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Rahman MK, Yamada T, Yamada NL, Hishida M, Higuchi Y, Seto H. Quasi-elastic neutron scattering reveals the relationship between the dynamical behavior of phospholipid headgroups and hydration water. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:044701. [PMID: 37637480 PMCID: PMC10449016 DOI: 10.1063/4.0000184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 08/04/2023] [Indexed: 08/29/2023]
Abstract
The dynamics of hydration water (HW) in 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE) was investigated by means of quasi-elastic neutron scattering (QENS) and compared with those observed in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). The headgroup dynamics of DMPE was investigated using a mixture of tail-deuterated DMPE and D2O, and the QENS profiles were interpreted as consisting of three modes. The fast mode comprised the rotation of hydrogen atoms in -NH3+ and -CH2- groups in the headgroup of DMPE, the medium-speed mode comprised fluctuations in the entire DMPE molecule, and the slow mode comprised fluctuations in the membrane. These interpretations were confirmed using molecular dynamics (MD) simulations. The HW dynamics analysis was performed on a tail-deuterated DMPE and H2O mixture. The QENS profiles were analyzed in terms of three modes: (1) a slow mode, identified as loosely bound HW in the DMPC membrane; (2) a medium-speed mode similar to free HW in the DMPC membrane; and (3) a fast mode, identified as rotational motion. The relaxation time for the fast mode was approximately six times shorter than that of rotational water in DMPC, consistent with the results of terahertz time-domain spectroscopy. The activation energy of medium-speed HW in DMPE differed from that of free HW in DMPC, suggesting the presence of different hydration states or hydrogen-bonded networks around the phosphocholine and phosphoethanolamine headgroups.
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Affiliation(s)
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), Tokai, Naka, Ibaraki 319-1106, Japan
| | | | - Mafumi Hishida
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Yuji Higuchi
- Research Institute for Information Technology, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Hideki Seto
- Authors to whom correspondence should be addressed: and
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2
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Malik S, Karmakar S, Debnath A. Relaxation time scales of interfacial water upon fluid to ripple to gel phase transitions of bilayers. J Chem Phys 2023; 158:114503. [PMID: 36948835 DOI: 10.1063/5.0138681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
The slow relaxation of interface water (IW) across three primary phases of membranes is relevant to understand the influence of IW on membrane functions at supercooled conditions. To this objective, a total of ∼16.26μs all-atom molecular dynamics simulations of 1,2-dimyristoyl-sn-glycerol-3-phosphocholine lipid membranes are carried out. A supercooling-driven drastic slow-down in heterogeneity time scales of the IW is found at the fluid to the ripple to the gel phase transitions of the membranes. At both fluid-to-ripple-to-gel phase transitions, the IW undergoes two dynamic crossovers in Arrhenius behavior with the highest activation energy at the gel phase due to the highest number of hydrogen bonds. Interestingly, the Stokes-Einstein (SE) relation is conserved for the IW near all three phases of the membranes for the time scales derived from the diffusion exponents and the non-Gaussian parameters. However, the SE relation breaks for the time scale obtained from the self-intermediate scattering functions. The behavioral difference in different time scales is universal and found to be an intrinsic property of glass. The first dynamical transition in the α relaxation time of the IW is associated with an increase in the Gibbs energy of activation of hydrogen bond breaking with locally distorted tetrahedral structures, unlike the bulk water. Thus, our analyses unveil the nature of the relaxation time scales of the IW across membrane phase transitions in comparison with the bulk water. The results will be useful to understand the activities and survival of complex biomembranes under supercooled conditions in the future.
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Affiliation(s)
- Sheeba Malik
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, India
| | - Ananya Debnath
- Department of Chemistry, IIT Jodhpur, Jodhpur, Rajasthan, India
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3
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Bicout DJ, Cisse A, Matsuo T, Peters J. The dynamical Matryoshka model: 1. Incoherent neutron scattering functions for lipid dynamics in bilayers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183944. [PMID: 35490712 DOI: 10.1016/j.bbamem.2022.183944] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 04/06/2022] [Accepted: 04/17/2022] [Indexed: 10/18/2022]
Abstract
Fluid lipid bilayers are the building blocks of biological membranes. Although there is a large amount of experimental data using incoherent quasi-elastic neutron scattering (QENS) techniques to study membranes, very little theoretical works have been developed to study the local dynamics of membranes. The main objective of this work is to build a theoretical framework to study and describe the local dynamics of lipids and derive analytical expressions of intermediate scattering functions (ISF) for QENS. As results, we developed the dynamical Matryoshka model which describes the local dynamics of lipid molecules in membrane layers as a nested hierarchical convolution of three motional processes: (i) individual motions described by the vibrational motions of H-atoms; (ii) internal motions including movements of the lipid backbone, head groups and tails, and (iii) molecule movements of the lipid molecule as a whole. The analytical expressions of the ISF associated with these movements are all derived. For use in analyzing the QENS experimental data, we also derived an analytical expression for the aggregate ISF of the Matryoshka model which involves an elastic term plus three inelastic terms of well-separated time scales and whose amplitudes and rates are functions of the lipid motions. And as an illustrative application, we used the aggregated ISF to analyze the experimental QENS data on a lipid sample of multilamellar bilayers of DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine). It is clear from this analysis that the dynamical Matryoshka model describes very well the experimental data and allow extracting the dynamical parameters of the studied system.
