1
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Matsuo T, Cisse A, Plazanet M, Natali F, Koza MM, Ollivier J, Bicout DJ, Peters J. The dynamical Matryoshka model: 3. Diffusive nature of the atomic motions contained in a new dynamical model for deciphering local lipid dynamics. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183949. [PMID: 35508224 DOI: 10.1016/j.bbamem.2022.183949] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 04/06/2022] [Accepted: 04/25/2022] [Indexed: 11/17/2022]
Abstract
In accompanying papers [Bicout et al., BioRxiv https://doi.org/10.1101/2021.09.21.461198 (2021); Cissé et al., BioRxiv https://doi.org/10.1101/2022.03.30.486370 (2022)], a new model called Matryoshka model has been proposed to describe the geometry of atomic motions in phospholipid molecules in bilayers and multilamellar vesicles based on their quasielastic neutron scattering (QENS) spectra. Here, in order to characterize the relaxational aspects of this model, the energy widths of the QENS spectra of the samples were analyzed first in a model-free way. The spectra were decomposed into three Lorentzian functions, which are classified as slow, intermediate, and fast motions depending on their widths. The analysis provides the diffusion coefficients, residence times, and geometrical parameters for the three classes of motions. The results corroborate the parameter values such as the amplitudes and the mobile fractions of atomic motions obtained by the application of the Matryoshka model to the same samples. Since the current analysis was carried out independently of the development of the Matryoshka model, the present results enhance the validity of the model. The model will serve as a powerful tool to decipher the dynamics of lipid molecules not only in model systems, but also in more complex systems such as mixtures of different kinds of lipids or natural cell membranes.
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Affiliation(s)
- Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, F-38000 Grenoble, France; Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France; Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Aline Cisse
- Univ. Grenoble Alpes, CNRS, LiPhy, F-38000 Grenoble, France; Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Marie Plazanet
- Univ. Grenoble Alpes, CNRS, LiPhy, F-38000 Grenoble, France
| | - Francesca Natali
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France; CNR-IOM, OGG, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Michael Marek Koza
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Jacques Ollivier
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Dominique J Bicout
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France; Univ. Grenoble Alpes, CNRS, Grenoble INP, VetAgro Sup, TIMC, 38000 Grenoble, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, F-38000 Grenoble, France; Institut Laue-Langevin, 71 avenue des Martyrs, 38042 Grenoble Cedex 9, France; Institut Universitaire de France, France.
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2
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Mamontov E, Bordallo HN, Delaire O, Nickels J, Peters J, Schneider GJ, Smith JC, Sokolov AP. Broadband Wide-Angle VElocity Selector (BWAVES) neutron spectrometer designed for the SNS Second Target Station. EPJ WEB OF CONFERENCES 2022. [DOI: 10.1051/epjconf/202227202003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A recently proposed wide-angle velocity selector (WAVES) device for choosing the velocity of detected neutrons after they have been scattered by the sample paves the way for inverted geometry neutron spectrometers with continuously adjustable final neutron wavelength. BWAVES broadband inverted geometry spectrometer proposed for the Second Target Station at the Spallation Neutron Source at Oak Ridge National Laboratory is designed using WAVES to simultaneously probe dynamic processes spanning 4.5 decades in time (energy transfer). This makes BWAVES a uniquely flexible instrument which can be viewed as either a quasielasitc neutron scattering (QENS) spectrometer with a practically unlimited (overlapping with the vibrational excitations) range of energy transfers, or a broadband inelastic vibrational neutron spectrometer with QENS capabilities, including a range of accessible momentum transfer (Q) and a sufficiently high energy resolution at the elastic line. The new capabilities offered by BWAVES will expand the application of neutron scattering in ways not possible with existing neutron spectrometers.
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3
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Cisse A, Schachner-Nedherer AL, Appel M, Beck C, Ollivier J, Leitinger G, Prassl R, Kornmueller K, Peters J. Dynamics of Apolipoprotein B-100 in Interaction with Detergent Probed by Incoherent Neutron Scattering. J Phys Chem Lett 2021; 12:12402-12410. [PMID: 34939807 DOI: 10.1021/acs.jpclett.1c03141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Apolipoprotein B-100 (apo B-100) is the protein moiety of both low- and very-low-density lipoproteins, whose role is crucial to cholesterol and triglyceride transport. Aiming at the molecular dynamics' details of apo B-100, scarcely studied, we performed elastic and quasi-elastic incoherent neutron scattering (EINS, QENS) experiments combining different instruments and time scales. Similar to classical membrane proteins, the solubilization results in remaining detergent, here Nonidet P-40 (NP40). Therefore, we propose a framework for QENS studies of protein-detergent complexes, with the introduction of a combined model, including the experimental apo B-100/NP40 ratio. Relying on the simultaneous analysis of all QENS amplitudes, this approach is sensitive enough to separate both contributions. Its application identified two points: (i) apo B-100 slow dynamics and (ii) the acceleration of NP40 dynamics in the presence of apo B-100. Direct translation of the exposed methodology now makes the investigation of more membrane proteins by neutron spectroscopy achievable.
