The dynamical transition of proteins, concepts and misconceptions

Hydration-induced dynamical changes in lyophilised and weakly hydrated apoferritin: insights from molecular dynamics simulation

The dynamics and functionality of proteins are significantly influenced by their interaction with water. For lyophilised (i.e. h ≤ 0.05 where h = g of H2O per g of protein) and weakly hydrated systems (i.e. h ≤ 0.38) hydration generally enhances protein mobility above the so-called 'dynamical transition' temperature (Td > 220 K). However, water-induced mobility hindrance at low temperatures (T < 175 K) has been reported in various proteins of varying secondary structure; namely green fluorescent protein (GFP), pig liver esterase, lysozyme, ribonuclease A (RNAse A) and apoferritin. By focussing on the dynamic behaviour of the apoferritin molecule, this study proposes mechanisms driving these hydration-induced mobility changes, particularly the less understood hindrance at low temperatures. Using atomistic molecular dynamics (MD) simulations of horse spleen apoferritin in the lyophilised (h = 0.05) and weakly hydrated (h = 0.31) states, we report here the impact of water on protein dynamics as a function of temperature. Through residue-specific mean squared displacement (MSD), radial distribution function (RDF), solvent accessible surface area (SASA), local hydration degree and hydrogen bonding analyses, we demonstrate that while water proximity directly correlates with mobility enhancement at high temperatures, the hydration-induced mobility reduction observed at temperatures below 175 K is primarily propagated through the protein backbone.

Dynamic-to-static switch of hydrogen bonds induces a metal-insulator transition in an organic-inorganic superlattice

Hydrogen bonds profoundly influence the fundamental chemical, physical and biological properties of molecules and materials. Owing to their relatively weaker interactions compared to other chemical bonds, hydrogen bonds alone are generally insufficient to induce substantial changes in electrical properties, thus imposing severe constraints on their applications in related devices. Here we report a metal-insulator transition controlled by hydrogen bonds for an organic-inorganic (1,3-diaminopropane)0.5SnSe2 superlattice that exhibits a colossal on-off ratio of 107 in electrical resistivity. The key to inducing the transition is a change in the amino group's hydrogen-bonding structure from dynamic to static. In the dynamic state, thermally activated free rotation continuously breaks and forms transient hydrogen bonds with adjacent Se anions. In the static state, the amino group forms three fixed-angle positions, each separated by 120°. Our findings contribute to the understanding of electrical phenomena in organic-inorganic hybrid materials and may be used for the design of future molecule-based electronic materials.

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

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

Inelastic neutron scattering and spectroscopy methods to characterize dynamics in colloidal and soft matter systems

Colloidal systems and soft materials are well suited to neutron scattering, and the community has readily adopted elastic scattering techniques to investigate their structure. Due to their unique properties, neutrons may also be used to characterize the dynamics of soft materials over a wide range of length and time scales in situ. Both static structures and an understanding of how molecules move about their equilibrium positions is essential if we are to deliver on the promise of rationally designing soft materials. In this review we introduce the basics of neutron spectroscopy and explore the ways in which inelastic neutron scattering can be used to study colloidal and soft materials. Illustrative examples are chosen that highlight the phenomena suitable for investigation using this suite of techniques.

Persistence of Methionine Side Chain Mobility at Low Temperatures in a Nine-Residue Low Complexity Peptide, as Probed by 2 H Solid-State NMR

Methionine side chains are flexible entities which play important roles in defining hydrophobic interfaces. We utilize deuterium static solid-state NMR to assess rotameric inter-conversions and other dynamic modes of the methionine in the context of a nine-residue random-coil peptide (RC9) with the low-complexity sequence GGKGMGFGL. The measurements in the temperature range of 313 to 161 K demonstrate that the rotameric interconversions in the hydrated solid powder state persist to temperatures below 200 K. Removal of solvation significantly reduces the rate of the rotameric motions. We employed 2 H NMR line shape analysis, longitudinal and rotation frame relaxation, and chemical exchange saturation transfer methods and found that the combination of multiple techniques creates a significantly more refined model in comparison with a single technique. Further, we compare the most essential features of the dynamics in RC9 to two different methionine-containing systems, characterized previously. Namely, the M35 of hydrated amyloid-β1-40 in the three-fold symmetric polymorph as well as Fluorenylmethyloxycarbonyl (FMOC)-methionine amino acid with the bulky hydrophobic group. The comparison suggests that the driving force for the enhanced methionine side chain mobility in RC9 is the thermodynamic factor stemming from distributions of rotameric populations, rather than the increase in the rate constant.

Native and nonnative reactions in ethanolamine ammonia-lyase are actuated by different dynamics

We address the contribution of select classes of solvent-coupled configurational fluctuations to the complex choreography involved in configurational and chemical steps in an enzyme by comparing native and nonnative reactions conducted at different protein internal sites. The low temperature, first-order kinetics of covalent bond rearrangement of the cryotrapped substrate radical in coenzyme B12-dependent ethanolamine ammonia-lyase (EAL) from Salmonella enterica display a kink, or increase in slope, of the Arrhenius plot with decreasing temperature. The event is associated with quenching of a select class of reaction-actuating collective fluctuations in the protein hydration layer. For comparison, a nonnative, radical reaction of the protein interior cysteine sulfhydryl group with hydrogen peroxide (H2O2) is introduced by cryotrapping EAL in an aqueous H2O2 eutectic system. The low-temperature aqueous H2O2 protein hydration and mesodomain solvent phases surrounding cryotrapped EAL are characterized by using TEMPOL spin probe electron paramagnetic resonance spectroscopy, including a freezing transition of the eutectic phase that orders the protein hydration layer. Kinetics of the cysteine-H2O2 reaction in the EAL protein interior are monitored by DEPMPO spin trapping of hydroxyl radical product. In contrast to the native reaction, the linear Arrhenius relation for the nonnative cysteine-H2O2 reaction is maintained through the solvent-protein ordering transition. The nonnative reaction is coupled to the generic local, incremental fluctuations that are intrinsic to globular proteins. The comparative approach supports the proposal that select coupled solvent-protein configurational fluctuations actuate the native reaction, and suggests that select dynamical coupling contributes to the degree of catalysis in enzymes.