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Affiliation(s)
- Dominique J Bicout
- Univ. Grenoble Alpes, CNRS, Grenoble INP, VetAgro Sup, TIMC, 38000 Grenoble, France; Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France.
| | - Aline Cisse
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France; Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France; Institute for Quantum Life Science, National Institutes for Quantum Science and Technology (QST), Tokai, Ibaraki 319-1106, Japan; Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, Grenoble, France; Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France; Institut Universitaire de France, France
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4
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Cisse A, Matsuo T, Plazanet M, Natali F, Koza MM, Ollivier J, Bicout DJ, Peters J. The dynamical Matryoshka model: 2. Modeling of local lipid dynamics at the sub-nanosecond timescale in phospholipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183950. [PMID: 35525301 DOI: 10.1016/j.bbamem.2022.183950] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 04/06/2022] [Accepted: 04/25/2022] [Indexed: 12/12/2022]
Abstract
Biological membranes are generally formed by lipids and proteins. Often, the membrane properties are studied through model membranes formed by phospholipids only. They are molecules composed by a hydrophilic head group and hydrophobic tails, which can present a panoply of various motions, including small localized movements of a few atoms up to the diffusion of the whole lipid or collective motions of many of them. In the past, efforts were made to measure these motions experimentally by incoherent neutron scattering and to quantify them, but with upcoming modern neutron sources and instruments, such models can now be improved. In the present work, we expose a quantitative and exhaustive study of lipid dynamics on DMPC and DMPG membranes, using the Matryoshka model recently developed by our group. The model is confronted here to experimental data collected on two different membrane samples, at three temperatures and two instruments. Despite such complexity, the model describes reliably the data and permits to extract a series of parameters. The results compare also very well to other values found in the literature.
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Affiliation(s)
- Aline Cisse
- Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France; Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France
| | - Tatsuhito Matsuo
- Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France; Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France; Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Marie Plazanet
- Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France
| | - Francesca Natali
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France; CNR-IOM and INSIDE@ILL, c/o OGG, 38042 Grenoble Cedex 9, France
| | - Michael Marek Koza
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France
| | - Jacques Ollivier
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France
| | - Dominique J Bicout
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France; Univ. Grenoble Alpes, CNRS, Grenoble INP, VetAgro Sup, TIMC, 38000 Grenoble, France
| | - Judith Peters
- Univ. Grenoble Alpes, CNRS, LiPhy, 38000 Grenoble, France; Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, 7, France; Institut Universitaire de France, France.
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5
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Sharma VK, Mamontov E. Multiscale lipid membrane dynamics as revealed by neutron spectroscopy. Prog Lipid Res 2022; 87:101179. [PMID: 35780913 DOI: 10.1016/j.plipres.2022.101179] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 12/22/2022]
Abstract
The plasma membrane is one of the principal structural components of the cell and, therefore, one of the key components of the cellular life. Because the membrane's dynamics links the membrane's structure and function, the complexity and the broad range of the membrane's motions are essential for the enormously diverse functionality of the cell membrane. Even for the main membrane component, the lipid bilayer, considered alone, the range and complexity of the lipid motions are remarkable. Spanning the time scale from sub-picosecond to minutes and hours, the lipid motion in a bilayer is challenging to study even when a broad array of dynamic measurement techniques is employed. Neutron scattering plays a special role among such dynamic measurement techniques, particularly, because it involves the energy transfers commensurate with the typical intra- and inter- molecular dynamics and the momentum transfers commensurate with intra- and inter-molecular distances. Thus, using neutron scattering-based techniques, the spatial and temporal information on the lipid motion can be obtained and analysed simultaneously. Protium vs. deuterium sensitivity and non-destructive character of the neutron probe add to the remarkable prowess of neutron scattering for elucidating the lipid dynamics. Herein we present an overview of the neutron scattering-based studies of lipid dynamics in model membranes, with a discussion of the direct relevance and implications to the real-life cell membranes. The latter are much more complex systems than simple model membranes, consisting of heterogeneous non-stationary domains composed of lipids, proteins, and other small molecules, such as carbohydrates. Yet many fundamental aspects of the membrane behavior and membrane interactions with other molecules can be understood from neutron scattering measurements of the model membranes. For example, such studies can provide a great deal of information on the interactions of antimicrobial compounds with the lipid matrix of a pathogen membrane, or the interactions of drug molecules with the plasma membrane. Finally, we briefly discuss the recently emerging field of neutron scattering membrane studies with a reach far beyond the model membrane systems.