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Affiliation(s)
- Aline Cisse
- Université Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue Langevin, 38042 Grenoble, France
| | | | | | - Christian Beck
- Institut Laue Langevin, 38042 Grenoble, France
- Institut of Applied Physics, University of Tübingen, 72076 Tübingen, Germany
| | | | | | | | | | - Judith Peters
- Université Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
- Institut Laue Langevin, 38042 Grenoble, France
- Institut Universitaire de France, 75231 Paris, France
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4
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Cisse A, Marquette A, Altangerel M, Peters J, Bechinger B. Investigation of the Action of Peptides on Lipid Membranes. J Phys Chem B 2021; 125:10213-10223. [PMID: 34464136 DOI: 10.1021/acs.jpcb.1c06388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Calorimetric and incoherent neutron scattering methods were employed to investigate the action of magainin 2 and PGLa peptides on the phase behavior and molecular dynamics of lipids mimicking cytoplasmic membranes of Gram-negative bacteria. The impact of the peptides, tested individually and cooperatively by differential scanning calorimetry, presented a broadened peak, sometimes with a second shoulder, depicting the phase transition temperature around 21 °C. Neutron scattering revealed a small but significant variation of the membrane dynamics due to the peptides in both in-plane and out-of-plane directions. Although we did not find a clear hint for synergy in the interplay of the two peptides, the calorimetric and neutron data give compatible results in terms of a decrease of the enthalpy due to the presence of the peptides, which destabilize the membrane. The dynamics in the two directions was differentiated when the individual peptides were added to the membranes, but the impact was smaller when both peptides were added together.
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Affiliation(s)
- Aline Cisse
- Univ. Grenoble-Alpes, CNRS, LiPhy, 38000 Grenoble, France.,Institut Laue-Langevin, 38000 Grenoble, France
| | - Arnaud Marquette
- University of Strasbourg/CNRS, Chemistry Institute, Membrane Biophysics and NMR, UMR7177 Strasbourg, France
| | - Munkhtuguldur Altangerel
- Univ. Grenoble-Alpes, CNRS, LiPhy, 38000 Grenoble, France.,Institut Laue-Langevin, 38000 Grenoble, France
| | - Judith Peters
- Univ. Grenoble-Alpes, CNRS, LiPhy, 38000 Grenoble, France.,Institut Laue-Langevin, 38000 Grenoble, France.,Institut Universitaire de France, 75231 Paris, France
| | - Burkhard Bechinger
- University of Strasbourg/CNRS, Chemistry Institute, Membrane Biophysics and NMR, UMR7177 Strasbourg, France.,Institut Universitaire de France, 75231 Paris, France
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5
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Zeller D, Tan P, Hong L, Di Bari D, Garcia Sakai V, Peters J. Differences between calcium rich and depleted alpha-lactalbumin investigated by molecular dynamics simulations and incoherent neutron scattering. Phys Rev E 2020; 101:032415. [PMID: 32289905 DOI: 10.1103/physreve.101.032415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/21/2020] [Indexed: 11/07/2022]
Abstract
We present a study comparing atomic motional amplitudes in calcium rich and depleted alpha-lactalbumin. The investigations were performed by elastic incoherent neutron scattering (EINS) and molecular dynamics (MD) simulations. As the variations were expected to be very small, three different hydration levels and timescales (instrumental resolutions) were measured. In addition, we used two models to extract the mean square displacements (MSDs) from the EINS data, one taking into account the motional heterogeneity of the MSD. At a timescale of several nanoseconds, small differences in the amplitudes between the calcium enriched and depleted alpha-lactalbumin are visible, whereas at lower timescales no changes can be concluded within the statistics. The results are compared to MD simulations at 280 and 300 K by extracting the MSDs of the trajectories in two separate ways: first by direct calculation, and second by a virtual neutron experiment using the same models as for the experimental data. We show that the simulated data give qualitatively similar results as the experimental data but quantitatively there are differences. Furthermore, the distribution of the MSDs in the simulations suggests that the inclusion of heterogeneity is reasonable for alpha-lactalbumin, but a bi-or trimodal approach may be sufficient.
