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Conti Nibali V, Sacchetti F, Paciaroni A, Petrillo C, Tarek M, D'Angelo G. Intra-protein interacting collective modes in the terahertz frequency region. J Chem Phys 2023; 159:161101. [PMID: 37870134 DOI: 10.1063/5.0142381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
Understanding how proteins work requires a thorough understanding of their internal dynamics. Proteins support a wide range of motions, from the femtoseconds to seconds time scale, relevant to crucial biological functions. In this context, the term "protein collective dynamics" refers to the complex patterns of coordinated motions of numerous atoms throughout the protein in the sub-picosecond time scale (terahertz frequency region). It is hypothesized that these dynamics have a substantial impact on the regulation of functional dynamical mechanisms, including ligand binding and allosteric signalling, charge transport direction, and the regulation of thermodynamic and thermal transport properties. Using the theoretical framework of hydrodynamics, the collective dynamics of proteins had previously been described in a manner akin to that of simple liquids, i.e. in terms of a single acoustic-like excitation, related to intra-protein vibrational motions. Here, we employ an interacting-mode model to analyse the results from molecular dynamics simulations and we unveil that the vibrational landscape of proteins is populated by multiple acoustic-like and low-frequency optic-like modes, with mixed symmetry and interfering with each other. We propose an interpretation at the molecular level of the observed scenario that we relate to the side-chains and the hydrogen-bonded networks dynamics. The present insights provide a perspective for understanding the molecular mechanisms underlying the energy redistribution processes in the interior of proteins.
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Affiliation(s)
- Valeria Conti Nibali
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science, Messina University, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Francesco Sacchetti
- Department of Physics and Geology, Perugia University, Via Alessandro Pascoli, I-06123 Perugia, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, Perugia University, Via Alessandro Pascoli, I-06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, Perugia University, Via Alessandro Pascoli, I-06123 Perugia, Italy
| | - Mounir Tarek
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Giovanna D'Angelo
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science, Messina University, Viale Ferdinando Stagno D'Alcontres 31, 98166 Messina, Italy
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2
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Sala G, Mourigal M, Boone C, Butch NP, Christianson AD, Delaire O, DeSantis AJ, Hart CL, Hermann RP, Huegle T, Kent DN, Lin JYY, Lumsden MD, Manley ME, Quirinale DG, Stone MB, Z Y. CHESS: The future direct geometry spectrometer at the second target station. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:065109. [PMID: 35778024 DOI: 10.1063/5.0089740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
CHESS, chopper spectrometer examining small samples, is a planned direct geometry neutron chopper spectrometer designed to detect and analyze weak signals intrinsic to small cross sections (e.g., small mass, small magnetic moments, or neutron absorbing materials) in powders, liquids, and crystals. CHESS is optimized to enable transformative investigations of quantum materials, spin liquids, thermoelectrics, battery materials, and liquids. The broad dynamic range of the instrument is also well suited to study relaxation processes and excitations in soft and biological matter. The 15 Hz repetition rate of the Second Target Station at the Spallation Neutron Source enables the use of multiple incident energies within a single source pulse, greatly expanding the information gained in a single measurement. Furthermore, the high flux grants an enhanced capability for polarization analysis. This enables the separation of nuclear from magnetic scattering or coherent from incoherent scattering in hydrogenous materials over a large range of energy and momentum transfer. This paper presents optimizations and technical solutions to address the key requirements envisioned in the science case and the anticipated uses of this instrument.
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Affiliation(s)
- G Sala
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M Mourigal
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - C Boone
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - N P Butch
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - A D Christianson
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - O Delaire
- Department of Physics, Duke University, Durham, North Carolina 27708, USA
| | - A J DeSantis
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - C L Hart
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - R P Hermann
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - T Huegle
- Neutron Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D N Kent
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J Y Y Lin
- Spallation Neutron Source, Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M D Lumsden
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M E Manley
- Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - D G Quirinale
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - M B Stone
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Y Z
- Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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3
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Zhai Y, Luo P, Waller J, Self JL, Harriger LW, Z Y, Faraone A. Dynamics of molecular associates in methanol/water mixtures. Phys Chem Chem Phys 2022; 24:2287-2299. [PMID: 35015001 DOI: 10.1039/d1cp04726d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of molecular associates in a methanol/water mixture was investigated using quasielastic neutron scattering. By measuring the signal from four methanol/water samples differing only by their isotopic composition, the relative motion of the water to methanol molecules, i.e. their mutual dynamics, was determined at the nanoscale. The thus obtained nanoscopic mutual diffusion coefficient signals a significantly slower process than the single particle diffusion of either methanol or water in the system as well as their macroscopic mutual diffusion. The data do not provide any indication of microsegregation in this preeminent alcohol/water mixture; however, they do indicate the existence of long lived but dynamic molecular associates of water and methanol molecules. Analysis of the structural relaxation shows that the lifetime of molecular association through hydrogen bonding determines the fact that viscosity of the mixtures at intermediate concentrations is higher than that of both pure components.