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Affiliation(s)
- V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Mumbai 400094, India.
| | - E Mamontov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Nguan H, Ishak KA, Zahid NI, Martinez-Felipe A, Hashim R, Aripin NFK. Incommensurate lamellar phase from long chain Mannosides: Investigation by X-Ray scattering and replica exchange molecular dynamics (REMD). J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Tominaga T, Sahara M, Kawakita Y, Nakagawa H, Yamada T. Evaluation of sample cell materials for aqueous solutions used in quasi-elastic neutron scattering measurements. J Appl Crystallogr 2021. [DOI: 10.1107/s1600576721009687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
For quasi-elastic neutron scattering (QENS) studies, sample cells made of pure or alloyed aluminium are frequently employed. Although the Al surface is protected by a passivating film, this film is not robust. Therefore, when the sample is an aqueous solution, chemical interactions between the Al surface and sample, promoted by corrosive entities such as chloride ions and certain conditions of pH, can compromise the integrity of the cell and interfere with the experiment. In this study, the corrosion susceptibilities of Al and its alloys were investigated by subjecting them to various treatments; the results were compared with those of other candidate materials with low chemical reactivity. This work showed that alloys with higher Al content and boehmite-coated surfaces are resistant to corrosion. In particular, for Al, the resistance is due to a reduction in the contact area achieved by reducing the surface roughness. QENS measurements of empty sample cells made of these materials revealed two results: (1) the profile of the cell fabricated with a copper-free Al alloy showed a minor dependence on the scattering vector magnitude Q and (2) reducing the real surface area of Al effectively suppresses its scattering intensity, while boehmite coating strengthens the scattering. Cells fabricated with Mo, Nb and single-crystal sapphire can be used as alternatives to Al because of their low scattering intensity and reduced dependence on Q.
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8
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Malik S, Debnath A. Dehydration induced dynamical heterogeneity and ordering mechanism of lipid bilayers. J Chem Phys 2021; 154:174904. [PMID: 34241050 DOI: 10.1063/5.0044614] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding the influence of dehydration on the membrane structure is crucial to control membrane functionality related to domain formation and cell fusion under anhydrobiosis conditions. To this end, we perform all-atom molecular dynamic simulations of 1,2-dimyristoyl-sn-glycero-3-phosphocholine dimyristoylphosphatidylcholine lipid membranes at different hydration levels at 308 K. As dehydration increases, the lipid area per head group decreases with an increase in bilayer thickness and lipid order parameters indicating bilayer ordering. Concurrently, translational and rotational dynamics of interfacial water (IW) molecules near membranes slow down. On the onset of bilayer ordering, the IW molecules exhibit prominent features of dynamical heterogeneity evident from non-Gaussian parameters and one-dimensional van Hove correlation functions. At a fully hydrated state, diffusion constants (D) of the IW follow a scaling relation, D∼τα -1, where the α relaxation time (τα) is obtained from self-intermediate scattering functions. However, upon dehydration, the relation breaks and the D of the IW follows a power law behavior as D∼τα -0.57, showing the signature of glass dynamics. τα and hydrogen bond lifetime calculated from intermittent hydrogen bond auto-correlation functions undergo a similar crossover in association with bilayer ordering on dehydration. The bilayer ordering is accompanied with an increase in fraction of caged lipids spanned over the bilayer surface and a decrease in fraction of mobile lipids due to the non-diffusive dynamics. Our analyses reveal that the microscopic mechanism of lipid ordering by dehydration is governed by dynamical heterogeneity. The fundamental understanding from this study can be applied to complex bio-membranes to trap functionally relevant gel-like domains at room temperature.