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Affiliation(s)
- Dominik Zeller
- University Grenoble Alpes, LiPhy, CNRS, F-38000 Grenoble, France and Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
| | - Pan Tan
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniele Di Bari
- University Grenoble Alpes, LiPhy, CNRS, F-38000 Grenoble, France and Institut Laue Langevin, F-38042 Grenoble Cedex 9, France.,Physics Department, University of Perugia, 06123 Perugia, Italy
| | - Victoria Garcia Sakai
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 0QX, United Kingdom
| | - Judith Peters
- University Grenoble Alpes, LiPhy, CNRS, F-38000 Grenoble, France and Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
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6
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Saouessi M, Peters J, Kneller GR. Frequency domain modeling of quasielastic neutron scattering from hydrated protein powders: Application to free and inhibited human acetylcholinesterase. J Chem Phys 2019; 151:125103. [PMID: 31575200 DOI: 10.1063/1.5121703] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
This article reports on a frequency domain analysis of quasielastic neutron scattering spectra from free and Huperzine-A-inhibited human acetylcholinesterase, extending a recent time domain analysis of the same experimental data [M. Saouessi et al., J. Chem. Phys. 150, 161104 (2019)]. An important technical point here is the construction of a semianalytical model for the resolution-broadened dynamic structure factor that can be fitted to the experimental spectra. We find comparable parameters as in our previous study and demonstrate that our model is sensitive to subpercent changes in the experimental data, which are caused by reversible binding of the inhibitor Huperzine A.
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Affiliation(s)
- Melek Saouessi
- Centre de Biophys. Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
| | - Judith Peters
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Gerald R Kneller
- Centre de Biophys. Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
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7
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Laulumaa S, Koza MM, Seydel T, Kursula P, Natali F. A Quasielastic Neutron Scattering Investigation on the Molecular Self-Dynamics of Human Myelin Protein P2. J Phys Chem B 2019; 123:8178-8185. [PMID: 31483648 DOI: 10.1021/acs.jpcb.9b05320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The human myelin protein P2 is a membrane binding protein believed to maintain correct lipid composition and organization in peripheral nerve myelin. Its function is related to its ability to stack membranes, and this function can be enhanced by the P38G mutation, whereby the overall protein structure does not change but the molecular dynamics increase. Mutations in P2 are linked to human peripheral neuropathy. Here, the dynamics of wild-type P2 and the P38G variant were studied using quasielastic neutron scattering on time scales from 10 ps to 1 ns at 300 K. The results suggest that the mutant protein dynamics are increased on both the fastest and the slowest measured time scales, by increasing the dynamics amplitude and/or the portion of atoms participating in the movement.
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Affiliation(s)
- Saara Laulumaa
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu , University of Oulu , Oulu , Finland.,European Spallation Source , Lund , Sweden
| | | | | | - Petri Kursula
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu , University of Oulu , Oulu , Finland.,Department of Biomedicine , University of Bergen , Bergen , Norway
| | - Francesca Natali
- Institut Laue-Langevin , Grenoble , France.,CNR-IOM, OGG , Grenoble , France
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8
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Saouessi M, Peters J, Kneller GR. Asymptotic analysis of quasielastic neutron scattering data from human acetylcholinesterase reveals subtle dynamical changes upon ligand binding. J Chem Phys 2019; 150:161104. [PMID: 31042885 DOI: 10.1063/1.5094625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, we show that subtle changes in the internal dynamics of human acetylcholinesterase upon ligand binding can be extracted from quasielastic neutron scattering data by employing a nonexponential relaxation model for the intermediate scattering function. The relaxation is here described by a stretched Mittag-Leffler function, which exhibits slow power law decay for long times. Our analysis reveals that binding of a Huperzine A ligand increases the atomic motional amplitudes of the enzyme and slightly slows down its internal diffusive motions. This result is interpreted within an energy landscape picture for the motion of the hydrogen atoms.