Correlating the Diffusion of Water to Performance in Model Reverse Osmosis Polyamides with Controlled Crosslink Densities

We systematically reduce the cross-link density of a PA network based on m-phenylene diamine by substituting a fraction of the trifunctional trimesoyl chloride cross-linking agent with a difunctional isophthaloyl analog that promotes chain extension, in order to elucidate robust design cues for improving the polyamide (PA) separation layer in reverse osmosis (RO) membranes for desalination. Thin films of these model PA networks are fully integrated into a composite membrane and evaluated in terms of their water flux and salt rejection. By incorporating 15 mol % of the difunctional chain extender, we reduce the cross-link density of the network by a factor of two, which leads to an 80 % increase in the free or unreacted amine content. The resulting swelling of the PA network in liquid water increases by a factor of two accompanied by a 30 % increase in the salt passage through the membrane. Surprisingly, this leads to a 30 % decrease in the overall permeance of water through the membrane. This conundrum is resolved by quantifying the microscopic diffusion coefficient of water inside the PA network with quasi-elastic neutron scattering. In the highest and lowest cross-link density networks, water shows strong signatures of confined diffusion. At short length scales, the water exhibits a translational diffusion that is consistent with the jump-diffusion mechanism. This translational diffusion coefficient is approximately five times slower in the lowest cross-linked density network, consistent with the reduced water permeance. This is interpreted as water molecules interacting more strongly with the increased free amine content. Over longer length scales the water diffusion is confined, exhibiting mobility that is independent of length scale. The length scales of confinement from the quasi-elastic neutron scattering experiments at which this transition from confined to translational diffusion occurs is on the order of (5 to 6) Å , consistent with complementary X-ray scattering, small angle neutron scattering, and positron annihilation lifetime spectroscopy measurements. The confinement appears to come from heterogeneities in the average inter-atomic distances, suggesting that diffusion occurs by water bouncing between chains and occasionally sticking to the polar functional groups. The results obtained here are compared with similar studies of water diffusion through both rigid porous silicates and ion exchange membranes, revealing robust design cues for engineering high-performance RO membranes.

Modeling of protein hydration dynamics is supported by THz spectroscopy of highly diluted solutions

In this investigation, we report the effect on the microscopic dynamics and interactions of the cytokine interferon gamma (IFN-γ) and antibodies to IFN-γ (anti-IFN-γ) and to the interferon gamma receptor 1 (anti-IFNGR1) prepared in highly dilute (HD) solutions of initial proteins. THz spectroscopy measurements have been conducted as a means to analyze and characterize the collective dynamics of the HD samples. MD simulations have also been performed that have successfully reproduced the observed signatures from experimental measurement. Using this joint experimental-computational approach we determine that the HD process associated with the preparation of the highly diluted samples used in this investigation induces a dynamical transition that results in collective changes in the hydrogen-bond network of the solvent. The dynamical transition in the solvent is triggered by changes in the mobility and hydrogen-bonding interactions of the surface molecules in the HD samples and is characterized by dynamical heterogeneity. We have uncovered that the reorganization of the sample surface residue dynamics at the solvent-protein interface leads to both structural and kinetic heterogeneous dynamics that ultimately create interactions that enhance the binding probability of the antigen binding site. Our results indicate that the modified interfacial dynamics of anti-IFN-γ and anti-IFGNR1 that we probe experimentally are directly associated with alterations in the complementarity regions of the distinct antibodies that designate both antigen-antibody affinity and recognition.

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.

Confinement dependence of protein-associated solvent dynamics around different classes of proteins, from the EPR spin probe perspective

Protein function is modulated by coupled solvent fluctuations, subject to the degree of confinement from the surroundings. To identify universal features of the external confinement effect, the temperature dependence of the dynamics of protein-associated solvent over 200-265 K for proteins representative of different classes and sizes is characterized by using the rotational correlation time (detection bandwidth, 10-10-10-7 s) of the electron paramagnetic resonance (EPR, X-band) spin probe, TEMPOL, which is restricted to regions vicinal to protein in frozen aqueous solution. Weak (protein surrounded by aqueous-dimethylsulfoxide cryosolvent mesodomain) and strong (no added crysolvent) conditions of ice boundary confinement are imposed. The panel of soluble proteins represents large and small oligomeric (ethanolamine ammonia-lyase, 488 kDa; streptavidin, 52.8 kDa) and monomeric (myoglobin, 16.7 kDa) globular proteins, an intrinsically disordered protein (IDP, β-casein, 24.0 kDa), an unstructured peptide (protamine, 4.38 kDa) and a small peptide with partial backbone order (amyloid-β residues 1-16, 1.96 kDa). Expanded and condensate structures of β-casein and protamine are resolved by the spin probe under weak and strong confinement, respectively. At each confinement condition, the soluble globular proteins display common T-dependences of rotational correlation times and normalized weights, for two mobility components, protein-associated domain, PAD, and surrounding mesodomain. Strong confinement induces a detectable PAD component and emulation of globular protein T-dependence by the amyloid-β peptide. Confinement uniformly impacts soluble globular protein PAD dynamics, and is therefore a generic control parameter for modulation of soluble globular protein function.