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Affiliation(s)
- Sheeba Malik
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
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9
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Abstract
Water determines the properties of biological systems. Therefore, understanding the nature of the mutual interaction between water and biosystems is of primary importance for a proper assessment of any biological activity, e.g., the efficacy of new drugs or vaccines. A convenient way to characterize the interactions between biosystems and water is to analyze their impact on water density and dynamics in the proximity of the interfaces. It is commonly accepted that water bulk density and dynamical properties are recovered at distances of the order of 1 nm away from the surface of biological systems. This notion leads to the definition of hydration or biological water as the nanoscopic layer of water covering the surface of biosystems and to the expectation that all the effects of the water-interface interaction are limited to this thin region. Here, we review some of our latest contributions, showing that phospholipid membranes affect the water dynamics, structural properties, and hydrogen bond network at a distance that is more than twice as large as the commonly evoked ∼1nm thick layer and of the order of 2.4 nm. Furthermore, we unveil that at a shorter distance ∼0.5nm from the membrane, instead, there is an additional interface between lipid-bound and unbound water. Bound water has a structural role in the stability of the membrane. Our results imply that the concept of hydration water should be revised or extended and pave the way to a deeper understanding of the mutual interactions between water and biological systems.
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10
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Qian S, Sharma VK, Clifton LA. Understanding the Structure and Dynamics of Complex Biomembrane Interactions by Neutron Scattering Techniques. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:15189-15211. [PMID: 33300335 DOI: 10.1021/acs.langmuir.0c02516] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and therefore is involved in almost all biological processes. Membrane-specific interactions, such as drug binding to a membrane receptor or the interactions of an antimicrobial compound with the lipid matrix of a pathogen membrane, are of interest across the scientific disciplines. Herein we present a review, aimed at nonexperts, of the major neutron scattering techniques used in membrane studies: small-angle neutron scattering, neutron membrane diffraction, neutron reflectometry, quasielastic neutron scattering, and neutron spin echo. Neutron scattering techniques are well suited to studying biological membranes. The nondestructive nature of cold neutrons means that samples can be measured for long periods without fear of beam damage from ultraviolet, electron, or X-ray radiation, and neutron beams are highly penetrating, thus offering flexibility in samples and sample environments. Most important is the strong difference in neutron scattering lengths between the two most abundant forms of hydrogen, protium and deuterium. Changing the relative amounts of protium/deuterium in a sample allows the production of a series of neutron scattering data sets, enabling the observation of differing components within complex membrane architectures. This approach can be as simple as using the naturally occurring neutron contrast between different biomolecules to study components in a complex by changing the solution H2O/D2O ratio or as complex as selectively labeling individual components with hydrogen isotopes. This review presents an overview of each experimental technique with the neutron instrument configuration, related sample preparation and sample environment, and data analysis, highlighted by a special emphasis on using prominent neutron contrast to understand structure and dynamics. This review gives researchers a practical introduction to the often enigmatic suite of neutron beamlines, thereby lowering the barrier to taking advantage of these large-facility techniques to achieve new understandings of membranes and their interactions with other molecules.
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Affiliation(s)
- Shuo Qian
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Veerendra Kumar Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Luke A Clifton
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, U.K. OX11 0QX
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11
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Martelli F, Crain J, Franzese G. Network Topology in Water Nanoconfined between Phospholipid Membranes. ACS NANO 2020; 14:8616-8623. [PMID: 32578978 DOI: 10.1021/acsnano.0c02984] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Water provides the driving force for the assembly and stability of many cellular components. Despite its impact on biological functions, a nanoscale understanding of the relationship between its structure and dynamics under soft confinement has remained elusive. As expected, water in contact with biological membranes recovers its bulk density and dynamics at ∼1 nm from phospholipid headgroups but surprisingly enhances its intermediate range order (IRO) over a distance, at least, twice as large. Here, we explore how the IRO is related to the water's hydrogen-bond network (HBN) and its coordination defects. We characterize the increased IRO by an alteration of the HBN up to more than eight coordination shells of hydration water. The HBN analysis emphasizes the existence of a bound-unbound water interface at ∼0.8 nm from the membrane. The unbound water has a distribution of defects intermediate between bound and bulk water, but with density and dynamics similar to bulk, while bound water has reduced thermal energy and many more HBN defects than low-temperature water. This observation could be fundamental for developing nanoscale models of biological interactions and for understanding how alteration of the water structure and topology, for example, due to changes in extracellular ions concentration, could affect diseases and signaling. More generally, it gives us a different perspective to study nanoconfined water.
