Mean square displacements from elastic incoherent neutron scattering evaluated by spectrometers working with different energy resolution on dry and hydrated (H2O and D2O) lysozyme

Capturing Hydrated Vanadium Ion Dynamics in Ionomer Nanocomposites Used for Redox Flow Batteries

Herein, we employed high-flux backscattering spectroscopy to capture for the first time the motions of hydrated vanadyl ions in ionomer nanocomposites prepared by both solution-cast and in situ sol-gel condensation methods. Both local and jump diffusion coefficients of the hydrated vanadyl (VO2+) ions as well as the dynamic length scales of ion motions and the fraction of immobile hydrogen atoms were extracted from the scattering spectra. Notably, for solution-cast membranes, the jump and local diffusion coefficients of hydrated VO2+ ions were seen to decrease by over 10- and 4-fold, respectively, with the introduction of 10 mass % silica nanoparticles (SiNPs) compared to their neat counterparts. Further, the VO2+ diffusion coefficients were observed to decrease with thermal annealing, though the impact of annealing was less significant than that seen with the introduction of SiNPs. Finally, in general, thermal annealing and the introduction of SiNPs had no measurable impact on the fraction of immobile hydrogen atoms in both solution-cast and sol-gel ionomer nanocomposites. The data observed in this work, in conjunction with previous structural and chain dynamics studies on hydrated Nafion-SiNP nanocomposites, suggest that a combination of stiffening of the segmental dynamics as well as a decrease in available sulfonic acid groups facilitating transport leads to an overall decrease in mobility of vanadium ions in these ionomer nanocomposites.

The Structural and Dynamical Properties of the Hydration of SNase Based on a Molecular Dynamics Simulation

The dynamics of protein–water fluctuations are of biological significance. Molecular dynamics simulations were performed in order to explore the hydration dynamics of staphylococcal nuclease (SNase) at different temperatures and mutation levels. A dynamical transition in hydration water (at ~210 K) can trigger larger-amplitude fluctuations of protein. The protein–water hydrogen bonds lost about 40% in the total change from 150 K to 210 K, while the Mean Square Displacement increased by little. The protein was activated when the hydration water in local had a comparable trend in making hydrogen bonds with protein– and other waters. The mutations changed the local chemical properties and the hydration exhibited a biphasic distribution, with two time scales. Hydrogen bonding relaxation governed the local protein fluctuations on the picosecond time scale, with the fastest time (24.9 ps) at the hydrophobic site and slowest time (40.4 ps) in the charged environment. The protein dynamic was related to the water’s translational diffusion via the relaxation of the protein–water’s H-bonding. The structural and dynamical properties of protein–water at the molecular level are fundamental to the physiological and functional mechanisms of SNase.

Experimental demonstration of the novel "van-Hove integral method (vHI)" for measuring diffusive dynamics by elastic neutron scattering

Quasi-elastic neutron scattering (QENS)-based on the seminal work of Nobel Laureate Brockhouse-has been one of the major methods for studying pico-second to nano-second diffusive dynamics over the past 70 years. This is regarded as an "inelastic" method for dynamics. In contrast, we recently proposed a new neutron-scattering method for dynamics, which uses the elastic line of the scattering to access system dynamics directly in the time domain (Benedetto and Kearley in Sci Rep 9:11284, 2019). This new method has been denoted "vHI" that stands for "van Hove Integral". The reason is that, under certain conditions, the measured elastic intensity corresponds to the running-time integral of the intermediate scattering function, [Formula: see text], up to a time that is inversely proportional to the energy band-width incident on the sample. As a result, [Formula: see text] is accessed from the time derivative of the measured vHI profile. vHI has been supported by numerical and Monte-Carlo simulations, but has been difficult to validate experimentally due to the lack of a suitable instrument. Here we show that vHI works in practice, which we achieved by using a simple modification to the standard QENS backscattering spectrometer methodology. Basically, we varied the neutron-energy band-widths incident at the sample via a step-wise variation of the frequency of the monochromator Doppler-drive. This provides a measurement of the vHI profile at the detectors. The same instrument and sample were also used in standard QENS mode for comparison. The intermediate scattering functions, [Formula: see text], obtained by the two methods-vHI and QENS-are strikingly similar providing a direct experimental validation of the vHI method. Perhaps surprisingly, the counting statistics of the two methods are comparable even though the instrument used was expressly designed for QENS. This shows that the methodology modification adopted here can be used in practice to access vHI profiles at many of the backscattering spectrometers worldwide. We also show that partial integrations of the measured QENS spectrum cannot provide the vHI profile, which clarifies a common misconception. At the same time, we show a novel approach which does access [Formula: see text] from QENS spectra.