Triplet States Reveal Slow Local Dynamics in the Solvation Shell of Biomolecules

Protein hydration shell dynamics plays a pivotal role in biochemical processes such as protein folding, enzyme function, molecular recognition and interaction with biological membranes. Thus, it is crucial to understand the mobility of the solvation shell at the surface of biomolecules. Triplet state solvation dynamics can reveal the slow dynamics of the solvation shell. This is done in the present work without adding separate dye molecules but instead by using a phosphorescent subgroup of the biomolecule itself. In particular, we study a small heptapeptide in a glycerol-water mixture under cryoconservation conditions so that the system can be supercooled without crystallization. We find a significant slowing of molecules in the solvation shell in the millisecond range compared to the bulk. This opens up the possibility to unravel the nature of relaxation processes in the solvation shell usually overlapping at room temperature.

Temperature-Dependent Dynamics at Protein-Solvent Interfaces

We perform differential scanning calorimetry, broadband dielectric spectroscopy (BDS), and nuclear magnetic resonance (NMR) studies to ascertain the molecular dynamics in mixtures of ethylene glycol with elastin or lysozyme over broad temperature ranges. To focus on the protein-solvent interface, we use mixtures with about equal numbers of amino acids and solvent molecules. The elastin and lysozyme mixtures show similar glass transition steps, which extend over a broad temperature range of 157-185K. The BDS and NMR studies yield fully consistent results for the fastest process P1, which is caused by the structural relaxation of ethylene glycol between the protein molecules and follows an Arrhenius law with an activation energy of Ea=0.63eV. It involves quasi-isotropic reorientation and is very similar in the elastin and lysozyme matrices but different from the alpha and beta relaxations of bulk ethylene glycol. Two slower BDS processes P2 and P3 have protein-dependent time scales, but exhibit a similar Arrhenius-like temperature dependence with an activation energy of Ea~0.81eV. However, P2 and P3 do not have a clear NMR signature. In particular, the NMR results for the lysozyme mixture reveal that the protein backbone does not show isotropic alpha-like motion on the P2 and P3 time scales but only restricted beta-like reorientation. The different activation energies of the P1 and P2/P3 processes do not support an intimate coupling of protein and ethylene glycol dynamics. The present results are compared with previous findings for mixtures of proteins with water or glycerol, implying qualitatively different dynamical couplings at various protein-solvent interfaces.

A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks

Although proteins are considered as nonconductors that transfer electrons only up to 1 to 2 nanometers via tunneling, Geobacter sulfurreducens transports respiratory electrons over micrometers, to insoluble acceptors or syntrophic partner cells, via nanowires composed of polymerized cytochrome OmcS. However, the mechanism enabling this long-range conduction is unclear. Here, we demonstrate that individual nanowires exhibit theoretically predicted hopping conductance, at rate (>10¹⁰ s^-1) comparable to synthetic molecular wires, with negligible carrier loss over micrometers. Unexpectedly, nanowires show a 300-fold increase in their intrinsic conductance upon cooling, which vanishes upon deuteration. Computations show that cooling causes a massive rearrangement of hydrogen bonding networks in nanowires. Cooling makes hemes more planar, as revealed by Raman spectroscopy and simulations, and lowers their reduction potential. We find that the protein surrounding the hemes acts as a temperature-sensitive switch that controls charge transport by sensing environmental perturbations. Rational engineering of heme environments could enable systematic tuning of extracellular respiration.

Resolution and characterization of contributions of select protein and coupled solvent configurational fluctuations to radical rearrangement catalysis in coenzyme B12-dependent ethanolamine ammonia-lyase

Coenzyme B12 (adenosylcobalamin) -dependent ethanolamine ammonia-lyase (EAL) is the signature enzyme in ethanolamine utilization metabolism associated with microbiome homeostasis and disease conditions in the human gut. The enzyme conducts a complex choreography of bond-making/bond-breaking steps that rearrange substrate to products through a radical mechanism, with themes common to other coenzyme B12-dependent and radical enzymes. The methods presented are targeted to test the hypothesis that particular, select protein and coupled solvent configurational fluctuations contribute to enzyme function. The general approach is to correlate enzyme function with an introduced perturbation that alters the properties (for example, degree of concertedness, or collectiveness) of protein and coupled solvent dynamics. Methods for sample preparation and low-temperature kinetic measurements by using temperature-step reaction initiation and time-resolved, full-spectrum electron paramagnetic resonance spectroscopy are detailed. A framework for interpretation of results obtained in ensemble systems under conditions of statistical equilibrium within the reacting, globally unstable state is presented. The temperature-dependence of the first-order rate constants for decay of the cryotrapped paramagnetic substrate radical state in EAL, through the chemical step of radical rearrangement, displays a piecewise-continuous Arrhenius dependence from 203 to 295K, punctuated by a kinetic bifurcation over 219-220K. The results reveal the obligatory contribution of a class of select collective protein and coupled solvent fluctuations to the interconversion of two resolved, sequential configurational substates, on the decay time scale. The select class of collective fluctuations also contributes to the chemical step. The methods and analysis are generally applicable to other coenzyme B12-dependent and related radical enzymes.

Photo-Switching of Protein Dynamical Collectivity

We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins (RFP) mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy show in all cases an increase in the turn-on temperature in the bleached state. The result is surprising given that there is little change in the protein surface, and thus, the solvent dynamics held responsible for the transition should not change. A spectral analysis of the measurements guided by quasiharmonic calculations of the protein absorbance reveals that indeed the solvent dynamical turn-on temperature is independent of the thermal stability/photostate however the protein dynamical turn-on temperature shifts to higher temperatures. This is the first demonstration of switching the protein dynamical turn-on temperature with protein functional state. The observed shift in protein dynamical turn-on temperature relative to the solvent indicates an increase in the required mobile waters necessary for the protein picosecond motions, that is, these motions are more collective. Melting-point measurements reveal that the photobleached state is more thermally stable, and structural analysis of related RFP’s shows that there is an increase in internal water channels as well as a more uniform atomic root mean squared displacement. These observations are consistent with previous suggestions that water channels form with extended light excitation providing O2 access to the chromophore and subsequent fluorescence loss. We report that these same channels increase internal coupling enhancing thermal stability and collectivity of the picosecond protein motions. The terahertz spectroscopic characterization of the protein and solvent dynamical onsets can be applied generally to measure changes in collectivity of protein motions.