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Affiliation(s)
- Fausto Martelli
- Hartree Centre, IBM Research Europe, Daresbury WA4 4AD, United Kingdom
| | - Jason Crain
- Hartree Centre, IBM Research Europe, Daresbury WA4 4AD, United Kingdom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària, Departament de Física de la Matèria Condensada, and Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028 Barcelona, Spain
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12
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Srivastava A, Malik S, Karmakar S, Debnath A. Dynamic coupling of a hydration layer to a fluid phospholipid membrane: intermittency and multiple time-scale relaxations. Phys Chem Chem Phys 2020; 22:21158-21168. [DOI: 10.1039/d0cp02803g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Understanding the coupling of a hydration layer and a lipid membrane is crucial to gaining access to membrane dynamics and understanding its functionality towards various biological processes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Sheeba Malik
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
| | - Smarajit Karmakar
- Centre for Interdisciplinary Sciences
- Tata Institute of Fundamental Research
- Hyderabad 500107
- India
| | - Ananya Debnath
- Department of Chemistry
- Indian Institute of Technology Jodhpur
- Rajasthan
- India
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13
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Srivastava A, Karmakar S, Debnath A. Quantification of spatio-temporal scales of dynamical heterogeneity of water near lipid membranes above supercooling. SOFT MATTER 2019; 15:9805-9815. [PMID: 31746927 DOI: 10.1039/c9sm01725a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A hydrated 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) lipid membrane is investigated using an all atom molecular dynamics simulation at 308 K to determine the physical sources of universal slow relaxations of hydration layers and length-scale of the spatially heterogeneous dynamics. Continuously residing interface water (IW) molecules hydrogen bonded to different moieties of lipid heads in the membrane are identified. The non-Gaussian parameters of all classes of IW molecules show a cross-over from cage vibration to translational diffusion. A significant non-Gaussianity is observed for the IW molecules exhibiting large length correlations in translational van Hove functions. Two time-scales for the ballistic motions and hopping transitions are obtained from the self intermediate scattering functions of the IW molecules with an additional long relaxation, which disappears for bulk water. The long relaxation time-scales for the IW molecules obtained from the self intermediate scattering functions are in good accordance with the hydrogen bond relaxation time-scales irrespective of the nature of the chemical confinement and the confinement lifetime. Employing a block analysis approach, the length-scale of dynamical heterogeneities is captured from a transition from non-Gaussianity to Gaussianity in van Hove correlation functions of the IW molecules. The heterogeneity length-scale is comparable to the wave-length of the small and weak undulations of the membrane calculated by Fourier transforms of lipid tilts. This opens up a new avenue towards a possible correlation between heterogeneity length-scale and membrane curvature more significant for rippled membranes. Thus, our analyses provide a measure towards the spatio-temporal scale of dynamical heterogeneity of confined water near membranes.
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Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India.
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14
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Kadomura Y, Yamamoto N, Tominaga K. Broadband dielectric spectroscopy from sub GHz to THz of hydrated lipid bilayer of DMPC. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:139. [PMID: 31664606 DOI: 10.1140/epje/i2019-11901-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
In order to study the dynamics of a phospholipid and its hydration water, we measured complex dielectric spectra of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) from the sub-GHz to the THz frequency region with varying the temperature and hydration level of the sample. Spectra obtained from a vector network analyzer and two terahertz time-domain spectrometers are adjusted, which enables us to analyze the dielectric spectra from the sub-GHz region to the THz region by a model function. We confirmed a fast relaxational mode in the sub-THz region, which was suggested by the previous work which only used a THz spectrometer.
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Affiliation(s)
- Yu Kadomura
- Department of Chemistry, Graduate School of Science, Kobe University, 657-8501, Nada, Kobe, Japan
| | - Naoki Yamamoto
- Jichi Medical University, 3311-1 Yakushiji, 329-0498, Shimotsuke-shi, Tochigi-ken, Japan
| | - Keisuke Tominaga
- Department of Chemistry, Graduate School of Science, Kobe University, 657-8501, Nada, Kobe, Japan.
- Molecular Photoscience Research Center, Kobe University, 657-8501, Nada, Kobe, Japan.
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15
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Heterogeneity in structure and dynamics of water near bilayers using TIP3P and TIP4P/2005 water models. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2019.110396] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Elastic compliance as a tool to understand Hofmeister ion specific effect in DMPC liposomes. Biophys Chem 2019; 249:106148. [PMID: 30981138 DOI: 10.1016/j.bpc.2019.106148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 11/21/2022]
Abstract
Elastic compliance of DMPC liposomes with Hofmeister electrolytes: NaCl, Na2SO4, Na2CO3, NaNO3, KCl and MgCl2 studied using Quartz crystal microbalance with dissipation has been correlated with changes in their lamellar spacing from SAXS. The study suggests that hydration water of the different ions has an effect on the overall packing of the lipid bilayer that results as either a dehydrated liposome or where water smears the surface of the liposomes. Ratio of hydrogen bonded carbonyl and phosphate of polar region of the liposomes from ATR-FTIR spectroscopy, suggests that the polar groups are less hydrated due to the displacement of water by the electrolytes compared to pure DMPC and ordered in the sequence for cations as: K+ < Na+,Mg2+ and for anions as SO42- < CO32- < Cl- < NO3-. These findings show the usefulness of Elastic compliance for structural studies of composite phospholipid bilayers, lipid-protein complexes and lipid systems of reduced dimensionalities.
