydration changes in the amide group in combination with cooperative interactions of bound water along the backbone chain.

Peptide-Protein Binding Investigated by Far-IR Spectroscopy and Molecular Dynamics Simulations

Molecular dynamics (MD) simulations and far-infrared (far-IR) spectroscopy were combined to study peptide binding by the second PDZ domain (PDZ1) of MAGI1, which has been identified as an important target for the Human Papilloma Virus. PDZ1 recognizes and binds to the C-terminal end of the E6 protein from high-risk Human Papilloma Virus. The far-IR spectra of two forms of the protein, an unbound APO form and a HOLO form (where the PDZ1 is bound to an 11-residue peptide derived from the C terminus of HPV16 E6), were obtained. MD simulations were used to determine the most representative structure of each form and these were used to compute their respective IR spectra by normal mode analysis. Far-UV circular dichroism spectroscopy was used to confirm the secondary structure content and the stability through temperature-dependent studies. Both the experimental and calculated far-IR spectra showed a red shift of the low-frequency peaks upon peptide binding. The calculations show that this is coincident with an increased number of hydrogen bonds formed as the peptide augments the protein β-sheet. We further identified the contribution of surface-bound water molecules to bands in the far-IR and, through the calculations, identified potential pathways for allosteric communication. Together, these results demonstrate the utility of combining far-IR experiments and MD studies to study peptide binding by proteins.

Effective intermediate-spin iron in O2-transporting heme proteins

Proteins carrying an iron-porphyrin (heme) cofactor are essential for biological O2 management. The nature of Fe-O2 bonding in hemoproteins is debated for decades. We used energy-sampling and rapid-scan X-ray Kβ emission and K-edge absorption spectroscopy as well as quantum chemistry to determine molecular and electronic structures of unligated (deoxy), CO-inhibited (carboxy), and O2-bound (oxy) hemes in myoglobin (MB) and hemoglobin (HB) solutions and in porphyrin compounds at 20-260 K. Similar metrical and spectral features revealed analogous heme sites in MB and HB and the absence of low-spin (LS) to high-spin (HS) conversion. Amplitudes of Kβ main-line emission spectra were directly related to the formal unpaired Fe(d) spin count, indicating HS Fe(II) in deoxy and LS Fe(II) in carboxy. For oxy, two unpaired Fe(d) spins and, thus by definition, an intermediate-spin iron center, were revealed by our static and kinetic X-ray data, as supported by (time-dependent) density functional theory and complete-active-space self-consistent-field calculations. The emerging Fe-O2 bonding situation includes in essence a ferrous iron center, minor superoxide character of the noninnocent ligand, significant double-bond properties of the interaction, and three-center electron delocalization as in ozone. It resolves the apparently contradictory classical models of Pauling, Weiss, and McClure/Goddard into a unifying view of O2 bonding, tuned toward reversible oxygen transport.

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.

Dipolar Nanodomains in Protein Hydration Shells

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

Maillard Reaction Rate in Various Glassy Matrices

The Maillard Reaction (MR) rate below the glass transition temperature (T(g)) for various model glassy food systems was studied at temperatures between 40 degrees C and 70 degrees C. As a sample, freeze-dried glucose and lysine systems embedded in various glassy matrices (e.g., polyvinylpyrrolodone and trehalose) were used, and the MR rate below the T(g) was compared among the various glassy matrices. The extent of MR was estimated spectrophotometrically from the optical density at 280 nm (OD(280)), and the MR rate (k(280)) was determined as a pseudo zero order reaction rate from the time course of OD(280). Although k(280) was described by the Arrhenius plot, the temperature dependence of k(280) was almost the same and the intercept was different among the matrices. From the comparison of k(280), it was suggested that the MR rate in glassy matrix was affected not only by the T(g), but also by the hydrogen bonding between MR reactants and glassy matrix.