New insights into the microscopic interactions associated with the physical mechanism of action of highly diluted biologics

In this investigation, we report the effect on the microscopic dynamics and interactions of the cytokine interferon gamma (IFN-γ) and antibodies to IFN-γ (anti-IFN-γ) and to the interferon gamma receptor 1 (anti-IFNGR1) prepared in exceptionally dilute solutions of initial proteins. Using both THz spectroscopy and molecular dynamics simulations we have uncovered that the high dilution method of sample preparation results in the reorganization of the sample surface residue dynamics at the solvent-protein interface that leads to both structural and kinetic heterogeneous dynamics that ultimately create interactions that enhance the binding probability of the antigen binding site. Our results indicate that the modified interfacial dynamics of anti-IFN-γ and anti-IFGNR1 that we probe experimentally are directly associated with alterations in the complementarity regions of the distinct antibodies that designate both antigen-antibody affinity and recognition.

Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation

Understanding and describing the dynamics of proteins is one of the major challenges in biology. Here, we use multifield variable-temperature NMR longitudinal relaxation (R₁) measurements to determine the hierarchical activation energies of motions of four different proteins: two small globular proteins (GB1 and the SH3 domain of α-spectrin), an intrinsically disordered protein (the C-terminus of the nucleoprotein of the Sendai virus, Sendai Ntail), and an outer membrane protein (OmpG). The activation energies map the motions occurring in the side chains, in the backbone, and in the hydration shells of the proteins. We were able to identify similarities and differences in the average motions of the proteins. We find that the NMR relaxation properties of the four proteins do share similar features. The data characterizing average backbone motions are found to be very similar, the same for methyl group rotations, and similar activation energies are measured. The main observed difference occurs for the intrinsically disordered Sendai Ntail, where we observe much lower energy of activation for motions of protons associated with the protein-solvent interface as compared to the others. We also observe variability between the proteins regarding side chain ¹⁵N relaxation of lysine residues, with a higher activation energy observed in OmpG. This hints at strong interactions with negatively charged lipids in the bilayer and provides a possible mechanistic clue for the "positive-inside" rule for helical membrane proteins. Overall, these observations refine the understanding of the similarities and differences between hierarchical dynamics in proteins.

The Dynamics of Hydrated Proteins Are the Same as Those of Highly Asymmetric Mixtures of Two Glass-Formers

Customarily, the studies of dynamics of hydrated proteins are focused on the fast hydration water ν-relaxation, the slow structural α-relaxation responsible for a single glass transition, and the protein dynamic transition (PDT). Guided by the analogy with the dynamics of highly asymmetric mixtures of molecular glass-formers, we explore the possibility that the dynamics of hydrated proteins are richer than presently known. By providing neutron scattering, dielectric relaxation, calorimetry, and deuteron NMR data in two hydrated globular proteins, myoglobin and BSA, and the fibrous elastin, we show the presence of two structural α-relaxations, α1 and α2, and the hydration water ν-relaxation, all coupled together with interconnecting properties. There are two glass transition temperatures T _g ^α1and T _g ^α2 corresponding to vitrification of the α1 and α2 processes. Relaxation time τ_α2(T) of the α2-relaxation changes its Arrhenius temperature dependence to super-Arrhenius on crossing T _g ^α1 from below. The ν-relaxation responds to the two vitrifications by changing the T-dependence of its relaxation time τ_ν(T) on crossing consecutively T _g ^α2 and T _g ^α1. It generates the PDT at T _d where τ_ν(T _d) matches about five times the experimental instrument timescale τ_exp, provided that T _d > T _g ^α1. This condition is satisfied by the hydrated globular proteins considered in this paper, and the ν-relaxation is in the liquid state with τ_ν(T) having the super-Arrhenius temperature dependence. However, if T _d < T _g ^α1, the ν-relaxation fails to generate the PDT because it is in the glassy state and τ_ν(T) has Arrhenius T-dependence, as in the case of hydrated elastin. Overall, the dynamics of hydrated proteins are the same as the dynamics of highly asymmetric mixtures of glass-formers. The results from this study have expanded the knowledge of the dynamic processes and their properties in hydrated proteins, and impact on research in this area is expected.

Quasielastic neutron scattering studies on couplings of protein and water dynamics in hydrated elastin

Performing quasielastic neutron scattering measurements and analyzing both elastic and quasielasic contributions, we study protein and water dynamics of hydrated elastin. At low temperatures, hydration-independent methyl group rotation dominates the findings. It is characterized by a Gaussian distribution of activation energies centered at about E_m = 0.17 eV. At ∼195 K, coupled protein-water motion sets in. The hydration water shows diffusive motion, which is described by a Gaussian distribution of activation energies with E_m = 0.57 eV. This Arrhenius behavior of water diffusion is consistent with previous results for water reorientation, but at variance with a fragile-to-strong crossover at ∼225 K. The hydration-related elastin backbone motion is localized and can be attributed to the cage rattling motion. We speculate that its onset at ∼195 K is related to a secondary glass transition, which occurs when a β relaxation of the protein has a correlation time of τ_β ∼ 100 s. Moreover, we show that its temperature-dependent amplitude has a crossover at the regular glass transition T_g = 320 K of hydrated elastin, where the α relaxation of the protein obeys τ_α ∼ 100 s. By contrast, we do not observe a protein dynamical transition when water dynamics enters the experimental time window at ∼240 K.