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Affiliation(s)
- Yanqin Zhai
- Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Peng Luo
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jackson Waller
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Jeffrey L Self
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Leland W Harriger
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
| | - Y Z
- Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
| | - Antonio Faraone
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
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4
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Zheng L, Liu Z, Zhang Q, Li S, Huang J, Zhang L, Zan B, Tyagi M, Cheng H, Zuo T, Sakai VG, Yamada T, Yang C, Tan P, Jiang F, Chen H, Zhuang W, Hong L. Universal dynamical onset in water at distinct material interfaces. Chem Sci 2022; 13:4341-4351. [PMID: 35509458 PMCID: PMC9006901 DOI: 10.1039/d1sc04650k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Interfacial water remains liquid and mobile much below 0 °C, imparting flexibility to the encapsulated materials to ensure their diverse functions at subzero temperatures. However, a united picture that can describe the dynamical differences of interfacial water on different materials and its role in imparting system-specific flexibility to distinct materials is lacking. By combining neutron spectroscopy and isotope labeling, we explored the dynamics of water and the underlying substrates independently below 0 °C across a broad range of materials. Surprisingly, while the function-related anharmonic dynamical onset in the materials exhibits diverse activation temperatures, the surface water presents a universal onset at a common temperature. Further analysis of the neutron experiment and simulation results revealed that the universal onset of water results from an intrinsic surface-independent relaxation: switching of hydrogen bonds between neighboring water molecules with a common energy barrier of ∼35 kJ mol−1. We demonstrated that the dynamical onset of interfacial water is an intrinsic property of water itself, resulting from a surface independent relaxation process in water with an approximately universal energy barrier of ∼35 kJ mol−1.![]()
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Affiliation(s)
- Lirong Zheng
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Zhuo Liu
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Zhang
- College of Chemistry and Materials Science, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028043, China
| | - Song Li
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Zhang
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Zan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - He Cheng
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Taisen Zuo
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Victoria García Sakai
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, UK
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
| | - Chenxing Yang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pan Tan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Liang Hong
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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5
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Nakagawa H, Appavou MS, Wuttke J, Zamponi M, Holderer O, Schrader TE, Richter D, Doster W. Nanosecond structural dynamics of intrinsically disordered β-casein micelles by neutron spectroscopy. Biophys J 2021; 120:5408-5420. [PMID: 34717964 PMCID: PMC8715185 DOI: 10.1016/j.bpj.2021.10.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 09/17/2021] [Accepted: 10/13/2021] [Indexed: 10/20/2022] Open
Abstract
β-casein undergoes a reversible endothermic self-association, forming protein micelles of limited size. In its functional state, a single β-casein monomer is unfolded, which creates a high structural flexibility, which is supposed to play a major role in preventing the precipitation of calcium phosphate particles. We characterize the structural flexibility in terms of nanosecond molecular motions, depending on the temperature by quasielastic neutron scattering. Our major questions are: Does the self-association reduce the chain flexibility? How does the dynamic spectrum of disordered caseins differ from a compactly globular protein? How does the dynamic spectrum of β-casein in solution differ from that of a protein in hydrated powder states? We report on two relaxation processes on a nanosecond and a sub-nanosecond timescale for β-casein in solution. Both processes are analyzed by Brownian oscillator model, by which the spring constant can be defined in the isotropic parabolic potential. The slower process, which is analyzed by neutron spin echo, seems a characteristic feature of the unfolded structure. It requires bulk solvent and is not seen in hydrated protein powders. The faster process, which is analyzed by neutron backscattering, has a smaller amplitude and requires hydration water, which is also observed with folded proteins in the hydrated state. The self-association had no significant influence on internal relaxation, and thus, a β-casein protein monomer flexibility is preserved in the micelle. We derive spring constants of the faster and slower motions of β-caseins in solution and compared them with those of some proteins in various states (folded or hydrated powder).
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Affiliation(s)
- Hiroshi Nakagawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan; Forschungszentrum Jülich, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Germany; J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan.
| | - Marie-Sousai Appavou
- Forschungszentrum Jülich, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Germany
| | - Joachim Wuttke
- Forschungszentrum Jülich, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Germany
| | - Michaela Zamponi
- Forschungszentrum Jülich, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Germany
| | - Olaf Holderer
- Forschungszentrum Jülich, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Germany
| | - Tobias E Schrader
- Forschungszentrum Jülich, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Germany
| | - Dieter Richter
- Forschungszentrum Jülich, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Germany
| | - Wolfgang Doster
- Technische Universität München, Physik-Department, Garching, Germany
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6
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Okudaira T, Ueda Y, Hiroi K, Motokawa R, Inamura Y, Takata SI, Oku T, Suzuki JI, Takahashi S, Endo H, Iwase H. Polarization analysis for small-angle neutron scattering with a 3He spin filter at a pulsed neutron source. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721001643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Neutron polarization analysis (NPA) for small-angle neutron scattering (SANS) experiments using a pulsed neutron source was successfully achieved by applying a 3He spin filter as a spin analyzer for the neutrons scattered from the sample. The cell of the 3He spin filter gives a weak small-angle scattering intensity (background) and covers a sufficient solid angle for performing SANS experiments. The relaxation time of the 3He polarization is sufficient for continuous use for approximately 2 days, thus reaching the typical duration required for a complete set of SANS experiments. Although accurate evaluation of the incoherent neutron scattering, which is predominantly attributable to the extremely large incoherent scattering cross section of hydrogen atoms in samples, is difficult using calculations based on the sample elemental composition, the developed NPA approach with consideration of the influence of multiple neutron scattering enabled reliable decomposition of the SANS intensity distribution into the coherent and incoherent scattering components. To date, NPA has not been well established as a standard technique for SANS experiments at pulsed neutron sources such as the Japan Proton Accelerator Research Complex (J-PARC) and the US Spallation Neutron Source. It is anticipated that this work will contribute significantly to the accurate determination of the coherent neutron scattering component for scatterers in various types of organic sample systems in SANS experiments at J-PARC, particularly for systems involving competition between the coherent and incoherent scattering intensity.
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7
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Zhai Y, Luo P, Nagao M, Nakajima K, Kikuchi T, Kawakita Y, Kienzle PA, Z Y, Faraone A. Relevance of hydrogen bonded associates to the transport properties and nanoscale dynamics of liquid and supercooled 2-propanol. Phys Chem Chem Phys 2021; 23:7220-7232. [PMID: 33876082 DOI: 10.1039/d0cp05481j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2-Propanol was investigated, in both the liquid and supercooled states, as a model system to study how hydrogen bonds affect the structural relaxation and the dynamics of mesoscale structures, of approximately several Ångstroms, employing static and quasi-elastic neutron scattering and molecular dynamics simulation. Dynamic neutron scattering measurements were performed over an exchanged wave-vector range encompassing the pre-peak, indicative of the presence of H-bonding associates, and the main peak. The dynamics observed at the pre-peak is associated with the formation and disaggregation of the H-bonded associates and is measured to be at least one order of magnitude slower than the dynamics at the main peak, which is identified as the structural relaxation. The measurements indicate that the macroscopic shear viscosity has a similar temperature dependence as the dynamics of the H-bonded associates, which highlights the important role played by these structures, together with the structural relaxation, in defining the macroscopic rheological properties of the system. Importantly, the characteristic relaxation time at the pre-peak follows an Arrhenius temperature dependence whereas at the main peak it exhibits a non-Arrhenius behavior on approaching the supercooled state. The origin of this differing behavior is attributed to an increased structuring of the hydrophobic domains of 2-propanol accommodating a more and more encompassing H-bond network, and a consequent set in of dynamic cooperativity.