Cα-H carries information of a hydrogen bond involving the geminal hydroxyl group: a case study with a hydrogen-bonded complex of 1,1,1,3,3,3-hexafluoro-2-propanol and tertiary amines

Experimental measurement of the contribution of H-bonding to intermolecular and intramolecular interactions that provide specificity to biological complex formation is an important aspect of macromolecular chemistry and structural biology. However, there are very few viable methods available to determine the energetic contribution of an individual hydrogen bond to binding and catalysis in biological systems. Therefore, the methods that use secondary deuterium isotope effects analyzed by NMR or equilibrium or kinetic isotope effect measurements are attractive ways to gain information on the H-bonding properties of an alcohol system, particularly in a biological environment. Here, we explore the anharmonic contribution to the C-H group when the O-H group of 1,1,1,3,3,3-hexafluoro-2-propanol (HFP) forms an intermolecular H-bond with the amines by quantum mechanical calculations and by experimentally measuring the H/D effect by NMR. Within the framework of density functional theory, ab initio calculations were carried out for HFP in its two different conformational states and their H-bonded complexes with tertiary amines to determine the (13)C chemical shielding, change in their vibrational equilibrium distances, and the deuterium isotope effect on (13)C2 (secondary carbon) of HFP upon formation of complexes with tertiary amines. When C2-OH was involved in hydrogen bond formation (O-H as hydrogen donor), it weakened the geminal C2-H bond; it was reflected in the NMR chemical shift, coupling constant, and the equilibrium distances of the C-H bond. The first derivative of nuclear shielding at C2 in HFP was -48.94 and -50.73 ppm Å(-1) for anti and gauche conformations, respectively. In the complex, the values were -50.28 and -50.76 ppm Å(-1), respectively. The C-H stretching frequency was lower than the free monomer, indicating enhanced anharmonicity in the C-H bond in the complex form. In chloroform, HFP formed a complex with the amine; δC2 was 69.107 ppm for HFP-triethylamine and 68.766 ppm for HFP-d2-triethylamine and the difference in chemical shift, the ΔδC2 was 341 ppb. The enhanced anharmonicity in the hydrogen-bonded complex resulted in a larger vibrational equilibrium distance in C-H/D bonds. An analysis with the Morse potential function indicated that the enhanced anharmonicity encountered in the bond was the origin of a larger isotope effect and the equilibrium distances. Change in vibrational equilibrium distance and the deuterium isotope effect, as observed in the complex, could be used as parameters in monitoring the strength of the H-bond in small model systems with promising application in biomacromolecules.

Non-Gaussian statistics and nanosecond dynamics of electrostatic fluctuations affecting optical transitions in proteins

We show that electrostatic fluctuations of the protein-water interface are globally non-Gaussian. The electrostatic component of the optical transition energy (energy gap) in a hydrated green fluorescent protein is studied here by classical molecular dynamics simulations. The distribution of the energy gap displays a high excess in the breadth of electrostatic fluctuations over the prediction of the Gaussian statistics. The energy gap dynamics include a nanosecond component. When simulations are repeated with frozen protein motions, the statistics shifts to the expectations of linear response and the slow dynamics disappear. We therefore suggest that both the non-Gaussian statistics and the nanosecond dynamics originate largely from global, low-frequency motions of the protein coupled to the interfacial water. The non-Gaussian statistics can be experimentally verified from the temperature dependence of the first two spectral moments measured at constant-volume conditions. Simulations at different temperatures are consistent with other indicators of the non-Gaussian statistics. In particular, the high-temperature part of the energy gap variance (second spectral moment) scales linearly with temperature and extrapolates to zero at a temperature characteristic of the protein glass transition. This result, violating the classical limit of the fluctuation-dissipation theorem, leads to a non-Boltzmann statistics of the energy gap and corresponding non-Arrhenius kinetics of radiationless electronic transitions, empirically described by the Vogel-Fulcher-Tammann law.