From protein and its hydration water dynamics to controlling mechano-elasticity of cellular lipid membranes and cell migration via ionic liquids

In this invited Commentary, as requested, I will walk the reader through my research path starting from my first works on proteins and their hydration water dynamics to my most recent activity on the use of ionic liquids (ILs) as molecular handles to control and manipulate cell membrane mechano-elasticity and cell migration. In doing so I will comment on my research activity on polymers, proteins, natural bioprotectants, phospholipid bilayers, amyloids and cells, which I have carried out by combining several different experimental and computational approaches including neutron scattering, atomic force microscopy, classical molecular dynamics and ab initio calculations, used in tandem with several biological assays and a palette of complementary techniques ranging from calorimetry to static and dynamic light scattering. In parallel to this biophysical/chemical-physical core activity, a smaller portion of my interest and effort has been-I may say always-dedicated to the development of a new neutron scattering method/spectroscopy for dynamics based on "elastic" scattering. I will comment on this instrumental side of my research as well and show its relationship with the biophysical core of my activity. The overall picture that emerges is, from my personal prospective, of a coherent 13-year research path based on curiosity and a problem-solving approach, in which the fundamental importance of inter- and trans-disciplinary approaches and collaborations is emerging on the way, forecasting a prosper and intriguing future for physics in biology and in nanomedicine and bionanotechnology applications.

Evolution of the structure and dynamics of bovine serum albumin induced by thermal denaturation

Protein denaturation in concentrated solutions consists of the unfolding of the native protein structure, and subsequent cross-linking into clusters or gel networks. While the kinetic evolution of structure has been studied for some cases, the underlying microscopic dynamics of proteins has so far been neglected. However, protein dynamics is essential to understand the specific nature of assembly processes, such as diffusion-limited growth, or vitrification of dense liquids. Here, we present a study on thermal denaturation of concentrated solutions of bovine serum albumin (BSA) in D₂O with and without NaCl. Using small-angle scattering, we provide information on structure before, during and after denaturation. Using quasi-elastic neutron scattering, we monitor in real-time the microscopic dynamics and dynamical confinement throughout the entire denaturation process covering protein unfolding and cross-linking. After denaturation, the protein dynamics is slowed down in salty solutions compared to those in pure water, while the stability and dynamics of the native solution appears unaffected by salt. The approach presented here opens opportunities to link microscopic dynamics to emerging structural properties, with implications for assembly processes in soft and biological matter.

A Quantitative Comparison of the Counting Significance of van Hove Integral Spectroscopy and Quasielastic Neutron Scattering

We have recently proposed a new method to access system dynamics via neutron scattering based on measuring the elastic scattered intensity: By varying the energy band-width that impinges on the sample (also known as instrumental energy resolution), the purely elastic-scattering from this variation is the running time-integral of the intermediate scattering function (I(t)) [Benedetto and Kearley, Sci. Rep. 9, 11284, 2019]. In this correspondence we denote our method "vHI", which stands for "van Hove Integral". The method is now widely accepted as "valid" and here we focus on the efficiency of the vHI method compared with the standard quasi-elastic neutron scattering (QENS) method. We use a numerical Monte-Carlo simulation of an instrument that is equally capable of measuring QENS and vHI under identical conditions. For an "experiment" in which the same number of neutrons enter the instrument, we present comparisons between QENS and vHI at three levels of data-reduction. Firstly, at the raw-data level vHI achieves 100 times more neutrons at the detector than QENS. Secondly, vHI has a factor of 2 less statistical error, which would translate to an overall gain of 4 for vHI in counting-time. Lastly, we compare the distortions caused in obtaining the final I(t) via time-Fourier transform (QENS) and polynomial time-derivative (vHI). Here, the statistical error is 10 times smaller for vHI. This last comparison is the most important result where the 10 times smaller residual for vHI gives a net gain in counting time of 100 better than QENS to obtain the same underlying dynamics of the system under study.

Dynamics from elastic neutron-scattering via direct measurement of the running time-integral of the van Hove distribution function

We present a new neutron-scattering approach to access the van Hove distribution function directly in the time domain, I(t), which reflects the system dynamics. Currently, I(t) is essentially determined from neutron energy-exchange. Our method consists of the straightforward measurement of the running time-integral of I(t), by computing the portion of scattered neutrons corresponding to species at rest within a time t, (conceptually elastic scattering). Previous attempts failed to recognise this connection. Starting from a theoretical standpoint, a practical realisation is assessed via numerical methods and an instrument simulation.