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Affiliation(s)
- Yanqin Zhai
- Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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8
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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
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.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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9
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Yamaguchi T, Faraone A, Nagao M. Collective Mesoscale Dynamics of Liquid 1-Dodecanol Studied by Neutron Spin-Echo Spectroscopy with Isotopic Substitution and Molecular Dynamics Simulation. J Phys Chem B 2019; 123:239-246. [PMID: 30511874 PMCID: PMC11168703 DOI: 10.1021/acs.jpcb.8b10299] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The collective dynamics of liquid 1-dodecanol was investigated at a length scale matching the mesoscale structure arising from the segregation of hydrophilic and hydrophobic domains. To this end, neutron spin-echo experiments were performed on a series of partially deuterated samples and the relevant collective dynamics of the hydroxyl groups with respect to the alkyl chains was extracted from the linear combination of the intermediate scattering functions of these samples. The resulting collective dynamics is slower than the single particle dynamics as determined by the measurement on the nondeuterated sample. The experimental results are in excellent agreement with molecular dynamics simulation, which allows further insight into the mechanism of the molecular motions. The results indicate that two factors are responsible for the slower collective dynamics. The first one is the slower dynamics of the hydroxyl group, with respect to the alkyl chains, owing to hydrogen bonding, and the second one is the presence of mesoscale structuring.
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Affiliation(s)
- Tsuyoshi Yamaguchi
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8603, Japan
| | - Antonio Faraone
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, United States
| | - Michihiro Nagao
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, United States
- Center for Exploration of Energy and Matter, Indiana University, Bloomington, Indiana 47408-1398, United States
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10
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Ito K, Faraone A, Tyagi M, Yamaguchi T, Chen SH. Nanoscale dynamics of water confined in ordered mesoporous carbon. Phys Chem Chem Phys 2019; 21:8517-8528. [DOI: 10.1039/c8cp07704e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The single particle dynamics of water confined in ordered mesoporous carbon matrix was investigated in the temperature range from 290 K to 170 K by quasielastic neutron scattering using three high resolution neutron spectrometers.
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Affiliation(s)
- Kanae Ito
- Department of Nuclear Science and Engineering
- Massachusetts Institute of Technology
- 77 Massachusetts Avenue
- Cambridge
- USA
| | - Antonio Faraone
- NIST Center for Neutron Research
- National Institute of Standards and Technology
- 100 Bureau Drive
- Gaithersburg
- USA
| | - Madhusudan Tyagi
- NIST Center for Neutron Research
- National Institute of Standards and Technology
- 100 Bureau Drive
- Gaithersburg
- USA
| | - Toshio Yamaguchi
- Department of Chemistry
- Faculty of Science
- Fukuoka University
- 8-19-1 Nanakuma
- Jonan-ku
| | - Sow-Hsin Chen
- Department of Nuclear Science and Engineering
- Massachusetts Institute of Technology
- 77 Massachusetts Avenue
- Cambridge
- USA
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11
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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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12
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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13
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Linking Structure to Dynamics in Protic Ionic Liquids: A Neutron Scattering Study of Correlated and Single-Particle Motions. Sci Rep 2018; 8:16400. [PMID: 30401950 PMCID: PMC6219547 DOI: 10.1038/s41598-018-34481-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/18/2018] [Indexed: 11/22/2022] Open
Abstract
Coupling between dynamical heterogeneity of ionic liquids and their structural periodicity on different length-scales can be directly probed by quasielastic neutron scattering with polarization analysis. The technique provides the tools to investigate single-particle and cooperative ion motions separately and, thus, dynamics of ion associations affecting the net charge transport can be experimentally explored. The focus of this study is the structure-dynamic relationship in the protic ionic liquid, triethylammonium triflate, characterized by strong hydrogen bonds between cations and anions. The site-selective deuterium/hydrogen-isotope substitution was applied to modulate the relative contributions of different atom groups to the total coherent and incoherent scattering signal. This approach in combination with molecular dynamics simulations allowed us to obtain a sophisticated description of cation self-diffusion and confined ion pair dynamics from the incoherent spectral component by using the acidic proton as a tagged particle. The coherent contribution of the neutron spectra demonstrated substantial ion association leading to collective ion migration that preserves charge alteration on picosecond time scale, as well as correlation of the localized dynamics occurring between adjacent ions.
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14
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Golub M, Rusevich L, Irrgang KD, Pieper J. Rigid versus Flexible Protein Matrix: Light-Harvesting Complex II Exhibits a Temperature-Dependent Phonon Spectral Density. J Phys Chem B 2018; 122:7111-7121. [DOI: 10.1021/acs.jpcb.8b02948] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Leonid Rusevich
- Institute of Physical Energetics, Krivu 11, LV-1006 Riga, Latvia
- Institute of Solid State Physics, University of Latvia, Kengaraga 8, LV-1063 Riga, Latvia
| | - Klaus-Dieter Irrgang
- Department of Life Science & Technology, Laboratory of Biochemistry, University for Applied Sciences, 10318 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
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15
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Malo de Molina P, Alvarez F, Frick B, Wildes A, Arbe A, Colmenero J. Investigation of the dynamics of aqueous proline solutions using neutron scattering and molecular dynamics simulations. Phys Chem Chem Phys 2017; 19:27739-27754. [PMID: 28984889 DOI: 10.1039/c7cp05474b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We applied quasielastic neutron scattering (QENS) techniques to samples with two different contrasts (deuterated solute/hydrogenated solvent and the opposite label) to selectively study the component dynamics of proline/water solutions. Results on diluted and concentrated solutions (31 and 6 water molecules/proline molecule, respectively) were analyzed in terms of the susceptibility and considering a recently proposed model for water dynamics [Arbe et al., Phys. Rev. Lett., 2016, 117, 185501] which includes vibrations and the convolution of localized motions and diffusion. We found that proline molecules not only reduce the average diffusion coefficient of water but also extend the time/frequency range of the crossover region ('cage') between the vibrations and purely diffusive behavior. For the high proline concentration we also found experimental evidence of water heterogeneous dynamics and a distribution of diffusion coefficients. Complementary molecular dynamics simulations show that water molecules start to perform rotational diffusion when they escape the cage regime but before the purely diffusive behavior is established. The rotational diffusion regime is also retarded by the presence of proline molecules. On the other hand, a strong coupling between proline and water diffusive dynamics which persists with decreasing temperature is directly observed using QENS. Not only are the temperature dependences of the diffusion coefficients of both components the same, but their absolute values also approach each other with increasing proline concentration. We compared our results with those reported using other techniques, in particular using dielectric spectroscopy (DS). A simple approach based on molecular hydrodynamics and a molecular treatment of DS allows rationalizing the a priori puzzling inconsistency between QENS and dielectric results regarding the dynamic coupling of the two components. The interpretation proposed is based on general grounds and therefore should be applicable to other biomolecular solutions.