Near-infrared spectroscopy for in-line monitoring of protein unfolding and its interactions with lyoprotectants during freeze-drying

This work presents near-infrared spectroscopy (NIRS) as an in-line process analyzer for monitoring protein unfolding and protein-lyoprotectant hydrogen bond interactions during freeze-drying. By implementing a noncontact NIR probe in the freeze-drying chamber, spectra of formulations containing a model protein immunoglobulin G (IgG) were collected each process minute. When sublimation was completed in the cake region illuminated by the NIR probe, the frequency of the amide A/II band (near 4850 cm(-1)) was monitored as a function of water elimination. These two features were well correlated during protein dehydration in the absence of protein unfolding (desired process course), whereas consistent deviations from this trend to higher amide A/II frequencies were shown to be related to protein unfolding. In formulations with increased sucrose concentrations, the markedly decreased amide A/II frequencies seen immediately after sublimation indicated an increased extent of hydrogen bond interaction between the protein's backbone and surrounding molecules. At the end of drying, there was evidence of nearly complete water substitution for formulations with 1%, 5%, and 10% sucrose. The presented approach shows promising perspectives for early fault detection of protein unfolding and for obtaining mechanistic process information on actions of lyoprotectants.

Electrostatics of the protein-water interface and the dynamical transition in proteins

Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.

Dynamical transition of protein-hydration water

Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [Proc. Natl. Acad. Sci. U.S.A. 103, 9012 (2006)]10.1073/pnas.0602474103 suggested that anomalies near 220 K observed by quasielastic neutron scattering can be explained by a hidden critical point of bulk water. Based on more sensitive measurements of water on perdeuterated phycocyanin, using the new neutron backscattering spectrometer SPHERES, and an improved data analysis, we present results that show no sign of such a fragile-to-strong transition. The inflection of the elastic intensity at 220 K has a dynamic origin that is compatible with a calorimetric glass transition at 170 K. The temperature dependence of the relaxation times is highly sensitive to data evaluation; it can be brought into perfect agreement with the results of other techniques, without any anomaly.

Osmolyte-induced perturbations of hydrogen bonding between hydration layer waters: correlation with protein conformational changes

Gadolinium vibronic sideband luminescence spectroscopy (GVSBLS) is used to probe osmolyte-induced changes in the hydrogen bond strength between first and second shell waters on the surface of free Gd(3+) and Gd(3+) coordinated to EDTA and to structured calcium binding peptides in solution. In parallel, Raman is used to probe the corresponding impact of the same set of osmolytes on hydrogen bonding among waters in the bulk phase. Increasing concentration of added urea is observed to progressively weaken the hydrogen bonding within the hydration layer but has minimal observed impact on bulk water. In contrast, polyols are observed to enhance hydrogen bonding in both the hydration layer and the bulk with the amplitude being polyol dependent with trehalose being more effective than sucrose, glucose, or glycerol. The observed patterns indicate that the size and properties of the osmolyte as well as the local architecture of the specific surface site of hydration impact preferential exclusion effects and local hydrogen bond strength. Correlation of the vibronic spectra with CD measurements on the peptides as a function of added osmolytes shows an increase in secondary structure with added polyols and that the progressive weakening of the hydrogen bonding upon addition of urea first increases water occupancy within the peptide and only subsequently does the peptide unfold. The results support models in which the initial steps in the unfolding process involve osmolyte-induced enhancement of water occupancy within the interior of the protein.

Dynamical transition in a small helical peptide and its implication for vibrational energy transport

The two-dimensional infrared spectrum of an octameric helical peptide in chloroform was measured as a function of temperature. Isotope labeling of the carbonyl group of one of the amino acids was used to obtain information for an isolated vibration. The antidiagonal width of the 2D-IR signal, which is a measure of the homogeneous dephasing time T(2), is constant from 220 to 260 K (within experimental error), and increases steeply above. The homogeneous dephasing time of the carbonyl vibration is attributed to the flexibility of the system and/or its immediate surrounding. The system undergoes a dynamical transition at about 270 K, with similarities to the protein dynamical transition. Furthermore, the temperature dependence of the antidiagonal width strongly resembles that of the efficiency of vibrational energy transport along the helix, which has been studied in a recent paper (J. Phys. Chem. B 2008, 112, 15487). The connection between the two processes, structural flexibility and energy transport mechanism, is discussed.