On the microscopic origins of relaxation processes in aqueous peptide solutions undergoing a glass transition

We combine broadband dielectric spectroscopy (BDS) with ¹H and ²H nuclear magnetic resonance (NMR) to study molecular dynamics in mixtures of ε-polylysine with H₂O or D₂O. In BDS, four relaxation processes can be attributed to molecular dynamics. While the fastest process P1 obeys the Arrhenius law, the slowest process P4 shows prominent non-Arrhenius behavior typical of structural α relaxation. For the intermediate processes P2 and P3, the temperature dependence changes at the glass transition temperature T_g. The ¹H and ²H NMR results yield insights into the molecular origins of these relaxation phenomena. In these NMR analyses, we exploit, in addition to the isotope selectivity of the method, the possibility to distinguish between various types of motion based on their respective line-shape effects and the capability to single out specific molecular moieties based on different spin-lattice relaxation behaviors. In this way, we reveal that process P1 results from the rotation of side and end groups of the peptide, while process P2 is caused by a reorientation of essentially all water molecules, which are quasi-isotropic and survive well below T_g. As for the peptide backbone dynamics, we find evidence that rotational motion of polar groups is involved in process P3 and that nonpolar regions show a dynamical process, which is located between P3 and P4. Thus, the NMR analyses do not yield evidence for coexisting fast peptide-decoupled and slow peptide-coupled water species, which contribute to BDS processes P2 and P3, respectively, but minor bimodality of water motion may remain undetected. Finally, it is demonstrated that the proton/deuteron exchange needs to be considered when interpreting experimental results for molecular dynamics in aqueous peptide solutions.

Role of hydration water in the onset of protein structural dynamics

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

Solid-state NMR reveals a comprehensive view of the dynamics of the flexible, disordered N-terminal domain of amyloid-β fibrils

Amyloid fibril deposits observed in Alzheimer's disease comprise amyloid-β (Aβ) protein possessing a structured hydrophobic core and a disordered N-terminal domain (residues 1-16). The internal flexibility of the disordered domain is likely essential for Aβ aggregation. Here, we used ²H static solid-state NMR methods to probe the dynamics of selected side chains of the N-terminal domain of Aβ_1-40 fibrils. Line shape and relaxation data suggested a two-state model in which the domain's free state undergoes a diffusive motion that is quenched in the bound state, likely because of transient interactions with the structured C-terminal domain. At 37 °C, we observed freezing of the dynamics progressively along the Aβ sequence, with the fraction of the bound state increasing and the rate of diffusion decreasing. We also found that without solvation, the diffusive motion is quenched. The solvent acted as a plasticizer reminiscent of its role in the onset of global dynamics in globular proteins. As the temperature was lowered, the fraction of the bound state exhibited sigmoidal behavior. The midpoint of the freezing curve coincided with the bulk solvent freezing for the N-terminal residues and increased further along the sequence. Using ²H R _1ρ measurements, we determined the conformational exchange rate constant between the free and bound states under physiological conditions. Zinc-induced aggregation leads to the enhancement of the dynamics, manifested by the faster conformational exchange, faster diffusion, and lower freezing-curve midpoints.

Evidence of a low-temperature dynamical transition in concentrated microgels

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

Molecular Dynamics Simulations of Water, Silica, and Aqueous Mixtures in Bulk and Confinement

Aqueous systems are omnipresent in nature and technology. They show complex behaviors, which often originate in the existence of hydrogen-bond networks. Prominent examples are the anomalies of water and the non-ideal behaviors of aqueous solutions. The phenomenology becomes even richer when aqueous liquids are subject to confinement. To this day, many properties of water and its mixtures, in particular, under confinement, are not understood. In recent years, molecular dynamics simulations developed into a powerful tool to improve our knowledge in this field. Here, our simulation results for water and aqueous mixtures in the bulk and in various confinements are reviewed and some new simulation data are added to improve our knowledge about the role of interfaces. Moreover, findings for water are compared with results for silica, exploiting that both systems form tetrahedral networks.

Hydrogen-bond dynamics at the bio-water interface in hydrated proteins: a molecular-dynamics study

Water is fundamental to the biochemistry of enzymes. It is well known that without a minimum amount of water, enzymes are not biologically active. Bare minimal solvation for biological function corresponds to about a single layer of water covering enzymes' surfaces. Many contradictory studies on protein-hydration-water-coupled dynamics have been published in recent decades. Following prevailing wisdom, a dynamical crossover in hydration water (at around 220 K for hydrated lysozymes) can trigger larger-amplitude motions of the protein, activating, in turn, biological functions. Here, we present a molecular-dynamics-simulation study on a solvated model protein (hen egg-white lysozyme), in which we determine, inter alia, the relaxation dynamics of the hydrogen-bond network between the protein and its hydration water molecules on a residue-per-residue basis. Hydrogen-bond breakage/formation kinetics is rather heterogeneous in temperature dependence (due to the heterogeneity of the free-energy surface), and is driven by the magnitude of thermal motions of various different protein residues which provide enough thermal energy to overcome energy barriers to rupture their respective hydrogen bonds with water. In particular, arginine residues exhibit the highest number of such hydrogen bonds at low temperatures, losing almost completely such bonding above 230 K. This suggests that hydration water's dynamical crossover, observed experimentally for hydrated lysozymes at ∼220 K, lies not at the origin of the protein residues' larger-amplitude motions, but rather arises as a consequence thereof. This highlights the need for new experimental investigations, and new interpretations to link protein dynamics to functions, in the context of key interrelationships with the solvation layer.