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Affiliation(s)
- Paula Malo de Molina
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU) - Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain.
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16
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Matsuo T, Tominaga T, Kono F, Shibata K, Fujiwara S. Modulation of the picosecond dynamics of troponin by the cardiomyopathy-causing mutation K247R of troponin T observed by quasielastic neutron scattering. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1781-1789. [PMID: 28923663 DOI: 10.1016/j.bbapap.2017.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/18/2017] [Accepted: 09/14/2017] [Indexed: 11/16/2022]
Abstract
Troponin (Tn), consisting of three subunits (TnC, TnI, and TnT), regulates cardiac muscle contraction in a Ca2+-dependent manner. Various point mutations of human cardiac Tn are known to cause familial hypertrophic cardiomyopathy due to aberration of the regulatory function. In this study, we investigated the effects of one of these mutations, K247R of TnT, on the picosecond dynamics of the Tn core domain (Tn-CD), consisting of TnC, TnI and TnT2 (183-288 residues of TnT), by carrying out the quasielastic neutron scattering measurements on the reconstituted Tn-CD containing either the wild-type TnT2 (wtTn-CD) or the mutant TnT2 (K247R-Tn-CD) in the absence and presence of Ca2+. It was found that Ca2+-binding to the wtTn-CD decreases the residence time of atomic motions in the Tn-CD with slight changes in amplitudes, suggesting that the regulatory function mainly requires modulation of frequency of atomic motions. On the other hand, the K247R-Tn-CD shows different dynamic behavior from that of the wtTn-CD both in the absence and presence of Ca2+. In particular, the K247R-Tn-CD exhibits a larger amplitude than the wtTn-CD in the presence of Ca2+, suggesting that the mutant can explore larger conformational space than the wild-type. This increased flexibility should be relevant to the functional aberration of this mutant.
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Affiliation(s)
- Tatsuhito Matsuo
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, Tokai, Ibaraki 319-1106, Japan
| | - Fumiaki Kono
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Kaoru Shibata
- Neutron Science Section, J-PARC Center, Tokai, Ibaraki 319-1195, Japan
| | - Satoru Fujiwara
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, Tokai, Ibaraki 319-1106, Japan.
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17
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Fujiwara S, Chatake T, Matsuo T, Kono F, Tominaga T, Shibata K, Sato-Tomita A, Shibayama N. Ligation-Dependent Picosecond Dynamics in Human Hemoglobin As Revealed by Quasielastic Neutron Scattering. J Phys Chem B 2017; 121:8069-8077. [DOI: 10.1021/acs.jpcb.7b05182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Satoru Fujiwara
- Quantum
Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Toshiyuki Chatake
- Research
Reactor Institute, Kyoto University, 2 Asashiro-Nishi, Kumatori, Osaka 590-0494, Japan
| | - Tatsuhito Matsuo
- Quantum
Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Fumiaki Kono
- Quantum
Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taiki Tominaga
- Neutron
Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Kaoru Shibata
- Neutron
Science Section, J-PARC Center, 2-4 Shirakata, Tokai, Ibaraki 319-1195, Japan
| | - Ayana Sato-Tomita
- Division
of Biophysics, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
| | - Naoya Shibayama
- Division
of Biophysics, Department of Physiology, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, Tochigi 329-0498, Japan
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18
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Liu Z, Huang J, Tyagi M, O'Neill H, Zhang Q, Mamontov E, Jain N, Wang Y, Zhang J, Smith JC, Hong L. Dynamical Transition of Collective Motions in Dry Proteins. PHYSICAL REVIEW LETTERS 2017; 119:048101. [PMID: 29341744 DOI: 10.1103/physrevlett.119.048101] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 06/07/2023]
Abstract
Water is widely assumed to be essential for protein dynamics and function. In particular, the well-documented "dynamical" transition at ∼200 K, at which the protein changes from a rigid, nonfunctional form to a flexible, functional state, as detected in hydrogenated protein by incoherent neutron scattering, requires hydration. Here, we report on coherent neutron scattering experiments on perdeuterated proteins and reveal that a transition occurs in dry proteins at the same temperature resulting primarily from the collective heavy-atom motions. The dynamical transition discovered is intrinsic to the energy landscape of dry proteins.
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Affiliation(s)
- Zhuo Liu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, USA and Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37931, USA
| | - Qiu Zhang
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37931, USA
| | - Eugene Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Nitin Jain
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Yujie Wang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Zhang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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19
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Bertrand CE, Self JL, Copley JRD, Faraone A. Nanoscopic length scale dependence of hydrogen bonded molecular associates' dynamics in methanol. J Chem Phys 2017; 146:194501. [PMID: 28527447 PMCID: PMC5648548 DOI: 10.1063/1.4983179] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/25/2017] [Indexed: 11/14/2022] Open
Abstract
In a recent paper [C. E. Bertrand et al., J. Chem. Phys. 145, 014502 (2016)], we have shown that the collective dynamics of methanol shows a fast relaxation process related to the standard density-fluctuation heat mode and a slow non-Fickian mode originating from the hydrogen bonded molecular associates. Here we report on the length scale dependence of this slow relaxation process. Using quasielastic neutron scattering and molecular dynamics simulations, we show that the dynamics of the slow process is affected by the structuring of the associates, which is accessible through polarized neutron diffraction experiments. Using a series of partially deuterated samples, the dynamics of the associates is investigated and is found to have a similar time scale to the lifetime of hydrogen bonding in the system. Both the structural relaxation and the dynamics of the associates are thermally activated by the breaking of hydrogen bonding.