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17
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Calero C, Franzese G. Membranes with different hydration levels: The interface between bound and unbound hydration water. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.10.074] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Nanda H, García Sakai V, Khodadadi S, Tyagi MS, Schwalbach EJ, Curtis JE. Relaxation dynamics of saturated and unsaturated oriented lipid bilayers. SOFT MATTER 2018; 14:6119-6127. [PMID: 29998268 PMCID: PMC6262841 DOI: 10.1039/c7sm01720k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We present experimental measurements and analysis of the dynamics and the phase behaviour of saturated DMPC and unsaturated DOPC oriented multi-lamellar bilayers. Elastic and inelastic neutron scattering were used to directly probe the dynamical processes of these membrane systems on time and length scales relevant to the internal and localized motion of lipid monomers. Mobility in this regime can be informative in elucidating the local interactions responsible for material properties of these fluid lipid systems. DMPC and DOPC are structurally similar in terms of their membrane hydrophobic thickness; however, they exhibit different mechanical properties in terms of both elastic compressibility and bending moduli. The analyses suggest that the constraint imposed by the double bonds in DOPC acyl chains restricts atomic motion in both liquid and gel phases compared to DMPC. We discuss applications of molecular dynamics to further elucidate the atomic details of the dynamical processes. Such an understanding may suggest how membrane properties can be tuned using a variety of different lipid species.
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Affiliation(s)
- Hirsh Nanda
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA.
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Sharma VK, Mukhopadhyay R. Deciphering interactions of ionic liquids with biomembrane. Biophys Rev 2018; 10:721-734. [PMID: 29549587 DOI: 10.1007/s12551-018-0410-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 02/27/2018] [Indexed: 12/24/2022] Open
Abstract
Ionic liquids (ILs) are a special class of low-temperature (typically < 100 °C) molten salts, which have huge upsurge interest in the field of chemical synthesis, catalysis, electrochemistry, pharmacology, and biotechnology, mainly due to their highly tunable nature and exceptional properties. However, practical uses of ILs are restricted mainly due to their adverse actions on organisms. Understanding interactions of ILs with biomembrane is prerequisite to assimilate the actions of these ionic compounds on the organism. Here, we review different biophysical methods to characterize interactions between ILs and phospholipid membrane, a model biomembrane. All these studies indicate that ILs interact profoundly with the lipid bilayer and modulate the structure, microscopic dynamics, and phase behavior of the membrane, which could be the fundamental cause of the observed toxicity of ILs. Effects of ILs on the membrane are found to be strongly dependent on the lipophilicity of the IL and are found to increase with the alkyl chain length of IL. This can be correlated with the observed higher toxicity of IL with the longer alkyl chain length. These informations would be useful to tune the toxicity of IL which is required in designing environment-friendly nontoxic solvents of the so-called green chemistry for various practical applications.
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Affiliation(s)
- V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
| | - R Mukhopadhyay
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
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20
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Sharma VK, Ghosh SK, Mandal P, Yamada T, Shibata K, Mitra S, Mukhopadhyay R. Effects of ionic liquids on the nanoscopic dynamics and phase behaviour of a phosphatidylcholine membrane. SOFT MATTER 2017; 13:8969-8979. [PMID: 29152634 DOI: 10.1039/c7sm01799e] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ionic liquids (ILs) are potential candidates for new antimicrobials due to their tunable antibacterial and antifungal properties that are required to keep pace with the growing challenge of bacterial resistance. To a great extent their antimicrobial actions are related to the interactions of ILs with cell membranes. Here, we report the effects of ILs on the nanoscopic dynamics and phase behaviour of a dimyristoylphosphatidylcholine (DMPC) membrane, a model cell membrane, as studied using neutron scattering techniques. Two prototypical imidazolium-based ILs 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM[BF4]) and 1-decyl-3-methylimidazolium tetrafluoroborate (DMIM[BF4]), which differ only in terms of the alkyl chain length of cations, have been used for the present study. Fixed Elastic Window Scan (FEWS) shows that the incorporation of ILs affects the phase behaviour of the phospholipid membrane significantly and the transition from a solid gel to a fluid phase shifts to lower temperature. This is found to be consistent with our differential scanning calorimetry measurements. DMIM[BF4], which has a longer alkyl chain cation, affects the phase behaviour more strongly in comparison to BMIM[BF4]. The pressure-area isotherms of the DMPC monolayer measured at the air-water interface show that in the presence of ILs, isotherms shift towards higher area-per lipid molecule. DMIM[BF4] is found to shift the isotherm to a greater extent compared to BMIM[BF4]. Quasielastic neutron scattering (QENS) data show that both ILs act as a plasticizer, which enhances the fluidity of the membrane. DMIM[BF4] is found to be a stronger plasticizing agent in comparison to BMIM[BF4] that has a cation with a shorter alkyl chain. The incorporation of DMIM[BF4] enhances not only the long range lateral motion but also the localised internal motion of the lipids. On the other hand, BMIM[BF4] acts weakly in comparison to DMIM[BF4] and mainly alters the localised internal motion of the lipids. Any subtle change in the dynamical properties of the membrane can profoundly affect the stability of the cell. Hence, the dominant effect of the IL with the longer chain length on the dynamics of the phospholipid membrane might be correlated with its cytotoxic activity. QENS data analysis has provided a quantitative description of the effects of the two imidazolium-based ILs on the dynamical and phase behaviour of the model cell membrane, which is essential for a detailed understanding of their action mechanism.