Charge density-dependent modifications of hydration shell waters by Hofmeister ions

Gadolinium (Gd(3+)) vibronic sideband luminescence spectroscopy (GVSBLS) is used to probe, as a function of added Hofmeister series salts, changes in the OH stretching frequency derived from first-shell waters of aqueous Gd(3+) and of Gd(3+) coordinated to three different types of molecules: (i) a chelate (EDTA), (ii) structured peptides (mSE3/SE2) of the lanthanide-binding tags (LBTs) family with a single high-affinity binding site, and (iii) a calcium-binding protein (calmodulin) with four binding sites. The vibronic sideband (VSB) corresponding to the OH stretching mode of waters coordinated to Gd(3+), whose frequency is inversely correlated with the strength of the hydrogen bonding to neighboring waters, exhibits an increase in frequency when Gd(3+) becomes coordinated to either EDTA, calmodulin, or mSE3 peptide. In all of these cases, the addition of cation chloride or acetate salts to the solution increases the frequency of the vibronic band originating from the OH stretching mode of the coordinated waters in a cation- and concentration-dependent fashion. The cation dependence of the frequency increase scales with charge density of the cations, giving rise to an ordering consistent with the Hofmeister ordering. On the other hand, water Raman spectroscopy shows no significant change upon addition of these salts. Additionally, it is shown that the cation effect is modulated by the specific anion used. The results indicate a mechanism of action for Hofmeister series ions in which hydrogen bonding among hydration shell waters is modulated by several factors. High charge density cations sequester waters in a configuration that precludes strong hydrogen bonding to neighboring waters. Under such conditions, anion effects emerge as anions compete for hydrogen-bonding sites with the remaining free waters on the surface of the hydration shell. The magnitude of the anion effect is both cation and Gd(3+)-binding site specific.

The dynamical transition of proteins, concepts and misconceptions

The dynamics of hydrated proteins and of protein crystals can be studied within a wide temperature range, since the water of hydration does not crystallize at low temperature. Instead it turns into an amorphous glassy state below 200 K. Extending the temperature range facilitates the spectral separation of different molecular processes. The conformational motions of proteins show an abrupt enhancement near 180 K, which has been called a "dynamical transition". In this contribution various aspects of the transition are critically reviewed: the role of the instrumental resolution function in extracting displacements from neutron elastic scattering data and the question of the appropriate dynamic model, discrete transitions between states of different energy versus continuous diffusion inside a harmonic well, are discussed. A decomposition of the transition involving two motional components is performed: rotational transitions of methyl groups and small scale librations of side-chains, induced by water at the protein surface. Both processes create an enhancement of the observed amplitude. The onset occurs, when their time scale becomes compatible with the resolution of the spectrometer. The reorientational rate of hydration water follows a super-Arrhenius temperature dependence, a characteristic feature of a dynamical transition. It occurs only with hydrated proteins, while the torsional motion of methyl groups takes place also in the dehydrated or solvent-vitrified system. Finally, the role of fast hydrogen bond fluctuations contributing to the amplitude enhancement is discussed.

Molecular level probing of preferential hydration and its modulation by osmolytes through the use of pyranine complexed to hemoglobin

Two spectroscopic probes are used to expose molecular level changes in hydration shell water interactions that directly relate to such issues as preferential hydration and protein stability. The major focus of the present study is on the use of pyranine (HPT) fluorescence to probe as a function of added osmolytes (PEG, urea, trehalose, and magnesium), the extent to which glycerol is preferentially excluded from the hydration shell of free HPT and HPT localized in the diphosphoglycerate (DPG) binding site of hemoglobin in both solution and in Sol-Gel matrices. The pyranine study is complemented by the use of vibronic side band luminescence from the gadolinium cation that directly exposes the changes in hydrogen bonding between first and second shell waters as a function of added osmolytes. Together the results form the basis for a water partitioning model that can account for both preferential hydration and water/osmolyte-mediated conformational changes in protein structure.