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Affiliation(s)
- C E Bertrand
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - J L Self
- McKetta Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
| | - J R D Copley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - A Faraone
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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20
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Shrestha UR, Bhowmik D, Van Delinder KW, Mamontov E, O’Neill H, Zhang Q, Alatas A, Chu XQ. Collective Excitations in Protein as a Measure of Balance Between its Softness and Rigidity. J Phys Chem B 2017; 121:923-930. [DOI: 10.1021/acs.jpcb.6b10245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Utsab R. Shrestha
- Department
of Physics and Astronomy, Wayne State University, Detroit, MI 48201, United States
| | - Debsindhu Bhowmik
- Computational
Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Kurt W. Van Delinder
- Department
of Physics and Astronomy, Wayne State University, Detroit, MI 48201, United States
| | - Eugene Mamontov
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Hugh O’Neill
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Qiu Zhang
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Ahmet Alatas
- Advanced
Photon Source, Argonne National laboratory, Argonne, IL 60439, United States
| | - Xiang-Qiang Chu
- Department
of Physics and Astronomy, Wayne State University, Detroit, MI 48201, United States
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21
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Biological Structures. NEUTRON SCATTERING - APPLICATIONS IN BIOLOGY, CHEMISTRY, AND MATERIALS SCIENCE 2017. [DOI: 10.1016/b978-0-12-805324-9.00001-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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Hong L, Jain N, Cheng X, Bernal A, Tyagi M, Smith JC. Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering. SCIENCE ADVANCES 2016; 2:e1600886. [PMID: 27757419 PMCID: PMC5065251 DOI: 10.1126/sciadv.1600886] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 09/02/2016] [Indexed: 06/06/2023]
Abstract
Protein function often depends on global, collective internal motions. However, the simultaneous quantitative experimental determination of the forms, amplitudes, and time scales of these motions has remained elusive. We demonstrate that a complete description of these large-scale dynamic modes can be obtained using coherent neutron-scattering experiments on perdeuterated samples. With this approach, a microscopic relationship between the structure, dynamics, and function in a protein, cytochrome P450cam, is established. The approach developed here should be of general applicability to protein systems.
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Affiliation(s)
- Liang Hong
- Institute of Natural Sciences and Department of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Nitin Jain
- Department of Biochemistry & 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
| | - Ana Bernal
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - 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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23
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Amann-Winkel K, Bellissent-Funel MC, Bove LE, Loerting T, Nilsson A, Paciaroni A, Schlesinger D, Skinner L. X-ray and Neutron Scattering of Water. Chem Rev 2016; 116:7570-89. [DOI: 10.1021/acs.chemrev.5b00663] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Katrin Amann-Winkel
- Department
of Physics, AlbaNova University Center, Stockholm University, SE-106
91, Stockholm, Sweden
| | | | - Livia E. Bove
- IMPMC, CNRS-UMR 7590, Université P&M Curie, 75252 Paris, France
- Institute
of Condensed Matter Physics, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas Loerting
- Institute
of Physical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Anders Nilsson
- Department
of Physics, AlbaNova University Center, Stockholm University, SE-106
91, Stockholm, Sweden
| | - Alessandro Paciaroni
- Dipartimento
di Fisica e Geologia, Università di Perugia, Via Alessandro
Pascoli, I-06123 Perugia, Italy
| | - Daniel Schlesinger
- Department
of Physics, AlbaNova University Center, Stockholm University, SE-106
91, Stockholm, Sweden
| | - Lawrie Skinner
- Mineral
Physics Institute, Stony Brook University, Stony Brook, New York 11794-2100, United States
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24
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Grimaldo M, Roosen-Runge F, Hennig M, Zanini F, Zhang F, Jalarvo N, Zamponi M, Schreiber F, Seydel T. Hierarchical molecular dynamics of bovine serum albumin in concentrated aqueous solution below and above thermal denaturation. Phys Chem Chem Phys 2016; 17:4645-55. [PMID: 25587698 DOI: 10.1039/c4cp04944f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of proteins in solution is a complex and hierarchical process, affected by the aqueous environment as well as temperature. We present a comprehensive study on nanosecond time and nanometer length scales below, at, and above the denaturation temperature Td. Our experimental data evidence dynamical processes in protein solutions on three distinct time scales. We suggest a consistent physical picture of hierarchical protein dynamics: (i) self-diffusion of the entire protein molecule is confirmed to agree with colloid theory for all temperatures where the protein is in its native conformational state. At higher temperatures T > Td, the self-diffusion is strongly obstructed by cross-linking or entanglement. (ii) The amplitude of backbone fluctuations grows with increasing T, and a transition in its dynamics is observed above Td. (iii) The number of mobile side-chains increases sharply at Td while their average dynamics exhibits only little variations. The combination of quasi-elastic neutron scattering and the presented analytical framework provides a detailed microscopic picture of the protein molecular dynamics in solution, thereby reflecting the changes of macroscopic properties such as cluster formation and gelation.
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Affiliation(s)
- Marco Grimaldo
- Institut Max von Laue - Paul Langevin (ILL), CS 20156, F-38042 Grenoble, France.
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25
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Fujiwara S, Araki K, Matsuo T, Yagi H, Yamada T, Shibata K, Mochizuki H. Dynamical Behavior of Human α-Synuclein Studied by Quasielastic Neutron Scattering. PLoS One 2016; 11:e0151447. [PMID: 27097022 PMCID: PMC4838215 DOI: 10.1371/journal.pone.0151447] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/29/2016] [Indexed: 12/02/2022] Open
Abstract
α-synuclein (αSyn) is a protein consisting of 140 amino acid residues and is abundant in the presynaptic nerve terminals in the brain. Although its precise function is unknown, the filamentous aggregates (amyloid fibrils) of αSyn have been shown to be involved in the pathogenesis of Parkinson's disease, which is a progressive neurodegenerative disorder. To understand the pathogenesis mechanism of this disease, the mechanism of the amyloid fibril formation of αSyn must be elucidated. Purified αSyn from bacterial expression is monomeric but intrinsically disordered in solution and forms amyloid fibrils under various conditions. As a first step toward elucidating the mechanism of the fibril formation of αSyn, we investigated dynamical behavior of the purified αSyn in the monomeric state and the fibril state using quasielastic neutron scattering (QENS). We prepared the solution sample of 9.5 mg/ml purified αSyn, and that of 46 mg/ml αSyn in the fibril state, both at pD 7.4 in D2O. The QENS experiments on these samples were performed using the near-backscattering spectrometer, BL02 (DNA), at the Materials and Life Science Facility at the Japan Accelerator Research Complex, Japan. Analysis of the QENS spectra obtained shows that diffusive global motions are observed in the monomeric state but largely suppressed in the fibril state. However, the amplitude of the side chain motion is shown to be larger in the fibril state than in the monomeric state. This implies that significant solvent space exists within the fibrils, which is attributed to the αSyn molecules within the fibrils having a distribution of conformations. The larger amplitude of the side chain motion in the fibril state than in the monomeric state implies that the fibril state is entropically favorable.