2H NMR Studies on the Dynamics of Pure and Mixed Hydrogen-Bonded Liquids in Confinement

2H NMR is used to ascertain dynamical behaviors of pure and mixed hydrogen-bonded liquids in bulk and in confinement. Detailed comparisons of previous and new results in broad dynamic and temperature ranges reveal that confinement effects differ for various liquids and confinements. For water, molecular reorientation strongly depends on the confinement size, with much slower and less fragile structural relaxation under more severe geometrical restriction. Moreover, a dynamical crossover occurs when a fraction of solid water forms so that the dynamics of the fraction of liquid water becomes even more restricted and, as a consequence, changes from bulk-like to interface-dominated. For glycerol, by contrast, confinement has weak effects on the reorientation dynamics. Mixed hydrogen-bonded liquids show even more complex dynamical behaviors. For aqueous solutions, the temperature dependence of the structural relaxation becomes discontinuous when the concentration changes due to a freezing of water fractions. This tendency for partial crystallization is enhanced rather than reduced by confinement, because different liquid-matrix interactions of the molecular species induce micro-phase segregation, which facilitates ice formation in water-rich regions. In addition, dynamical couplings at solvent-protein interfaces are discussed. It is shown that, on the one hand, solvent dynamics are substantially slowed down at protein surfaces and, on the other hand, protein dynamics significantly depend on the composition and, thus, the viscosity of the solvent. Furthermore, a protein dynamical transition occurs when the amplitude of water-coupled restricted backbone dynamics vanishes upon cooling.

Triplet Solvation Dynamics of Hydrogen Bonding Liquids in Confinement

We have developed a flexible experimental setup to conduct triplet solvation dynamics (TSD) experiments. The setup is capable of exciting dyes at 355, 320 and 266 nm. Phosphorescence spectra can be recorded up to a 10 ns-resolution usually covering three decades using a grating spectrograph and a CCD camera. In this contribution, we describe the experimental setup as well as first investigations on water-alcohol mixtures, microemulsions and new dyes for TSD, i.e. naphthalene derivates, which take full advantage of this experimental method sensitive to the local environment of the dyes.

Comparative Dynamics of Methionine Side-Chain in FMOC-Methionine and in Amyloid Fibrils

We compared the dynamics of key methionine methyl groups in the water-accessible hydrophobic cavity of amyloid fibrils and Fluorenylmethyloxycarbonyl-Methionine (FMOC-Met), which renders general hydrophobicity to the environment without the complexity of the protein. Met35 in the hydrated cavity was recently found to undergo a dynamical cross-over from the dominance of methyl rotations at low temperatures to the dominance of diffusive motion of methyl axis at high temperatures. Current results indicate that in FMOC-Met this cross-over is suppressed, similar to what was observed for the dry fibrils, indicating that hydration of the cavity is driving the onset of the dynamical transition.

What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes

Nuclear resonance vibrational spectroscopy (NRVS; also known as nuclear inelastic scattering, NIS) is a synchrotron-based method that reveals the full spectrum of vibrational dynamics for Mössbauer nuclei. Another major advantage, in addition to its completeness (no arbitrary optical selection rules), is the unique selectivity of NRVS. The basics of this recently developed technique are first introduced with descriptions of the experimental requirements and data analysis including the details of mode assignments. We discuss the use of NRVS to probe ⁵⁷Fe at the center of heme and heme protein derivatives yielding the vibrational density of states for the iron. The application to derivatives with diatomic ligands (O₂, NO, CO, CN^–) shows the strong capabilities of identifying mode character. The availability of the complete vibrational spectrum of iron allows the identification of modes not available by other techniques. This permits the correlation of frequency with other physical properties. A significant example is the correlation we find between the Fe–Im stretch in six-coordinate Fe(XO) hemes and the trans Fe–N(Im) bond distance, not possible previously. NRVS also provides uniquely quantitative insight into the dynamics of the iron. For example, it provides a model-independent means of characterizing the strength of iron coordination. Prediction of the temperature-dependent mean-squared displacement from NRVS measurements yields a vibrational “baseline” for Fe dynamics that can be compared with results from techniques that probe longer time scales to yield quantitative insights into additional dynamical processes.

Solvent-Driven Dynamical Crossover in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by 2H NMR Relaxation

Aromatic residues are important markers of dynamical changes in proteins' hydrophobic cores. In this work we investigated the dynamics of the F19 side-chain in the core of amyloid fibrils across a wide temperature range of 300 to 140 K. We utilized solid-state 2H NMR relaxation to demonstrate the presence of a solvent-driven dynamical crossover between different motional regimes, often also referred to as the dynamical transition. In particular, the dynamics are dominated by small-angle fluctuations at low temperatures and by π-flips of the aromatic ring at high temperatures. The crossover temperature is more than 43 degrees lower for the hydrated state of the fibrils compared to the dry state, indicating that interactions with water facilitate π-flips. Further, crossover temperatures are shown to be very sensitive to polymorphic states of the fibrils, such as the 2-fold and 3-fold symmetric morphologies of the wild-type protein as well as D23N mutant protofibrils. We speculate that these differences can be attributed, at least partially, to enhanced interactions with water in the 3-fold polymorph, which has been shown to have a water-accessible cavity. Combined with previous studies of methyl group dynamics, the results highlight the presence of multiple dynamics modes in the core of the fibrils, which was originally believed to be quite rigid.

Static solid-state 2H NMR methods in studies of protein side-chain dynamics

In this review, we discuss the experimental static deuteron NMR techniques and computational approaches most useful for the investigation of side-chain dynamics in protein systems. Focus is placed on the interpretation of line shape and relaxation data within the framework of motional modeling. We consider both jump and diffusion models and apply them to uncover glassy behaviors, conformational exchange and dynamical transitions in proteins. Applications are chosen from globular and membrane proteins, amyloid fibrils, peptide adsorbed on surfaces and proteins specific to connective tissues.

