Biomolecular motion characterization by a self-distribution-function procedure in elastic incoherent neutron scattering

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.

Stiffening Effect of the [Bmim][Cl] Ionic Liquid on the Bending Dynamics of DMPC Lipid Vesicles

The elastic properties of the cellular lipid membrane play a crucial role for life. Their alteration can lead to cell malfunction, and in turn, being able to control them holds the promise of effective therapeutic and diagnostic approaches. In this context, due to their proven strong interaction with lipid bilayers, ionic liquids (ILs)-a vast class of organic electrolytes-may play an important role. This work focuses on the effect of the model imidazolium-IL [bmim][Cl] on the bending modulus of DMPC lipid vesicles, a basic model of cellular lipid membranes. Here, by combining small-angle neutron scattering and neutron spin-echo spectroscopy, we show that the IL, dispersed at low concentrations at the bilayer-water interface, (i) diffuses into the lipid region, accounting for five IL-cations for every 11 lipids, and (ii) causes an increase of the lipid bilayer bending modulus, up to 60% compared to the neat lipid bilayer at 40 °C.

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.

Room-temperature ionic liquids meet bio-membranes: the state-of-the-art

Room-temperature ionic liquids (RTIL) are a new class of organic salts whose melting temperature falls below the conventional limit of 100 °C. Their low vapor pressure, moreover, has made these ionic compounds the solvents of choice of the so-called green chemistry. For these and other peculiar characteristics, they are increasingly used in industrial applications. However, studies of their interaction with living organisms have highlighted mild to severe health hazards. Since their cytotoxicity shows a positive correlation with their lipophilicity, several chemical-physical studies of their interactions with biomembranes have been carried out in the last few years, aiming to identify the molecular mechanisms behind their toxicity. Cation chain length and anion nature of RTILs have seemed to affect lipophilicity and, in turn, their toxicity. However, the emerging picture raises new questions, points to the need to assess toxicity on a case-by-case basis, but also suggests a potential positive role of RTILs in pharmacology, bio-medicine and bio-nanotechnology. Here, we review this new subject of research, and comment on the future and the potential importance of this emerging field of study.

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".

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.

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.

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.

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].

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

The main aim of the present paper is the evaluation of the effects of the instrumental energy resolution on the mean square displacement (MSD) obtained by elastic incoherent neutron scattering (EINS). In particular, this study is performed in the time domain, through the time-Fourier transform of the elastically scattered neutron intensity, and is mainly focused on the connection between the system MSD and the measured MSD. It is shown how in the case of EINS, the instrumental energy resolution gives rise to the time integration of the time-dependent system MSD function weighted in time by the resolution function. The formulated approach is applied to the data collected on dry and hydrated (H(2)O and D(2)O with h = 0.4) lysozyme samples by two spectrometers working with a different instrumental resolution (the IN10 and IN13 spectrometers of the Institute Laue-Langevin). As a result, the procedure furnishes an excellent agreement for the system MSD evaluated in the low temperature range up to T = 40 K.

Motion characterization by self-distribution-function procedure

In the present paper a procedure for the biomolecular motion characterization based on the evaluation of the Mean Square Displacement (MSD), through the Self Distribution Function (SDF), is presented. In particular it will be shown how the MSD, which represents a good observable for the characterization of the dynamical properties in disordered systems, can be decomposed into partial contributions associated to the system dynamical processes within a specific spatial scale. It will be shown how the SDF procedure allows to evaluate both the total MSD and the partial MSDs through the total SFD and the partial SDFs. As a result, the total MSD is the weighed sum of the partial MSD contributions in which the weights are obtained by the fitting procedure of measured EINS intensity data. We apply the SDF procedure at EINS data collected, by the IN13 backscattering spectrometer at the Institute Laue-Langevin, Grenoble, on aqueous mixtures of two homologous disaccharides (sucrose and trehalose) and on dry myoglobin in trehalose environment. It emerges that the hydrogen bond imposed network of the water-trehalose mixture appears to be stronger with respect to that of the water-sucrose mixture and this result can justify the highest bioprotectant effectiveness of trehalose in comparison with sucrose. Furthermore it emerges that, the partial MSD behaviours of sucrose and trehalose are equivalent in the low Q domain (0-1.7) A(-1) whereas they are different in the high Q domain (1.7-4) A(-)(1). This circumstance suggests that the higher structure sensitivity of sucrose in respect to trehalose should be related to the small spatial observation windows.