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Affiliation(s)
- Satoru Fujiwara
- Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
- * E-mail:
| | - Katsuya Araki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Tatsuhito Matsuo
- Quantum Beam Science Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Hisashi Yagi
- Center for Research on Green Sustainable Chemistry, Tottori University, Tottori, Japan
| | - Takeshi Yamada
- Research Center for Neutron Science and Technology, CROSS-Tokai, Tokai, Ibaraki, Japan
| | - Kaoru Shibata
- Neutron Science Section, J-PARC Center, Tokai, Ibaraki, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
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26
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Pluhackova K, Morhenn H, Lautner L, Lohstroh W, Nemkovski KS, Unruh T, Böckmann RA. Extension of the LOPLS-AA Force Field for Alcohols, Esters, and Monoolein Bilayers and its Validation by Neutron Scattering Experiments. J Phys Chem B 2015; 119:15287-99. [DOI: 10.1021/acs.jpcb.5b08569] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Kristyna Pluhackova
- Computational
Biology, Department of Biology, University of Erlangen-Nürnberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Humphrey Morhenn
- Lehrstuhl
für Kristallografie und Strukturphysik, Department Physik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 3, 91058 Erlangen, Germany
| | - Lisa Lautner
- Lehrstuhl
für Kristallografie und Strukturphysik, Department Physik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 3, 91058 Erlangen, Germany
| | - Wiebke Lohstroh
- Heinz
Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85748 Garching b. München, Germany
| | - Kirill S. Nemkovski
- Jülich
Center for Neutron Science JCNS, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstrasse 1, 85747 Garching b. München, Germany
| | - Tobias Unruh
- Lehrstuhl
für Kristallografie und Strukturphysik, Department Physik, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 3, 91058 Erlangen, Germany
| | - Rainer A. Böckmann
- Computational
Biology, Department of Biology, University of Erlangen-Nürnberg, Staudtstrasse 5, 91058 Erlangen, Germany
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27
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Rusevich L, Embs J, Bektas I, Paulsen H, Renger G, Pieper J. Protein and solvent dynamics of the water-soluble chlorophyll-binding protein (WSCP). EPJ WEB OF CONFERENCES 2015. [DOI: 10.1051/epjconf/20158302016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Busch S, Lorenz CD, Taylor J, Pardo LC, McLain SE. Short-Range Interactions of Concentrated Proline in Aqueous Solution. J Phys Chem B 2014; 118:14267-77. [DOI: 10.1021/jp508779d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sebastian Busch
- Department
of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | | | - Luis Carlos Pardo
- Departament
de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, 08028 Barcelona, Catalonia, Spain
| | - Sylvia E. McLain
- Department
of Biochemistry, University of Oxford, Oxford, United Kingdom
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29
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Schmiele M, Schindler T, Westermann M, Steiniger F, Radulescu A, Kriele A, Gilles R, Unruh T. Mesoscopic Structures of Triglyceride Nanosuspensions Studied by Small-Angle X-ray and Neutron Scattering and Computer Simulations. J Phys Chem B 2014; 118:8808-18. [DOI: 10.1021/jp502580a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Schmiele
- Friedrich-Alexander-Universität Erlangen—Nürnberg, Physik
Department, Staudtstrasse
3, 91058 Erlangen, Germany
| | - Torben Schindler
- Friedrich-Alexander-Universität Erlangen—Nürnberg, Physik
Department, Staudtstrasse
3, 91058 Erlangen, Germany
| | - Martin Westermann
- Center for Electron Microscopy of the Jena University Hospital, Ziegelmühlenweg 1, 07743 Jena, Germany
| | - Frank Steiniger
- Center for Electron Microscopy of the Jena University Hospital, Ziegelmühlenweg 1, 07743 Jena, Germany
| | - Aurel Radulescu
- Jülich Centre for Neutron Science (JCNS), Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Armin Kriele
- Outstation
at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht (HZG), Lichtenbergstrasse
1, 85747 Garching, Germany
| | - Ralph Gilles
- Heinz
Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - Tobias Unruh
- Friedrich-Alexander-Universität Erlangen—Nürnberg, Physik
Department, Staudtstrasse
3, 91058 Erlangen, Germany
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30
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Doster W, Nakagawa H, Appavou MS. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments. J Chem Phys 2014; 139:045105. [PMID: 23902030 DOI: 10.1063/1.4816513] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
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.
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Affiliation(s)
- W Doster
- Physik-Department, Technische Universität München, D-85748 Garching, Germany.
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31
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Schiró G. Anharmonic onsets in polypeptides revealed by neutron scattering: Experimental evidences and quantitative description of energy resolution dependence. Biophys Chem 2013; 180-181:29-36. [DOI: 10.1016/j.bpc.2013.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/26/2013] [Accepted: 05/26/2013] [Indexed: 10/26/2022]
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32
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Nickels JD, García Sakai V, Sokolov AP. Dynamics in Protein Powders on the Nanosecond–Picosecond Time Scale Are Dominated by Localized Motions. J Phys Chem B 2013; 117:11548-55. [DOI: 10.1021/jp4058884] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan D. Nickels
- Joint
Institute for Neutron Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee 37831, United States
- Department
of Chemistry, University of Tennessee, 552 Buehler Hall, Knoxville, Tennessee 37996, United States
| | - Victoria García Sakai
- ISIS Neutron and Muon Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
| | - Alexei P. Sokolov
- Joint
Institute for Neutron Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee 37831, United States
- Department
of Chemistry, University of Tennessee, 552 Buehler Hall, Knoxville, Tennessee 37996, United States
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33
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Ngai KL, Capaccioli S, Paciaroni A. Change of caged dynamics at Tg in hydrated proteins: Trend of mean squared displacements after correcting for the methyl-group rotation contribution. J Chem Phys 2013; 138:235102. [DOI: 10.1063/1.4810752] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Schmiele M, Schindler T, Unruh T, Busch S, Morhenn H, Westermann M, Steiniger F, Radulescu A, Lindner P, Schweins R, Boesecke P. Structural characterization of the phospholipid stabilizer layer at the solid-liquid interface of dispersed triglyceride nanocrystals with small-angle x-ray and neutron scattering. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062316. [PMID: 23848684 DOI: 10.1103/physreve.87.062316] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Indexed: 06/02/2023]
Abstract
Dispersions of crystalline nanoparticles with at least one sufficiently large unit cell dimension can give rise to Bragg reflections in the small-angle scattering range. If the nanocrystals possess only a small number of unit cells along these particular crystallographic directions, the corresponding Bragg reflections will be broadened. In a previous study of phospholipid stabilized dispersions of β-tripalmitin platelets [Unruh, J. Appl. Crystallogr. 40, 1008 (2007)], the x-ray powder pattern simulation analysis (XPPSA) was developed. The XPPSA method facilitates the interpretation of the rather complicated small-angle x-ray scattering (SAXS) curves of such dispersions of nanocrystals. The XPPSA method yields the distribution function of the platelet thicknesses and facilitates a structural characterization of the phospholipid stabilizer layer at the solid-liquid interface between the nanocrystals and the dispersion medium from the shape of the broadened 001 Bragg reflection. In this contribution an improved and extended version of the XPPSA method is presented. The SAXS and small-angle neutron scattering patterns of dilute phospholipid stabilized tripalmitin dispersions can be reproduced on the basis of a consistent simulation model for the particles and their phospholipid stabilizer layer on an absolute scale. The results indicate a surprisingly flat arrangement of the phospholipid molecules in the stabilizer layer with a total thickness of only 12 Å. The stabilizer layer can be modeled by an inner shell for the fatty acid chains and an outer shell including the head groups and additional water. The experiments support a dense packing of the phospholipid molecules on the nanocrystal surfaces rather than isolated phospholipid domains.