Dynamic Neutron Scattering by Biological Systems

Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions detectable using neutrons in biological systems at physiological temperatures. New techniques for deriving information on collective motions using coherent scattering are also reviewed.

A high pressure study of calmodulin-ligand interactions using small-angle X-ray and elastic incoherent neutron scattering

Calmodulin (CaM) is a Ca²⁺ sensor and mediates Ca²⁺ signaling through binding of numerous target ligands. The binding of ligands by Ca²⁺-saturated CaM (holo-CaM) is governed by attractive hydrophobic and electrostatic interactions that are weakened under high pressure in aqueous solutions. Moreover, the potential formation of void volumes upon ligand binding creates a further source of pressure sensitivity. Hence, high pressure is a suitable thermodynamic variable to probe protein-ligand interactions. In this study, we compare the binding of two different ligands to holo-CaM as a function of pressure by using X-ray and neutron scattering techniques. The two ligands are the farnesylated hypervariable region (HVR) of the K-Ras4B protein, which is a natural binding partner of holo-CaM, and the antagonist trifluoperazine (TFP), which is known to inhibit holo-CaM activity. From small-angle X-ray scattering experiments performed up to 3000 bar, we observe a pressure-induced partial unfolding of the free holo-CaM in the absence of ligands, where the two lobes of the dumbbell-shaped protein are slightly swelled. In contrast, upon binding TFP, holo-CaM forms a closed globular conformation, which is pressure stable at least up to 3000 bar. The HVR of K-Ras4B shows a different binding behavior, and the data suggest the dissociation of the holo-CaM/HVR complex under high pressure, probably due to a less dense protein contact of the HVR as compared to TFP. The elastic incoherent neutron scattering experiments corroborate these findings. Below 2000 bar, pressure induces enhanced atomic fluctuations in both holo-CaM/ligand complexes, but those of the holo-CaM/HVR complex seem to be larger. Thus, the inhibition of holo-CaM by TFP is supported by a low-volume ligand binding, albeit this is not associated with a rigidification of the complex structure on the sub-ns Å-scale.

Inhibition of GNNQQNY prion peptide aggregation by trehalose: a mechanistic view

Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose concentration leads to faster expulsion of water molecules than interpeptide interactions. These expelled water molecules have larger translational movement, suggesting an entropy factor to favor the assembly process. Different conformations observed under this condition suggest the role of water molecules in guiding the morphology of the aggregates as well. A similar scenario exists on increasing peptide concentration.

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.

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.

The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering

Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.

Protein dynamics as seen by (quasi) elastic neutron scattering

BACKGROUND

Elastic and quasielastic neutron scattering studies proved to be efficient probes of the atomic mean square displacement (MSD), a fundamental parameter for the characterization of the motion of individual atoms in proteins and its evolution with temperature and compositional environment.

SCOPE OF REVIEW

We present a technical overview of the different types of experimental situations and the information quasi-elastic neutron scattering approaches can make available. In particular, MSD can crucially depend on the time scale over which the averaging (building of the "mean") takes place, being defined by the instrumental resolution. Due to their high neutron scattering cross section, hydrogen atoms can be particularly sensitively observed with little interference by the other atoms in the sample. A few examples, including new data, are presented for illustration.

MAJOR CONCLUSIONS

The incoherent character of neutron scattering on hydrogen atoms restricts the information obtained to the self-correlations in the motion of individual atoms, simplifying at the same time the data analysis. On the other hand, the (often overlooked) exploration of the averaging time dependent character of MSD is crucial for unambiguous interpretation and can provide a wealth of information on micro- and nanoscale atomic motion in proteins.

GENERAL SIGNIFICANCE

By properly exploiting the broad range capabilities of (quasi)elastic neutron scattering techniques to deliver time dependent characterization of atomic displacements, they offer a sensitive, direct and simple to interpret approach to exploration of the functional activity of hydrogen atoms in proteins. Partial deuteration can add most valuable selectivity by groups of hydrogen atoms. "This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".

Quasielastic neutron scattering in biology: Theory and applications

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Finally, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.

New generation non-stationary portable neutron generators for biophysical applications of Neutron Activation Analysis

BACKGROUND

Neutron sources are increasingly employed in a wide range of research fields. For some specific purposes an alternative to existing large-scale neutron scattering facilities, can be offered by the new generation of portable neutron devices.