Hydrogen Mobility and Protein-Water Interactions in Proteins in the Solid State

In this work the groundwork is laid for characterizing the mobility of hydrogen-hydrogen pairs (proton-proton radial vectors) in proteins in the solid state that contain only residual water. In this novel approach, we introduce new ways of analyzing and interpreting data: 1) by representing hydrogen mobility (HM) and melting diagram (MD) data recorded by wide-line ¹ H NMR spectroscopic analysis as a function of fundamental temperature (thermal excitation energy); 2) by suggesting a novel mode of interpretation of these parameters that sheds light on details of protein-water interactions, such as the exact amount of water molecules and the distribution of barrier potentials pertaining to their rotational and surface translational mobility; 3) by relying on directly determined physical observables. We illustrate the power of this approach by studying the behavior of two proteins, the structured enzyme lysozyme and the intrinsically disordered ERD14.

Role of Hydration Layer in Dynamical Transition in Proteins: Insights from Translational Self-Diffusivity

Elucidation of the role of hydration water underpinning dynamical crossover in proteins has proven challenging. Indeed, many contradictory findings in the literature seek to establish either causal or correlative links between water and protein behavior. Here, via molecular dynamics, we compute the temperature dependence of mean-square displacement and translational self-diffusivities for both hen egg white lysozyme and its hydration layer from 190 to 300 K. We find that the protein's mobility increases sharply at ∼230 K, indicating dynamical onset; concerted motion with hydration-water molecules is evident up to ∼285 K, confirming dynamical correlation between them. Exploring underlying mechanisms of such concerted motion, we scrutinize the water-protein hydrogen-bonding network as a function of temperature, noting sharp deviation from linearity of the hydrogen bond number's profile with temperature originating near the protein dynamical transition. Our studies reveal a common temperature profile/dependence of self-diffusivity values of the protein, hydration water, and the bulk solvent, originating from a common dependence on the bulk solvent viscosity, η_S. The key mechanistic role adopted by the protein-water hydrogen bond network in relation to the onset of proteins' dynamical transition is also discussed.

Fast Motions of Key Methyl Groups in Amyloid-β Fibrils

Amyloid-β (Aβ) peptide is the major component of plaques found in Alzheimer's disease patients. Using solid-state 2H NMR relaxation performed on selectively deuterated methyl groups, we probed the dynamics in the threefold symmetric and twofold symmetric polymorphs of native Aβ as well as the protofibrils of the D23N mutant. Specifically, we investigated the methyl groups of two leucine residues that belong to the hydrophobic core (L17 and L34) as well as M35 residues belonging to the hydrophobic interface between the cross-β subunits, which has been previously found to be water-accessible. Relaxation measurements performed over 310-140 K and two magnetic field strengths provide insights into conformational variability within and between polymorphs. Core packing variations within a single polymorph are similar to what is observed for globular proteins for the core residues, whereas M35 exhibits a larger degree of variability. M35 site is also shown to undergo a solvent-dependent dynamical transition in which slower amplitude motions of methyl axes are activated at high temperature. The motions, modeled as a diffusion of methyl axis, have activation energy by a factor of 2.7 larger in the twofold compared with the threefold polymorph, whereas D23N protofibrils display a value similar to the threefold polymorph. This suggests enhanced flexibility of the hydrophobic interface in the threefold polymorph. This difference is only observed in the hydrated state and is absent in the dry fibrils, highlighting the role of solvent at the cavity. In contrast, the dynamic behavior of the core is hydration-independent.

Evidence of Coupling between the Motions of Water and Peptides

Studies of protein dynamics at low temperatures are generally performed on hydrated powders and not in biologically realistic solutions of water because of water crystallization. However, here we avoid the problem of crystallization by reducing the size of the biomolecules. We have studied oligomers of the amino acid l-lysine, fully dissolved in water, and our dielectric relaxation data show that the glass transition-related dynamics of the oligomers is determined by the water dynamics, in a way similar to that previously observed for solvated proteins. This implies that the crucial role of water for protein dynamics can be extended to other types of macromolecular systems, where water is also able to determine their conformational fluctuations. Using the energy landscape picture of macromolecules, the thermodynamic criterion for such solvent-slaved macromolecular motions may be that the macromolecules need the entropy contribution from the solvent to overcome the enthalpy barriers between different conformational substates.

Glass transitions in native silk fibres studied by dynamic mechanical thermal analysis

Silks are a family of semi-crystalline structural materials, spun naturally by insects, spiders and even crustaceans. Compared to the characteristic β-sheet crystalline structure in silks, the non-crystalline structure and its composition deserves more attention as it is equally critical to the filaments' high toughness and strength. Here we further unravel the structure-property relationship in silks using Dynamic Mechanical Thermal Analysis (DMTA). This technique allows us to examine the most important structural relaxation event of the disordered structure the disordered structure, the glass transition (GT), in native silk fibres of the lepidopteran Bombyx mori and Antheraea pernyi and the spider Nephila edulis. The measured glass transition temperature Tg, loss tangent tan δ and dynamic storage modulus are quantitatively modelled based on Group Interaction Modelling (GIM). The "variability" issue in native silks can be conveniently explained by the different degrees of structural disorder as revealed by DMTA. The new insights will facilitate a more comprehensive understanding of the structure-property relations for a wide range of biopolymers.

Dynamical and orientational structural crossovers in low-temperature glycerol

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

Water Determines the Structure and Dynamics of Proteins

Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.

Dynamics of hydrated proteins and bio-protectants: Caged dynamics, β-relaxation, and α-relaxation

BACKGROUND

The properties of the three dynamic processes, α-relaxation, ν-relaxation, and caged dynamics in aqueous mixtures and hydrated proteins are analogous to corresponding processes found in van der Waals and polymeric glass-formers apart from minor differences.