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Affiliation(s)
- Martin Schmiele
- Professur für Nanomaterialcharakterisierung (Streumethoden), Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 3, 91058 Erlangen, Germany
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35
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Incoherent Neutron Spin-Echo Spectroscopy as an Option to Study Long-Range Lipid Diffusion. ACTA ACUST UNITED AC 2013. [DOI: 10.1155/2013/439758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Diffusion is the fundamental mechanism for lipids and other molecules to move in a membrane. It is an important process to consider in modelling the formation of membrane structures, such as rafts. Lipid diffusion is mainly studied by two different techniques: incoherent neutron scattering and fluorescence microscopy. Both techniques access distinctly different length scales. While neutron scattering measures diffusion over about 3 lipid diameters, microscopic techniques access motions of lipids over micrometer distances. The diffusion constants which are determined by these two methods often differ by about an order of magnitude, with the neutrons usually seeing a faster lipid diffusion. Different theories are used to describe lipid diffusion in the two experiments. In order to close the “gap” between these two techniques, we propose to study lipid diffusion at mesoscopic length scales using a neutron spin-echo (NSE) spectrometer. We have conducted an experiment in highly oriented, solid supported lipid bilayers to prove the feasibility of performing incoherent NSE on biological samples. Lateral lipid diffusion was measured in a fluid phase model membrane system at a length scale of 12 Å. Using the high-energy resolution of the NSE technique, we find evidence for two dynamic processes.
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36
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Price DL, Fernandez-Alonso F. An Introduction to Neutron Scattering. EXPERIMENTAL METHODS IN THE PHYSICAL SCIENCES 2013. [DOI: 10.1016/b978-0-12-398374-9.00001-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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37
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Schiró G, Natali F, Cupane A. Physical origin of anharmonic dynamics in proteins: new insights from resolution-dependent neutron scattering on homomeric polypeptides. PHYSICAL REVIEW LETTERS 2012; 109:128102. [PMID: 23005991 DOI: 10.1103/physrevlett.109.128102] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Indexed: 06/01/2023]
Abstract
Neutron scattering reveals a complex dynamics in polypeptide chains, with two main onsets of anharmonicity whose physical origin and biological role are still debated. In this study the dynamics of strategically selected homomeric polypeptides is investigated with elastic neutron scattering using different energy resolutions and compared with that of a real protein. Our data spotlight the dependence of anharmonic transition temperatures and fluctuation amplitudes on energy resolution, which we quantitatively explain in terms of a two-site model for the protein-hydration water energy landscape. Experimental data strongly suggest that the protein dynamical transition is not a mere resolution effect but is due to a real physical effect. Activation barriers and free energy values obtained for the protein dynamical transition allow us to make a connection with the two-well interaction potential of supercooled-confined water proposed to explain a low-density→high-density liquid-liquid transition.
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38
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Busselez R, Arbe A, Cerveny S, Capponi S, Colmenero J, Frick B. Component dynamics in polyvinylpyrrolidone concentrated aqueous solutions. J Chem Phys 2012; 137:084902. [DOI: 10.1063/1.4746020] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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39
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Toppozini L, Armstrong CL, Kaye MD, Tyagi M, Jenkins T, Rheinstädter MC. Hydration Water Freezing in Single Supported Lipid Bilayers. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/520307] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present a high-temperature and high-energy resolution neutron scattering investigation of hydration water freezing in single supported lipid bilayers. Single supported lipid bilayers provide a well-defined biological interface to study hydration water dynamics and coupling to membrane degrees of freedom. Nanosecond molecular motions of membrane and hydration water were studied in the temperature range 240 K < T < 290 K in slow heating and cooling cycles using coherent and incoherent elastic neutron scattering on a backscattering spectrometer. Several freezing and melting transitions were observed. From the length scale dependence of the elastic scattering, these transitions could be assigned to freezing and melting of hydration water dynamics, diffusive lipid, and lipid acyl-tail dynamics. Coupling was investigated by comparing the different freezing and melting temperatures. While it is often speculated that membrane and hydration water dynamics are strongly coupled, we find that membrane and hydration water dynamics are at least partially decoupled in single bilayers.