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Affiliation(s)
- V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
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21
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Lee BL, Kuczera K. Simulating the free energy of passive membrane permeation for small molecules. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1407029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Brent L. Lee
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
| | - Krzysztof Kuczera
- Department of Chemistry, The University of Kansas , Lawrence, KS, USA
- Department of Molecular Biosciences, The University of Kansas , Lawrence, KS, USA
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22
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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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23
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Yamada T, Takahashi N, Tominaga T, Takata SI, Seto H. Dynamical Behavior of Hydration Water Molecules between Phospholipid Membranes. J Phys Chem B 2017; 121:8322-8329. [PMID: 28787155 DOI: 10.1021/acs.jpcb.7b01276] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamical behavior of hydration water sandwiched between 1,2-dimyristyl-sn-glycero-3-phosphocholine (DMPC) bilayers was investigated by quasi-elastic neutron scattering (QENS) in the range between 275 and 316 K, where the main transition temperature of DMPC is interposed. The results revealed that the hydration water could be categorized into three types of water: (1) free water, whose dynamical behavior is slightly different from that of bulk water; (2) loosely bound water, whose dynamical behavior is 1 order of magnitude slower than that of the free water; and (3) tightly bound water, whose dynamical behavior is comparable with that of DMPC molecules. The number of loosely bound and tightly bound water molecules per DMPC molecule monotonically decreased and increased with decreasing temperature, respectively, and the sum of these water molecules remained constant. The number of free water molecules per DMPC molecule was constant in the measured temperature range.
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Affiliation(s)
- Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS) , 162-1 Shirakata, Tokai, Naka, Ibaraki, Japan 319-1106
| | - Nobuaki Takahashi
- Institute for Chemical Research, Kyoto University Gokasho , Uji, Kyoto, Japan 611-0011
| | - Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS) , 162-1 Shirakata, Tokai, Naka, Ibaraki, Japan 319-1106
| | - Shin-Ichi Takata
- J-PARC Center, Japan Atomic Energy Agency , 2-4 Shirakata, Tokai, Japan 319-1195
| | - Hideki Seto
- J-PARC Center, High Energy Accelerator Research Organization , 203-1 Shirakata, Tokai, Ibaraki, Japan 319-1106
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24
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Dynamic processes in biological membrane mimics revealed by quasielastic neutron scattering. Chem Phys Lipids 2017; 206:28-42. [DOI: 10.1016/j.chemphyslip.2017.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 12/15/2022]
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25
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Peters J, Marion J, Natali F, Kats E, Bicout DJ. The Dynamical Transition of Lipid Multilamellar Bilayers as a Matter of Cooperativity. J Phys Chem B 2017. [PMID: 28650664 DOI: 10.1021/acs.jpcb.7b05167] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present study is the application of a two-state model formerly developed by Bicout and Zaccai [ Bicout , D. J. and Zaccai , G. Biophys. J. 2001 , 80 ( 3 ), 1115 - 1123 ] to describe the dynamical transition exhibited in the atomic mean square displacements of biological samples in terms of dynamic and thermodynamic parameters. Data were obtained by elastic incoherent neutron scattering on 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid membranes in various hydration states and on one partially per-deuterated lipid membrane. Fitting the data with the model allowed investigating which parts of lipid molecules were mainly involved in the dynamical transition, heads, tails, or both. Clear differences were found between the fully protonated and partially deuterated membranes. These findings shed light on the question of what is the degree of dynamical cooperativity of the atoms during the transition. Whereas the level of hydration does not significantly affect it, as the dry, the intermediate dry, and fully hydrated membranes all undergo a rather broad transition, the transition of the lipid tails is much sharper and sets in at much lower temperature than that of the heads. Therefore, the dynamical cooperativity appears high among the particles in the tails. Moreover, the transition of the lipid tails has to be completed first before the one of the head groups starts.
