Incoherent elastic neutron scattering as a function of temperature : A fast way to characterise in-situ biological dynamics in complex solutions (original) (raw)
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The Journal of Chemical Physics, 2013
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 T d 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 T g . The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature T d .
Journal of The Royal Society Interface, 2013
In vivo molecular dynamics in Halobacterium salinarum cells under stress conditions was measured by neutron scattering experiments coupled with microbiological characterization. Molecular dynamics alterations were detected with respect to unstressed cells, reflecting a softening of protein structures consistent with denaturation. The experiments indicated that the neutron scattering method provides a promising tool to study molecular dynamics modifications in the proteome of living cells induced by factors altering protein folds.
Protein dynamics studied by neutron scattering
Quarterly Reviews of Biophysics, 2002
1. Introduction 3282. Basic concepts of neutron scattering 3292.1 Introduction 3292.2 Neutron-scattering functions 3312.3 Coherent and incoherent neutron scattering. The particular role of hydrogen in incoherent scattering 3322.4 Total elastic scattering, EISF and mean square displacement (MSD) 3332.5 Quasielastic scattering and relaxation function 3342.6 Inelastic scattering and density of states 3353. Experimental aspects and instruments 3353.1 Energy and space resolution 3353.2 General sample aspects 3353.3 Potential effects of D2O on dynamics 3363.4 Experimental 2H (deuterium) labelling 3364. Physics of protein dynamics 3364.1 Models 3364.2 The dynamical transition 3384.3 Effective force constants 3395. Dynamics of hydrated protein powders 3395.1 First experiments on myoglobin 3405.2 Dynamical transitions in other proteins 3405.3 The role of hydration water 3415.4 Influence of the solvent 3445.5 Diffusional motions within proteins by QENS 3465.6 Inelastic neutron scattering and ...
The Journal of Chemical Physics, 2008
In the present work the role played by the instrumental resolution function in elastic incoherent neutron scattering (EINS) experiment is discussed. An important result consists in the definition of an equivalent time t*, which depends both on the characteristic system time and on the resolution time, for which the spatial Fourier transform of EINS intensity profile and the self-distribution function (SDF) evaluated at t=t* are proportional. Then the equivalent time t* is introduced in the SDF procedure, an operational recipe for the mean square displacement determination. The new revised procedure is applied on data of myoglobin in trehalose dry environment and of hydrated homologous disaccharides (sucrose and trehalose).
Temperature dependence of protein dynamics as affected by sugars: a neutron scattering study
2007
Neutron scattering data on lysozyme-trehalose and lysozyme-sucrose aqueous mixtures, and on trehalose and sucrose aqueous mixtures are presented for a wide temperature range. Although the degree of protein coupling to solvent seems to be an open question in the literature, we present evidence that seems to be a firm link between a local dynamics of the protein with that of the glassy host. One of the objectives of this study was to explore the relationship between protein dynamics and glassy host. Measuring the <u 2 > of lysozyme mixtures, we arrive at a qualitative description of how their thermal stability is affected by the presence of two sugars at different temperatures. Whereas the Q dependence of the elastic incoherent structure factor gives information about the geometry and the amplitudes of the motions.
Determination of Dynamical Heterogeneity from Dynamic Neutron-Scattering of Proteins
Biophysical journal, 2018
Motional displacements of hydrogen (H) in proteins can be measured using incoherent neutron-scattering methods. These displacements can also be calculated numerically using data from molecular dynamics simulations. An enormous amount of data on the average mean-square motional displacement (MSD) of H as a function of protein temperature, hydration, and other conditions has been collected. H resides in a wide spectrum of sites in a protein. Some H are tightly bound to molecular chains, and the H motion is dictated by that of the chain. Other H are quite independent. As a result, there is a distribution of motions and MSDs of H within a protein that is denoted dynamical heterogeneity. The goal of this paper is to incorporate a distribution of MSDs into models of the H incoherent intermediate scattering function, I(Q,t), that is calculated and observed. The aim is to contribute information on the distribution as well as on the average MSD from comparison of the models with simulations ...
Journal of Neutron Research, 2002
Neutron high resolution spectroscopic studies of biomolecular dynamics have been pursued actively in the last decade. They probe macromolecular thermal dynamics in a space-time window of about 1-10 Å and 10-1000 ps, which is involved in biological activity, because this window corresponds to the motions of H-atoms bound to larger groups such as the amino acid side chains. As a result of advances in instrumentation and data analysis methods, it is nowadays possible to obtain quantitative information on the complex low frequency motions exhibited by biologically active systems. In the near future, the advent of new sources and the availability of dedicated instruments will make it possible to extend these studies from "pure" systems, like single proteins, towards more complex ones as protein-lipid and protein-DNA complexes, glyco-lipid systems, ribosomes and even whole cells. Some selected examples highlighting possible future research areas will be illustrated.
The power of quasielastic neutron scattering to probe biophysical systems
Physica B: Condensed Matter, 1993
Neutron high-resolution spectroscopic studies of biomolecular dynamics have been pursued actively in the last decade due to the recognised role of the microscopic dynamics in determining the functional properties of many biomolecular assemblies. As a result of instrumental advances and progress in molecular dynamics simulations it is nowadays possible to describe quantitatively the complex low-frequency motions exhibited by biologically active systems. Some selected examples referring to different biopolymers and biological membranes will be illustrated.
Physica B: Condensed Matter, 2004
The dynamic structure factors in (Q,o)-space were calculated by using the results of biomolecular simulations at a wide range of temperature from 100 to 300 K. Three types of simulation, normal mode analysis, molecular dynamics in vacuum, and molecular dynamics in water were applied to HEW Lysozyme. The shapes of the three dynamic structure factors in (Q,o)-space are in good agreement in high-frequency regions (>10 meV), but considerably different in low-frequency regions (o10 meV) throughout the temperature range studied here. At cryogenic temperature, the socalled boson peak is observed only in the results of molecular dynamics in water. From these results, we discuss the (Q,o)-range and the resolution of a detector needed to observe function-related protein dynamics. Proposal of such a detector to be used in J-PARC is made. r