METHODS

Collection of various experimental data enables us to characterize the structural α-relaxation of the protein coupled to hydration water (HW), the secondary or ν-relaxation of HW, and the caged HW process.

RESULTS

From the T-dependence of the ν-relaxation time of hydrated myoglobin, lysozyme, and bovine serum albumin, we obtain Ton at which it enters the experimental time windows of Mössbauer and neutron scattering spectroscopies, coinciding with protein dynamical transition (PDT) temperature Td. However, for all systems considered, the α-relaxation time at Ton or Td is many orders of magnitude longer. The other step change of the mean-square-displacement (MSD) at Tg_alpha originates from the coupling of the nearly constant loss (NCL) of caged HW to density. The coupling of the NCL to density is further demonstrated by another step change at the secondary glass temperature Tg_beta in two bio-protectants, trehalose and sucrose.

CONCLUSIONS

The structural α-relaxation plays no role in PDT. Since PDT is simply due to the ν-relaxation of HW, the term PDT is a misnomer. NCL of caged dynamics is coupled to density and show transitions at lower temperature, Tg_beta and Tg_alpha.

GENERAL SIGNIFICANCE

The so-called protein dynamical transition (PDT) of hydrated proteins is not caused by the structural α-relaxation of the protein but by the secondary ν-relaxation of hydration water. "This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".

A neutron spectrometer concept implementing RENS for studies in life sciences

BACKGROUND

Resolution Elastic Neutron Scattering (RENS) method involves performing elastic scattering intensity scans as a function of the instrumental energy resolution and as a function of temperature.

METHODS

In the framework of RENS, numerical simulation and experimental data show that in the measured elastic scattering law against the logarithm of the instrumental energy resolution an inflection point occurs when the resolution time intersects the system relaxation time; conversely, in the measured elastic scattering law against temperature an inflection point turns up when the system relaxation time intersects the resolution time.

RESULTS

For practical implementation of the RENS technique, a dedicated neutron spectrometer would be needed. Here we propose a concept of such a spectrometer that utilizes mechanical velocity selection of both incident and scattered neutrons over a wide angular range. The instrument is able to collect intensity scans vs energy resolution where the instrumental resolution time changes crisscrossing the system relaxation time, and intensity scans vs temperature where the system relaxation time changes intersecting the instrumental resolution time.

CONCLUSIONS

We propose a RENS spectrometer concept based on velocity selection of incident neutrons and wide-angle velocity selection of scattered neutrons achieved by the same rotating collimator-type mechanical device with the optimized shape of blades.

GENERAL SIGNIFICANCE

RENS spectrometer is strongly appealing and innovative because of the simultaneous data collection as a function of energy resolution, wide wavevector range and temperature. Such a spectrometer would be the first practical implementation of RENS concept with a broad range of applications in Life Sciences. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.

Intrinsic Localized Modes in Proteins

Protein dynamics is essential for proteins to function. Here we predicted the existence of rare, large nonlinear excitations, termed intrinsic localized modes (ILMs), of the main chain of proteins based on all-atom molecular dynamics simulations of two fast-folder proteins and of a rigid α/β protein at 300 K and at 380 K in solution. These nonlinear excitations arise from the anharmonicity of the protein dynamics. The ILMs were detected by computing the Shannon entropy of the protein main-chain fluctuations. In the non-native state (significantly explored at 380 K), the probability of their excitation was increased by a factor between 9 and 28 for the fast-folder proteins and by a factor 2 for the rigid protein. This enhancement in the non-native state was due to glycine, as demonstrated by simulations in which glycine was mutated to alanine. These ILMs might play a functional role in the flexible regions of proteins and in proteins in a non-native state (i.e. misfolded or unfolded states).

Protein electron transfer: is biology (thermo)dynamic?

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

Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR

We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298-80 K temperature range. Our main tools were static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is nonexponential at all temperatures with the extent of nonexponentiality increasing from higher to lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al. J. Phys. Chem. B 2013, 117, 6129-6137), suggests that the hydrophobic core undergoes slow concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The crossover temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in softening the core and highlights aromatic residues as markers of the protein dynamical transitions.

(15)N CSA tensors and (15)N-(1)H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR

In this work, we assess the usefulness of static (15)N NMR techniques for the determination of the (15)N chemical shift anisotropy (CSA) tensor parameters and (15)N-(1)H dipolar splittings in powder protein samples. By using five single labeled samples of the villin headpiece subdomain protein in a hydrated lyophilized powder state, we determine the backbone (15)N CSA tensors at two temperatures, 22 and -35 °C, in order to get a snapshot of the variability across the residues and as a function of temperature. All sites probed belonged to the hydrophobic core and most of them were part of α-helical regions. The values of the anisotropy (which include the effect of the dynamics) varied between 130 and 156 ppm at 22 °C, while the values of the asymmetry were in the 0.32-0.082 range. The Leu-75 and Leu-61 backbone sites exhibited high mobility based on the values of their temperature-dependent anisotropy parameters. Under the assumption that most differences stem from dynamics, we obtained the values of the motional order parameters for the (15)N backbone sites. While a simple one-dimensional line shape experiment was used for the determination of the (15)N CSA parameters, a more advanced approach based on the "magic sandwich" SAMMY pulse sequence (Nevzorov and Opella, 2003) was employed for the determination of the (15)N-(1)H dipolar patterns, which yielded estimates of the dipolar couplings. Accordingly, the motional order parameters for the dipolar interaction were obtained. It was found that the order parameters from the CSA and dipolar measurements are highly correlated, validating that the variability between the residues is governed by the differences in dynamics. The values of the parameters obtained in this work can serve as reference values for developing more advanced magic-angle spinning recoupling techniques for multiple labeled samples.

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.