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Affiliation(s)
- Melek Saouessi
- Centre de Biophysique Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
| | - Judith Peters
- Institut Laue Langevin, 71 Avenue des Martyrs, 38042 Grenoble Cedex 9, France
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS and Université d'Orléans, Rue Charles Sadron, 45071 Orléans, France
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9
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Golub M, Guillon V, Gotthard G, Zeller D, Martinez N, Seydel T, Koza MM, Lafaye C, Clavel D, von Stetten D, Royant A, Peters J. Dynamics of a family of cyan fluorescent proteins probed by incoherent neutron scattering. J R Soc Interface 2019; 16:20180848. [PMID: 30836899 DOI: 10.1098/rsif.2018.0848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cyan fluorescent proteins (CFPs) are variants of green fluorescent proteins in which the central tyrosine of the chromophore has been replaced by a tryptophan. The increased bulk of the chromophore within a compact protein and the change in the positioning of atoms capable of hydrogen bonding have made it difficult to optimize their fluorescence properties, which took approximately 15 years between the availability of the first useable CFP, enhanced cyan fluorescent protein (ECFP), and that of a variant with almost perfect fluorescence efficiency, mTurquoise2. To understand the molecular bases of the progressive improvement in between these two CFPs, we have studied by incoherent neutron scattering the dynamics of five different variants exhibiting progressively increased fluorescence efficiency along the evolution pathway. Our results correlate well with the analysis of the previously determined X-ray crystallographic structures, which show an increase in flexibility between ECFP and the second variant, Cerulean, which is then hindered in the three later variants, SCFP3A (Super Cyan Fluorescent Protein 3A), mTurquoise and mTurquoise2. This confirms that increasing the rigidity of the direct environment of the fluorescent chromophore is not the sole parameter leading to brighter fluorescent proteins and that increased flexibility in some cases may be helpful.
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Affiliation(s)
- Maksym Golub
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Virginia Guillon
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Dominik Zeller
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
| | - Nicolas Martinez
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Tilo Seydel
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Michael M Koza
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France
| | - Céline Lafaye
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | - Damien Clavel
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France
| | | | - Antoine Royant
- 2 Univ. Grenoble Alpes, CNRS, CEA, IBS (Institut de Biologie Structurale) , 38000 Grenoble , France.,3 European Synchrotron Radiation Facility , 38043 Grenoble , France
| | - Judith Peters
- 1 Institut Laue Langevin , 71 avenue des Martyrs, 38042 Grenoble Cedex 9 , France.,4 Laboratoire Interdisciplinaire de Physique, Univ. Grenoble Alpes, CNRS , 38000 Grenoble , France
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10
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Andersson CD, Martinez N, Zeller D, Allgardsson A, Koza MM, Frick B, Ekström F, Peters J, Linusson A. Influence of Enantiomeric Inhibitors on the Dynamics of Acetylcholinesterase Measured by Elastic Incoherent Neutron Scattering. J Phys Chem B 2018; 122:8516-8525. [DOI: 10.1021/acs.jpcb.8b05485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | - Nicolas Martinez
- Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
- Université Grenoble Alpes, IBS and LiPhy, F-38000 Grenoble, France
| | - Dominik Zeller
- Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
- Université Grenoble Alpes, IBS and LiPhy, F-38000 Grenoble, France
| | - Anders Allgardsson
- CBRN Defence and Security, Swedish Defence Research Agency, SE-90621 Umeå, Sweden
| | | | - Bernhard Frick
- Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
| | - Fredrik Ekström
- CBRN Defence and Security, Swedish Defence Research Agency, SE-90621 Umeå, Sweden
| | - Judith Peters
- Institut Laue Langevin, F-38042 Grenoble Cedex 9, France
- Université Grenoble Alpes, IBS and LiPhy, F-38000 Grenoble, France
| | - Anna Linusson
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
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Abstract
Protein dynamics is characterized by fluctuations among different conformational substates, i.e. the different minima of their energy landscape. At temperatures above ~200 K, these fluctuations lead to a steep increase in the thermal dependence of all dynamical properties, phenomenon known as Protein Dynamical Transition. In spite of the intense studies, little is known about the effects of pressure on these processes, investigated mostly near room temperature. We studied by neutron scattering the dynamics of myoglobin in a wide temperature and pressure range. Our results show that high pressure reduces protein motions, but does not affect the onset temperature for the Protein Dynamical Transition, indicating that the energy differences and barriers among conformational substates do not change with pressure. Instead, high pressure values strongly reduce the average structural differences between the accessible conformational substates, thus increasing the roughness of the free energy landscape of the system.