SCOPE OF REVIEW

This review reports an overview for such recently available neutron generators mainly addressed to biophysics applications with specific reference to portable non-stationary neutron generators applied in Neutron Activation Analysis (NAA).

MAJOR CONCLUSIONS

The review reports a description of a typical portable neutron generator set-up addressed to biophysics applications.

GENERAL SIGNIFICANCE

New generation portable neutron devices, for some specific applications, can constitute an alternative to existing large-scale neutron scattering facilities. Deuterium-Deuterium pulsed neutron sources able to generate 2.5MeV neutrons, with a neutron yield of 1.0×10⁶n/s, a pulse rate of 250Hz to 20kHz and a duty factor varying from 5% to 100%, when combined with solid-state photon detectors, show that this kind of compact devices allow rapid and user-friendly elemental analysis. "This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".

Structural characterization in mixed lipid membrane systems by neutron and X-ray scattering

Lipids membranes, the primary component of the living cell, involve collective behaviour of numerous interacting molecules. The rich morphology and complex phase diagram of the lipid systems require different strategies in describing bio-membranes in order to capture the essential properties of self-assembly processes as well as the underling molecular collective phenomena involved in biological functions. Among the experimental methods used, the scattering techniques such as small angle neutrons and X-rays scattering (SANS and SAXS) are probably the most important experimental approaches for the structural investigation of bio-membranes and mixed lipids complex systems. In this tutorial review we describe the main approaches employed in the investigation of lipid bio-membranes by means of the neutron and x-ray scattering techniques. While introducing the main structural properties of lipid bio-membranes we highlight the important role of lipid components in different biological functions of living organisms. 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.

High-pressure dynamics of hydrated protein in bioprotective trehalose environment

We present a pressure-dependence study of the dynamics of lysozyme protein powder immersed in deuterated α,α-trehalose environment via quasielastic neutron scattering (QENS). The goal is to assess the baroprotective benefits of trehalose on biomolecules by comparing the findings with those of a trehalose-free reference study. While the mean-square displacement of the trehalose-free protein (hydrated to dD2O≃40 w%) as a whole, is reduced by increasing pressure, the actual observable relaxation dynamics in the picoseconds to nanoseconds time range remains largely unaffected by pressure--up to the maximum investigated pressure of 2.78(2) Kbar. Our observation is independent of whether or not the protein is mixed with the deuterated sugar. This suggests that the hydrated protein's conformational states at atmospheric pressure remain unaltered by hydrostatic pressures, below 2.78 Kbar. We also found the QENS response to be totally recoverable after ambient pressure conditions are restored. Small-angle neutron diffraction measurements confirm that the protein-protein correlation remains undisturbed. We observe, however, a clear narrowing of the QENS response as the temperature is decreased from 290 to 230 K in both cases, which we parametrize using the Kohlrausch-Williams-Watts stretched exponential model. Only the fraction of protons that are immobile on the accessible time window of the instrument, referred to as the elastic incoherent structure factor, is observably sensitive to pressure, increasing only marginally but systematically with increasing pressure.

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

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

Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and∕or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at Td from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature Tg. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature Td.

Protein dynamics by neutron scattering

Neutron scattering techniques represent a powerful tool for characterizing both the structure and dynamical properties of bio-systems, for example, proteins and membranes interacting with their solvents. In this paper, Elastic Neutron Scattering (ENS) data collected at the Institut Laue-Langevin (Grenoble, France) on dry and D2O hydrated lysozyme by varying hydration level are presented, and compared with previously published data on the same protein system, also with the addition of bio-protectants. The data have been collected with three different spectrometers, i.e. IN13, IN10 and IN4. This set of ENS data gives direct access to the temperature behavior of both (i) the Mean Square Displacement (MSD) and (ii) the characteristic system relaxation time. As a result, an explicative hypothesis on the relationship between the so-called "protein dynamical transition" (PDT) and the "fragile-to-strong dynamical crossover" (FSC) is formulated. Furthermore, by taking into proper account the effect of the finite instrumental energy resolution of the used spectrometers, the vibrational MSD of dry and hydrated lysozyme is calculated. The vibrational MSD of the lysozyme in the dry state resulted to be higher than the one in the hydrated state; the latter reaches the former at a temperature value of T=220K that corresponds to the temperature at which the FSC occurs. As a result, a cage effect resulting from the hydration water on the protein surface is hypothesized and subsequently linked to the FSC.