Infrared absorption study of the heme pocket dynamics of carbonmonoxyheme proteins

The temperature dependencies of the infrared absorption CO bands of carboxy complexes of horseradish peroxidase (HRP(CO)) in glycerol/water mixture at pH 6.0 and 9.3 are interpreted using the theory of optical absorption bandshape. The bands' anharmonic behavior is explained assuming that there is a higher-energy set of conformational substates (CSS(h)), which are populated upon heating and correspond to the protein substates with disordered water molecules in the heme pocket. Analysis of the second moments of the CO bands of the carboxy complexes of myoglobin (Mb(CO)) and hemoglobin (Hb(CO)), and of HRP(CO) with benzohydroxamic acid (HRP(CO)+BHA), shows that the low energy CSS(h) exists also in the open conformation of Mb(CO), where the heme pocket is spacious enough to accommodate a water molecule. In the HRP(CO)+BHA and closed conformations of Mb(CO) and Hb(CO), the heme pocket is packed with BHA and different amino acids, the CSS(h) has much higher energy and is hardly populated even at the highest temperatures. Therefore only motions of these amino acids contribute to the band broadening. These motions are linked to the protein surface and frozen in the glassy matrix, whereas in the liquid solvent they are harmonic. Thus the second moment of the CO band is temperature-independent in glass and is proportional to the temperature in liquid. The temperature dependence of the second moment of the CO peak of HRP(CO) in the trehalose glass exhibits linear coupling to an oscillator. This oscillator can be a moving water molecule locked in the heme pocket in the whole interval of temperatures or a trehalose molecule located in the heme pocket.

Low-temperature glass transitions of quenched and annealed bovine serum albumin aqueous solutions

To investigate the glass transition behaviors of a 20% (w/w) aqueous solution of bovine serum albumin, heat capacities and enthalpy relaxation rates were measured by adiabatic calorimetry at temperatures ranging from 80 to 300 K. One series of measurements was carried out after quenching from 300 down to 80 K and another after annealing in 200-240 K. The quenched sample showed a heat capacity jump indicating a glass transition temperature T(g) = 170 K, and the annealed sample showed a smaller jump with the T(g) shifted toward the higher temperature side. The temperature dependence of the enthalpy relaxation rates for the quenched sample indicated the presence of two enthalpy relaxation effects: one at around 110 K and the other over a wide temperature range (120-190 K). The annealed sample showed three separate relaxation effects giving 1) T(g) = 110 K, 2) 135 K, and 3) temperature higher than 180 K, whereas nothing around 170 K. These effects were thought to originate, respectively, from the rearrangement motions of 1) primary hydrate water forming a direct hydrogen bond with the protein, 2) part of the internal water localized in the opening of a protein structure, and 3) the disordered region in the protein.

Effects of Moisture on Glass Transition and Microstructure of Glycerol-Plasticized Soy Protein

The glass transition behavior of the glycerol-plasticized soy protein sheets (SL series) at various relative humidity (RH) was investigated by using differential scanning calorimetry with the aluminum pan and O-ring-sealed stainless steel capsule, and the microstructure of these sheets was detected on small-angle X-ray scattering. The results revealed that there were three glass transitions (Tg1, Tg2 and Tg3), corresponding to glycerol-rich, protein-rich and protein-water domains, in the protein-glycerol-water ternary system. The Tg1 values of the SL-series sheets at 75% RH decreased from -49.3 to -83.8 degrees C with an increase of glycerol content from 10 to 50 wt.-%, whereas Tg2 and Tg3 were almost invariable at about 60 degrees C and 3 degrees C, respectively. In addition, the Tg1, Tg2 and Tg3 values of the SL-25 containing 25 wt.-% glycerol at 0%, 35%, 58%, 75% and 98% RH were in the range of -12.7 - -83.2 degrees C, 65.8 - 53.1 degrees C and 3.5 - 1.9 degrees C, respectively. The result from small-angle X-ray scattering indicated that the radii of gyration (Rg) of protein-rich domain were in the range of 60-63 nm; this suggested the existence of protein macromolecules as aggregates in the stable protein-rich and protein-water domains. With an increase of RH, the tensile strength and Tg values of the SL-series sheets decreased, but the elongation at break increased. In view of the results above, the moisture in ambient environment significantly influenced the Tg values and microstructures of the glycerol-plasticized soy protein sheets, leading to the changes of the mechanical and thermal properties.