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12
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Peters J, Marion J, Becher FJ, Trapp M, Gutberlet T, Bicout DJ, Heimburg T. Thermodynamics of lipid multi-lamellar vesicles in presence of sterols at high hydrostatic pressure. Sci Rep 2017; 7:15339. [PMID: 29127413 PMCID: PMC5681575 DOI: 10.1038/s41598-017-15582-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/30/2017] [Indexed: 01/28/2023] Open
Abstract
We compared the effect of cholesterol at different concentration on the phase behaviour of DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) multilamellar vesicles. We used pressure perturbation differential scanning calorimetry (PPC) that studies a system on the whole by giving access to relevant thermodynamic quantities, and elastic incoherent neutron scattering (EINS) that probes local motions of a system at the atomic level by allowing extraction of dynamical parameters. PPC revealed that the volume expansion coefficient of DMPC and DMPC/Cholesterol samples with 13 and 25 mol% cholesterol is a linear function of the heat capacity measured by differential scanning calorimetry. Neutron backscattering spectroscopy showed that the mean square displacements of H atoms do exhibit an increase with temperature and a decrease under increasing pressure. Cholesterol added at concentrations of 25 and 50 mol% led to suppression of the main phase transition. Taking advantage of these results, the present study aims (i) to show that calorimetry and EINS using the Bicout and Zaccai model equally permit to get access to thermodynamic quantities characterizing pure DMPC and DMPC/cholesterol mixtures, thus directly confirming the theoretical method, and (ii) to validate our approach as function of temperature and of pressure, as both are equally important and complementary thermodynamic variables.
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Affiliation(s)
- J Peters
- Univ. Grenoble Alpes, LiPhy, 140 Rue de la Physique, 38402, Saint-Martin-d'Hères, France. .,Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble cedex 9, France.
| | - J Marion
- Univ. Grenoble Alpes, LiPhy, 140 Rue de la Physique, 38402, Saint-Martin-d'Hères, France.,Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble cedex 9, France
| | - F J Becher
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.,Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - M Trapp
- Helmholtz-Zentrum Berlin für Materialien und Energie, Lise-Meitner Campus, Hahn-Meitner-Platz 1, 14109, Berlin, Germany
| | - T Gutberlet
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Jülich GmbH, Lichtenbergstr. 1, 85748, Garching, Germany
| | - D J Bicout
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble cedex 9, France.,Biomathématiques et épidémiologie, EPSP - TIMC-IMAG, UMR CNRS 5525, Université Grenoble Alpes, VetAgro Sup Lyon, 69280, Marcy l'Etoile, France
| | - T Heimburg
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark
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13
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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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14
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Andersson CD, Martinez N, Zeller D, Rondahl SH, Koza MM, Frick B, Ekström F, Peters J, Linusson A. Changes in dynamics of α-chymotrypsin due to covalent inhibitors investigated by elastic incoherent neutron scattering. Phys Chem Chem Phys 2017; 19:25369-25379. [DOI: 10.1039/c7cp04041e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of chymotrypsin increases when bound to two different covalent inhibitors. These effects were analyzed by univariate and multivariate methods.
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Affiliation(s)
| | - N. Martinez
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- IBS and LiPhy
| | - D. Zeller
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- IBS and LiPhy
| | - S. H. Rondahl
- CBRN Defence and Security
- Swedish Defence Research Agency
- SE-90621 Umeå
- Sweden
| | - M. M. Koza
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
| | - B. Frick
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
| | - F. Ekström
- CBRN Defence and Security
- Swedish Defence Research Agency
- SE-90621 Umeå
- Sweden
| | - J. Peters
- Institut Laue Langevin
- F-38042 Grenoble Cedex 9
- France
- Univ. Grenoble Alpes
- IBS and LiPhy
| | - A. Linusson
- Department of Chemistry
- Umeå University
- SE-90187 Umeå
- Sweden
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Peters J, Martinez N, Trovaslet M, Scannapieco K, Koza MM, Masson P, Nachon F. Dynamics of human acetylcholinesterase bound to non-covalent and covalent inhibitors shedding light on changes to the water network structure. Phys Chem Chem Phys 2016; 18:12992-3001. [PMID: 27109895 DOI: 10.1039/c6cp00280c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the effects of non-covalent reversible and covalent irreversible inhibitors on human acetylcholinesterase and human butyrylcholinesterase. Remarkably a non-covalent inhibitor, Huperzine A, has almost no effect on the molecular dynamics of the protein, whereas the covalently binding nerve agent soman renders the molecular structure stiffer in its aged form. The modified movements were studied by incoherent neutron scattering on different time scales and they indicate a stabilization and stiffening of aged human acetylcholinesterase. It is not straightforward to understand the forces leading to this strong effect. In addition to the specific interactions of the adduct within the protein, some indications point towards an extensive water structure change for the aged conjugate as water Bragg peaks appeared at cryogenic temperature despite an identical initial hydration state for all samples. Such a change associated to an apparent increase in free water volume upon aging suggests higher ordering of the hydration shell that leads to the stiffening of protein. Thus, several additive contributions seem responsible for the improved flexibility or stiffening effect of the inhibitors rather than a single interaction.
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Affiliation(s)
- Judith Peters
- Univ. Grenoble Alpes, LiPhy, F-38044 Grenoble, France
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