Temperature Dependence of Logarithmic-like Relaxational Dynamics of Hydrated tRNA

The dynamics of RNA within the β-relaxation region of 10 ps to 1 ns is crucial to its biological function. Because of its simpler chemical building blocks and the lack of the side methyl groups, faster relaxational dynamics of RNA compared to proteins can be expected. However, the situation is actually opposite. In this work, the relaxational dynamics of tRNA is measured by quasielastic neutron scattering and analyzed using the mode coupling theory, originally developed for glass-forming liquids. Our results reveal that the dynamics of tRNA follows a log-decay within the β-relaxation region, which is an important trait demonstrated by the dynamics of proteins. The dynamics of hydrated tRNA and lysozyme compared in the time domain further demonstrate that the slower dynamics of tRNA relative to proteins originates from the difference in the folded states of tRNA and proteins, as well as the influence of their hydration water.

Dynamic behavior of oligomeric inorganic pyrophosphatase explored by quasielastic neutron scattering

The purpose of this investigation is to determine whether a large oligomeric protein, inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens with quaternary structural complexity, would have distinguishable dynamic characteristics compared to those of the small simple monomeric model protein, lysozyme. In this study, the β-relaxational dynamics of the two proteins, IPPase and lysozyme, are compared in the 10 ps to 0.5 ns time interval using quasi-elastic neutron scattering (QENS). Both of the protein dynamics show a characteristic logarithmic-like decay in the intermediate scattering function (ISF) of the hydrogen atoms. Distinguishable dynamical behavior found between two proteins reveals local flexibility and conformational substates unique to oligomeric structures. Moreover, the temperature dependence of the mean square displacement (MSD) of the hydrogen atoms in protein molecules, which is a traditional way to determine the "softness" of the protein molecule, is measured and shows no difference for the two proteins.

Intrinsic mean-square displacements in proteins

The thermal mean-square displacement (MSD) of hydrogen in proteins and its associated hydration water is measured by neutron scattering experiments and used an indicator of protein function. The observed MSD as currently determined depends on the energy resolution width of the neutron scattering instrument employed. We propose a method for obtaining the intrinsic MSD of H in the proteins, one that is independent of the instrument resolution width. The intrinsic MSD is defined as the infinite time value of (r(2)) that appears in the Debye-Waller factor. The method consists of fitting a model to the resolution broadened elastic incoherent structure factor or to the resolution dependent MSD. The model contains the intrinsic MSD, the instrument resolution width, and a rate constant characterizing the motions of H in the protein. The method is illustrated by obtaining the intrinsic MSD (r(2)) of heparan sulphate (HS-0.4), ribonuclease A, and staphysloccal nuclase (SNase) from data in the literature.

Dynamic properties of photosystem II membranes at physiological temperatures characterized by elastic incoherent neutron scattering. Increased flexibility associated with the inactivation of the oxygen evolving complex

Elastic incoherent neutron scattering (EINS), a non-invasive technique which is capable of measuring the mean square displacement of atoms in the sample, has been widely used in biology for exploring the dynamics of proteins and lipid membranes but studies on photosynthetic systems are scarce. In this study we investigated the dynamic characteristics of Photosystem II (PSII) membrane fragments between 280 and 340 K, i.e., in the physiological temperature range and in the range of thermal denaturation of some of the protein complexes. The mean square displacement values revealed the presence of a hydration-sensitive transition in the sample between 310 and 320 K, suggesting that the oxygen evolving complex (OEC) plays an important role in the transition. Indeed, in samples in which the OEC had been removed by TRIS- or heat-treatments (323 and 333 K) no such transition was found. Further support on the main role of OEC in these reorganizations is provided by data obtained from differential scanning calorimetry experiments, showing marked differences between the untreated and TRIS-treated samples. In contrast, circular dichroism spectra exhibited only minor changes in the excitonic interactions below 323 K, showing that the molecular organization of the pigment-protein complexes remains essentially unaffected. Our data, along with earlier incoherent neutron scattering data on PSII membranes at cryogenic temperatures (Pieper et al., Biochemistry 46:11398-11409, 2007), demonstrate that this technique can be applied to characterize the dynamic features of PSII membranes, and can be used to investigate photosynthetic membranes under physiologically relevant experimental conditions.