Internal dynamics and protein–matrix coupling in trehalose-coated proteins

We review recent studies on the role played by non-liquid, water-containing matrices on the dynamics and structure of embedded proteins. Two proteins were studied, in water-trehalose matrices: a water-soluble protein (carboxy derivative of horse heart myoglobin) and a membrane protein (reaction centre from Rhodobacter sphaeroides). Several experimental techniques were used: Mossbauer spectroscopy, elastic neutron scattering, FTIR spectroscopy, CO recombination after flash photolysis in carboxy-myoglobin, kinetic optical absorption spectroscopy following pulsed and continuous photoexcitation in Q(B) containing or Q(B) deprived reaction centre from R. sphaeroides. Experimental results, together with the outcome of molecular dynamics simulations, concurred to give a picture of how water-containing matrices control the internal dynamics of the embedded proteins. This occurs, in particular, via the formation of hydrogen bond networks that anchor the protein surface to the surrounding matrix, whose stiffness increases by lowering the sample water content. In the conclusion section, we also briefly speculate on how the protein-matrix interactions observed in our samples may shed light on the protein-solvent coupling also in liquid aqueous solutions.

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.

Protein–water displacement distributions

The statistical properties of fast protein-water motions are analyzed by dynamic neutron scattering experiments. Using isotopic exchange, one probes either protein or water hydrogen displacements. A moment analysis of the scattering function in the time domain yields model-independent information such as time-resolved mean square displacements and the Gauss-deviation. From the moments, one can reconstruct the displacement distribution. Hydration water displays two dynamical components, related to librational motions and anomalous diffusion along the protein surface. Rotational transitions of side chains, in particular of methyl groups, persist in the dehydrated and in the solvent-vitrified protein structure. The interaction with water induces further continuous protein motions on a small scale. Water acts as a plasticizer of displacements, which couple to functional processes such as open-closed transitions and ligand exchange.

Enzyme activity and flexibility at very low hydration

Recent measurements have demonstrated enzyme activity at hydrations as low as 3%. This raises the question of whether hydration-induced enzyme flexibility is important for activity. Here, to address this, picosecond dynamic neutron scattering experiments are performed on pig liver esterase powders at 0%, 3%, 12%, and 50% hydration by weight and at temperatures ranging from 120 to 300 K. At all temperatures and hydrations, significant quasielastic scattering intensity is found in the protein, indicating the presence of anharmonic, diffusive motion. As the hydration increases, a temperature-dependent dynamical transition appears and strengthens involving additional diffusive motion. The implication of these results is that, although the additional hydration-induced diffusive motion in the protein detected here may be related to increased activity, it is not required for the enzyme to function.

Picosecond thermometer in the amide I band of myoglobin

The amide I and II bands in myoglobin show a heterogeneous temperature dependence, with bands at 6.17 and 6.43 microm which are more intense at low temperatures. The amide I band temperature dependence is on the long wavelength edge of the band, while the short wavelength side has almost no temperature dependence. We compare concepts of anharmonic solid-state crystal physics and chemical physics for the origins of these bands. We suggest that the long wavelength side is composed of those amino acids which hydrogen bond to the hydration shell of the protein, and that temperature dependent bands can be used to determine the time it takes vibrational energy to flow into the hydration shell. We determine that vibrational energy flow to the hydration shell from the amide I takes approximately 20 ps to occur.