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Affiliation(s)
- Laura Toppozini
- Department of Physics & Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4M1
| | - Clare L. Armstrong
- Department of Physics & Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4M1
| | - Martin D. Kaye
- Department of Physics & Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4M1
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, NIST, Gaithersburg, MD 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Timothy Jenkins
- NIST Center for Neutron Research, NIST, Gaithersburg, MD 20899, USA
| | - Maikel C. Rheinstädter
- Department of Physics & Astronomy, McMaster University, 1280 Main Street West, Hamilton, ON, Canada L8S 4M1
- Canadian Neutron Beam Centre, National Research Council Canada, Chalk River, ON, Canada K0J 1J0
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40
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Schirò G, Vetri V, Frick B, Militello V, Leone M, Cupane A. Neutron Scattering Reveals Enhanced Protein Dynamics in Concanavalin A Amyloid Fibrils. J Phys Chem Lett 2012; 3:992-996. [PMID: 26286561 DOI: 10.1021/jz300082x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein aggregation is one of the most challenging topics in life sciences, and it is implicated in several human pathologies. The nature and the role of toxic species is highly debated, with amyloid fibrils being among the most relevant species for their peculiar structural and functional properties. Protein dynamics and in particular the ability to fluctuate through a large number of conformational substates are closely related to protein function. This Letter focuses on amyloid fibril dynamics, and, to our knowledge, it is the first neutron scattering study on a protein (Concanavalin A) isolated in its fibril state. Our results reveal enhanced atomic fluctuations in amyloid fibrils and indicate that the protein is "softer" in the fibril state with respect to the native and amorphous aggregate states. We discuss this finding in terms of a structural interpretation and suggest that the paradigm ordered structure ↔ lower flexibility can be questioned when considering the local fast side-chain protein dynamics.
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Affiliation(s)
- Giorgio Schirò
- †Dipartimento di Fisica, Università di Palermo, Palermo, Italy
| | - Valeria Vetri
- †Dipartimento di Fisica, Università di Palermo, Palermo, Italy
- ‡Istituto di Biofisica, CNR, Palermo, Italy
| | | | - Valeria Militello
- †Dipartimento di Fisica, Università di Palermo, Palermo, Italy
- ‡Istituto di Biofisica, CNR, Palermo, Italy
| | - Maurizio Leone
- †Dipartimento di Fisica, Università di Palermo, Palermo, Italy
- ‡Istituto di Biofisica, CNR, Palermo, Italy
| | - Antonio Cupane
- †Dipartimento di Fisica, Università di Palermo, Palermo, Italy
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41
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Paciaroni A, Orecchini A, Haertlein M, Moulin M, Conti Nibali V, De Francesco A, Petrillo C, Sacchetti F. Vibrational Collective Dynamics of Dry Proteins in the Terahertz Region. J Phys Chem B 2012; 116:3861-5. [DOI: 10.1021/jp211190q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alessandro Paciaroni
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
| | - Andrea Orecchini
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
- Institut Laue Langevin, 6 rue J. Horowitz, F-38042 Grenoble, France
| | | | - Martine Moulin
- Institut Laue Langevin, 6 rue J. Horowitz, F-38042 Grenoble, France
| | - Valeria Conti Nibali
- Dipartimento di Fisica, Università degli Studi di Messina, via Salita Sperone, I-98166 Messina, Italy
| | - Alessio De Francesco
- CNR, Istituto Officina dei Materiali, Unità di Grenoble, Institut Laue Langevin, 6 rue J. Horowitz, F-38042 Grenoble, France
| | - Caterina Petrillo
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy
- Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
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42
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Yoshida K, Hosokawa S, Baron AQR, Yamaguchi T. Collective dynamics of hydrated β-lactogloblin by inelastic x-ray scattering. J Chem Phys 2010; 133:134501. [DOI: 10.1063/1.3484238] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Stadler AM, van Eijck L, Demmel F, Artmann G. Macromolecular dynamics in red blood cells investigated using neutron spectroscopy. J R Soc Interface 2010; 8:590-600. [PMID: 20739313 DOI: 10.1098/rsif.2010.0306] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We present neutron scattering measurements on the dynamics of haemoglobin (Hb) in human red blood cells (RBCs) in vivo. Global and internal Hb dynamics were measured in the ps to ns time and Å length scales using quasi-elastic neutron backscattering spectroscopy. We observed the cross over from global Hb short-time to long-time self-diffusion. Both short- and long-time diffusion coefficients agree quantitatively with predicted values from the hydrodynamic theory of non-charged hard-sphere suspensions when a bound water fraction of around 0.23 gram H(2)O per gram Hb is taken into account. The higher amount of water in the cells facilitates internal protein fluctuations in the ps time scale when compared with fully hydrated Hb powder. Slower internal dynamics of Hb in RBCs in the ns time range were found to be rather similar to results obtained with fully hydrated protein powders, solutions and Escherichia coli cells.
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44
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Krycka KL, Booth RA, Hogg CR, Ijiri Y, Borchers JA, Chen WC, Watson SM, Laver M, Gentile TR, Dedon LR, Harris S, Rhyne JJ, Majetich SA. Core-shell magnetic morphology of structurally uniform magnetite nanoparticles. PHYSICAL REVIEW LETTERS 2010; 104:207203. [PMID: 20867056 DOI: 10.1103/physrevlett.104.207203] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Indexed: 05/15/2023]
Abstract
A new development in small-angle neutron scattering with polarization analysis allows us to directly extract the average spatial distributions of magnetic moments and their correlations with three-dimensional directional sensitivity in any magnetic field. Applied to a collection of spherical magnetite nanoparticles 9.0 nm in diameter, this enhanced method reveals uniformly canted, magnetically active shells in a nominally saturating field of 1.2 T. The shell thickness depends on temperature, and it disappears altogether when the external field is removed, confirming that these canted nanoparticle shells are magnetic, rather than structural, in origin.
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Affiliation(s)
- K L Krycka
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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45
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Doster W, Busch S, Gaspar AM, Appavou MS, Wuttke J, Scheer H. Dynamical transition of protein-hydration water. PHYSICAL REVIEW LETTERS 2010; 104:098101. [PMID: 20367013 DOI: 10.1103/physrevlett.104.098101] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Indexed: 05/10/2023]
Abstract
Thin layers of water on biomolecular and other nanostructured surfaces can be supercooled to temperatures not accessible with bulk water. Chen et al. [Proc. Natl. Acad. Sci. U.S.A. 103, 9012 (2006)]10.1073/pnas.0602474103 suggested that anomalies near 220 K observed by quasielastic neutron scattering can be explained by a hidden critical point of bulk water. Based on more sensitive measurements of water on perdeuterated phycocyanin, using the new neutron backscattering spectrometer SPHERES, and an improved data analysis, we present results that show no sign of such a fragile-to-strong transition. The inflection of the elastic intensity at 220 K has a dynamic origin that is compatible with a calorimetric glass transition at 170 K. The temperature dependence of the relaxation times is highly sensitive to data evaluation; it can be brought into perfect agreement with the results of other techniques, without any anomaly.
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Affiliation(s)
- W Doster
- Physik Department E 13 and ZWE FRM II, Technische Universität München, 85747 Garching, Germany.
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