Bio-protective effects of homologous disaccharides on biological macromolecules

In this contribution the effects of the homologous disaccharides trehalose and sucrose on both water and hydrated lysozyme dynamics are considered by determining the mean square displacement (MSD) from elastic incoherent neutron scattering (EINS) experiments. The self-distribution function (SDF) procedure is applied to the data collected, by use of IN13 and IN10 spectrometers (Institute Laue Langevin, France), on trehalose and sucrose aqueous mixtures (at a concentration corresponding to 19 water molecules per disaccharide molecule), and on dry and hydrated (H(2)O and D(2)O) lysozyme also in the presence of the disaccharides. As a result, above the glass transition temperature of water, the MSD of the water-trehalose system is lower than that of the water-sucrose system. This result suggests that the hydrogen-bond network of the water-trehalose system is stronger than that of the water-sucrose system. Furthermore, by taking into account instrumental resolution effects it was found that the system relaxation time of the water-trehalose system is longer than that of the water-sucrose system, and the system relaxation time of the protein in a hydrated environment in the presence of disaccharides increases sensitively. These results explain the higher bioprotectant effectiveness of trehalose. Finally, the partial MSDs of sucrose/water and trehalose/water have been evaluated. It clearly emerges from the analysis that these are almost equivalent in the low-Q domain (0-1.7 Å(-1)) but differ substantially in the high-Q range (1.7-4 Å(-1)). These findings reveal that the lower structural sensitivity of trehalose to thermal changes is connected with the local spatial scale.

Elastic incoherent neutron scattering operating by varying instrumental energy resolution: principle, simulations, and experiments of the resolution elastic neutron scattering (RENS)

The main aim of this paper is to present the scientific case of the resolution elastic neutron scattering (RENS) method that is based on the collection of elastic neutron scattering intensity as a function of the instrumental energy resolution and that is able to extract information on the system dynamical properties from an elastic signal. In this framework, it is shown that in the measured elastic scattering law, as a function of the instrumental energy resolution, an inflection point occurs when the instrumental energy resolution intersects the system relaxation time, and in an equivalent way, a transition in the temperature behavior of the measured elastic scattering law occurs when the characteristic system relaxation time crosses the instrumental energy resolution time. With regard to the latter, an operative protocol to determine the system characteristic time by different elastic incoherent neutron scattering (EINS) thermal scans at different instrumental energy resolutions is also proposed. The proposed method, hence, is not primarily addressed to collect the measured elastic scattering intensity with a great accuracy, but rather relies on determining an inflection point in the measured elastic scattering law versus instrumental energy resolution. The RENS method is tested both numerically and experimentally. As far as numerical simulations are concerned, a simple model system for which the temperature behavior of the relaxation time follows an Arrhenius law, while its scattering law follows a Gaussian behavior, is considered. It is shown that the system relaxation time used as an input for the simulations coincides with the one obtained by the RENS approach. Regarding the experimental findings, due to the fact that a neutron scattering spectrometer working following the RENS method has not been constructed yet, different EINS experiments with different instrumental energy resolutions were carried out on a complex model system, i.e., dry and D(2)O hydrated lysozyme, in an extended temperature range. The resulting temperature behavior of the system relaxation time, obtained with RENS method, agrees very well with the one obtained in literature, for the same system, following the quasi-elastic neutron scattering (QENS) approach. The proposed scientific case puts into evidence the challenges of an RENS spectrometer working by varying the instrumental energy resolution; in particular, in comparison with QENS, the proposed RENS method requires a smaller amount of sample, which is an important point in dealing with biological and exotic systems; it is not affected by the use of model functions for fitting spectra as in QENS, but furnishes a direct access to relevant information.

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.

Puzzle of protein dynamical transition

Despite recent extensive efforts, the nature of the dynamics of biological macromolecules still remains unclear. In particular, contradicting models have been proposed for explaining the temperature behavior of the mean square displacement, MSD, and of the system relaxation time, τ. To solve this puzzle, different neutron scattering experiments with different instrumental energy resolutions were performed on dry and hydrated lysozyme. The obtained results show that the so called dynamical transition: (i) is a finite instrumental energy resolution effect, and more specifically, it appears when the characteristic system relaxation time intersects the resolution time, (ii) it does not imply any transition in the dynamical properties of the systems, (iii) it is not due to the fragile-to-strong dynamical crossover (FSC) in the temperature behavior of the system relaxation time, differently to what S. H. Chen et al. proposed [Proc. Natl. Acad. Sci. U.S.A.2006, 103, 9012]. Furthermore, the obtained results confirm the change in the τ-temperature dependence at T = 220 K of S. H. Chen et al., and show that it is not due to finite instrumental energy resolution effects and it is not connected to numerical errors in the data analysis protocol, differently to what W. Doster et al. proposed [Phys. Rev. Lett.2010, 104, 098101].