Librational motion of spin-labeled lipids in high-cholesterol containing membranes from echo-detected EPR spectra

Two-pulse, echo-detected (ED) electron paramagnetic resonance (EPR) spectroscopy was used to study the librational motions of spin-labeled lipids in membranes of dipalmitoylphosphatidylcholine + 50 mol % cholesterol. The temperature dependence, over the range 77-240 K, and the dependence on position of spin-labeling in the sn-2 chain (n=5, 7, 10, 12, and 14) of the phospholipid, were characterized in detail. The experimental ED-spectra were corrected for instantaneous spin diffusion arising from static spin-spin interactions, by using spectra recorded at 77 K, where motional contributions are negligible. Simulations according to a model of rapid, small-amplitude librations about an axis whose direction is randomly distributed are able to describe the experimental spectra. Calibrations, in terms of the amplitude-correlation time product, alpha2tauc, were constructed for diagnostic spectral line-height ratios at different echo delay times, and for relaxation spectra obtained from the ratio of ED-spectra recorded at two different echo delays. The librational amplitude, alpha2, was determined for a spin label at the 14-C position of the lipid chain from the partially motionally averaged hyperfine splitting in the conventional EPR spectra. The librational correlation time, tauc, which is deduced from combination of the conventional and ED-EPR results, lies in the subnanosecond regime and depends only weakly on temperature. The temperature dependence of the ED-EPR spectra arises mainly from an increase in librational amplitude with increasing temperature, and position down the lipid chain. A gradual transition takes place at higher temperatures, from a situation in which segmental torsional librations are cumulative, i.e., the contributions of the individual segments add up progressively upon going down the chain, to one of concerted motion only weakly dependent on chain position. Such librational motions are important for glass-like states and are generally relevant to high lipid packing densities, e.g., in cholesterol-containing raft domains and condensed complexes.

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.

The 'glass transition' in protein dynamics: what it is, why it occurs, and how to exploit it

All proteins undergo a dramatic change in their dynamical properties at approximately 200 K. Above this temperature, their dynamic behavior is dominated by large-scale collective motions of bonded and nonbonded groups of atoms. At lower temperatures, simple harmonic vibrations predominate. The transition has been described as a 'glass transition' to emphasize certain similarities between the change in dynamic behavior of individual protein molecules and the changes in viscosity and other properties of liquids when they form a glass. The glass transition may reflect the intrinsic temperature dependence of the motions of atoms in the protein itself, in the bound solvent on the surface of the protein, or it may reflect contributions from both. Protein function is significantly altered below this transition temperature; a fact that can be exploited to trap normally unstable intermediates in enzyme-catalyzed reactions and stabilize them for periods long enough to permit their characterization by high-resolution protein crystallography.

Water induced effects on the thermal response of a protein

A model protein and surrounding water have been investigated at different temperatures. We have detected an anomalous compression of the protein near the freezing point of water-a compression not obviously related to the negative thermal expansion of the solvent. Moreover, the physiological protein working temperature (T=300 K) appears to be related to the activation of exchange of vicinal water with the bulk and the concomitant absorption of heat by hydrophilic amino acids. The inferred activation was interpreted on the basis of degenerate tetrahedral order between the hydration shell and the bulk. The results support the notion that the dynamics of vicinal water makes a substantial contribution to the activity optimum of proteins.

The role of dynamics in enzyme activity

Although protein function is thought to depend on flexibility, precisely how the dynamics of the molecule and its environment contribute to catalytic mechanisms is unclear. We review experimental and computational work relating to enzyme dynamics and function, including the role of solvent. The evidence suggests that fast motions on the 100 ps timescale, and any motions coupled to these, are not required for enzyme function. Proteins where the function is electron transfer, proton tunneling, or ligand binding may have different dynamical dependencies from those for enzymes, and enzymes with large turnover numbers may have different dynamical dependencies from those that turn over more slowly. The timescale differences between the fastest anharmonic fluctuations and the barrier-crossing rate point to the need to develop methods to resolve the range of motions present in enzymes on different time- and lengthscales.