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Zeller D, Telling MTF, Zamponi M, García Sakai V, Peters J. Analysis of elastic incoherent neutron scattering data beyond the Gaussian approximation. J Chem Phys 2018; 149:234908. [PMID: 30579322 DOI: 10.1063/1.5049938] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This work addresses the use of the Gaussian approximation as a common tool to extract atomic motions in proteins from elastic incoherent neutron scattering and whether improvements in data analysis and additional information can be obtained when going beyond that. We measured alpha-lactalbumin with different levels of hydration on three neutron backscattering spectrometers, to be able to resolve a wide temporal and spatial range for dynamics. We demonstrate that the Gaussian approximation gives qualitatively similar results to models that include heterogeneity, if one respects a certain procedure to treat the intercept of the elastic intensities with the momentum transfer axis. However, the inclusion of motional heterogeneity provides better fits to the data. Our analysis suggests an approach of limited heterogeneity, where including only two kinds of motions appears sufficient to obtain more quantitative results for the mean square displacement. Finally, we note that traditional backscattering spectrometers pose a limit on the lowest accessible momentum transfer. We therefore suggest that complementary information about the spatial evolution of the elastic intensity close to zero momentum transfer can be obtained using other neutron methods, in particular, neutron spin-echo together with polarization analysis.
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Affiliation(s)
- D Zeller
- Université Grenoble Alpes, CNRS, LiPhy, 140 av. de la Physique, 38000 Grenoble, France
| | - M T F Telling
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 0QX, United Kingdom
| | - M Zamponi
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748 Garching, Germany
| | - V García Sakai
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 0QX, United Kingdom
| | - J Peters
- Université Grenoble Alpes, CNRS, LiPhy, 140 av. de la Physique, 38000 Grenoble, France
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Mamontov E. A novel approach to neutron scattering instrumentation for probing multiscale dynamics in soft and biological matter. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:345201. [PMID: 27355223 DOI: 10.1088/0953-8984/28/34/345201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We present a concept and ray-tracing simulation of a mechanical device that will enable inelastic neutron scattering measurements where the data at energy transfers from a few μeV to several hundred meV can be collected in a single, gapless spectrum. Besides covering 5 orders of magnitude on the energy (time) scale, the device provides data over 2 orders of magnitude on the scattering momentum (length) scale in a single measurement. Such capabilities are geared primarily toward soft and biological matter, where the broad dynamical features of relaxation origin largely overlap with vibration features, thus necessitating gapless spectral coverage over several orders of magnitude in time and space. Furthermore, neutron scattering experiments with such a device are performed with a fixed neutron final energy, which enables measurements, with neutron energy loss in the sample, at arbitrarily low temperatures over the same broad spectral range. This capability is also invaluable in biological and soft matter research, as the variable temperature dependence of different relaxation components allows their separation in the scattering spectra as a function of temperature.
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Affiliation(s)
- Eugene Mamontov
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Vural D, Hu X, Lindner B, Jain N, Miao Y, Cheng X, Liu Z, Hong L, Smith JC. Quasielastic neutron scattering in biology: Theory and applications. Biochim Biophys Acta Gen Subj 2016; 1861:3638-3650. [PMID: 27316321 DOI: 10.1016/j.bbagen.2016.06.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/08/2016] [Accepted: 06/09/2016] [Indexed: 02/03/2023]
Abstract
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.
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Affiliation(s)
- Derya Vural
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Xiaohu Hu
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Benjamin Lindner
- Institute of Natural Sciences & Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240, China
| | - Nitin Jain
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Yinglong Miao
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Xiaolin Cheng
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Zhuo Liu
- Institute of Natural Sciences & Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240, China
| | - Liang Hong
- Institute of Natural Sciences & Department of Physics and Astronomy, Shanghai Jiao Tong University, 200240, China
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
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Aoun B, Pellegrini E, Trapp M, Natali F, Cantù L, Brocca P, Gerelli Y, Demé B, Marek Koza M, Johnson M, Peters J. Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of DMPC phase transitions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:48. [PMID: 27112937 DOI: 10.1140/epje/i2016-16048-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
Neutron scattering techniques have been employed to investigate 1,2-dimyristoyl-sn -glycero-3-phosphocholine (DMPC) membranes in the form of multilamellar vesicles (MLVs) and deposited, stacked multilamellar-bilayers (MLBs), covering transitions from the gel to the liquid phase. Neutron diffraction was used to characterise the samples in terms of transition temperatures, whereas elastic incoherent neutron scattering (EINS) demonstrates that the dynamics on the sub-macromolecular length-scale and pico- to nano-second time-scale are correlated with the structural transitions through a discontinuity in the observed elastic intensities and the derived mean square displacements. Molecular dynamics simulations have been performed in parallel focussing on the length-, time- and temperature-scales of the neutron experiments. They correctly reproduce the structural features of the main gel-liquid phase transition. Particular emphasis is placed on the dynamical amplitudes derived from experiment and simulations. Two methods are used to analyse the experimental data and mean square displacements. They agree within a factor of 2 irrespective of the probed time-scale, i.e. the instrument utilized. Mean square displacements computed from simulations show a comparable level of agreement with the experimental values, albeit, the best match with the two methods varies for the two instruments. Consequently, experiments and simulations together give a consistent picture of the structural and dynamical aspects of the main lipid transition and provide a basis for future, theoretical modelling of dynamics and phase behaviour in membranes. The need for more detailed analytical models is pointed out by the remaining variation of the dynamical amplitudes derived in two different ways from experiments on the one hand and simulations on the other.
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Affiliation(s)
- Bachir Aoun
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Eric Pellegrini
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Marcus Trapp
- Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120, Heidelberg, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Lise-Meitner Campus, Hahn-Meitner-Platz 1, 14109, Berlin, Germany
| | - Francesca Natali
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
- CNR-IOM-OGG, c/o Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Laura Cantù
- University of Milan, via F. lli Cervi 93, 20090, Segrate, Italy
| | - Paola Brocca
- University of Milan, via F. lli Cervi 93, 20090, Segrate, Italy
| | - Yuri Gerelli
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Bruno Demé
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Michael Marek Koza
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Mark Johnson
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Judith Peters
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France.
- LiPhy, UFR PhITEM, Univ. Grenoble Alpes, 71 avenue des Martyrs, CS 10090, 38044, Grenoble, France.
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