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Affiliation(s)
- Judith Peters
- Université 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
| | - Jérémie Marion
- Institut Laue-Langevin , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France.,Université Grenoble Alpes , IBS, 71 avenue des Martyrs, CS 10090, 38044 Grenoble, France
| | - Francesca Natali
- Institut Laue-Langevin , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France.,CNR-IOM, OGG , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France
| | - Efim Kats
- Institut Laue-Langevin , 71 avenue des Martyrs, CS 20156, 38042 Grenoble cedex 9, France.,Landau Institute for Theoretical Physics, RAS , 142432, Chernogolovka, Moscow region, Russia
| | - Dominique 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
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26
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Miskowiec A, Buck ZN, Hansen FY, Kaiser H, Taub H, Tyagi M, Diallo SO, Mamontov E, Herwig KW. On the structure and dynamics of water associated with single-supported zwitterionic and anionic membranes. J Chem Phys 2017; 146:125102. [DOI: 10.1063/1.4978677] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A. Miskowiec
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - Z. N. Buck
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - F. Y. Hansen
- Department of Chemistry, Technical University of Denmark, IK 207 DTU, DK-2800 Lyngby, Denmark
| | - H. Kaiser
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - H. Taub
- Department of Physics and Astronomy and University of Missouri Research Reactor, University of Missouri, Columbia, Missouri 65211, USA
| | - M. Tyagi
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6102, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - S. O. Diallo
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - E. Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - K. W. Herwig
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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27
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Inelastic and quasi-elastic neutron scattering spectrometers in J-PARC. Biochim Biophys Acta Gen Subj 2016; 1861:3651-3660. [PMID: 27156489 DOI: 10.1016/j.bbagen.2016.04.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 11/20/2022]
Abstract
J-PARC, Japan Proton Accelerator Research Complex provides short pulse proton beam at a repetition rate 25Hz and the maximum power is expected to be 1MW. Materials and Life Science Experimental Facility (MLF) has 23 neutron beam ports and 21 instruments have already been operated or under construction/commissioning. There are 6 inelastic/quasi-elastic neutron scattering spectrometers and the complementary use of these spectrometers will open new insight for life science. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics. MATERIALS 2016; 9:ma9050319. [PMID: 28773441 PMCID: PMC5503093 DOI: 10.3390/ma9050319] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/18/2016] [Accepted: 04/21/2016] [Indexed: 11/27/2022]
Abstract
Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs). We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i) to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii) to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii) to the higher probability of water–lipid HBs as the hydration decreases. Our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.
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29
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Aoun B, Pellegrini E, Trapp M, Natali F, Cantù L, Brocca P, Gerelli Y, Demé B, Marek Koza M, Johnson M, Peters J. Direct comparison of elastic incoherent neutron scattering experiments with molecular dynamics simulations of DMPC phase transitions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:48. [PMID: 27112937 DOI: 10.1140/epje/i2016-16048-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
Neutron scattering techniques have been employed to investigate 1,2-dimyristoyl-sn -glycero-3-phosphocholine (DMPC) membranes in the form of multilamellar vesicles (MLVs) and deposited, stacked multilamellar-bilayers (MLBs), covering transitions from the gel to the liquid phase. Neutron diffraction was used to characterise the samples in terms of transition temperatures, whereas elastic incoherent neutron scattering (EINS) demonstrates that the dynamics on the sub-macromolecular length-scale and pico- to nano-second time-scale are correlated with the structural transitions through a discontinuity in the observed elastic intensities and the derived mean square displacements. Molecular dynamics simulations have been performed in parallel focussing on the length-, time- and temperature-scales of the neutron experiments. They correctly reproduce the structural features of the main gel-liquid phase transition. Particular emphasis is placed on the dynamical amplitudes derived from experiment and simulations. Two methods are used to analyse the experimental data and mean square displacements. They agree within a factor of 2 irrespective of the probed time-scale, i.e. the instrument utilized. Mean square displacements computed from simulations show a comparable level of agreement with the experimental values, albeit, the best match with the two methods varies for the two instruments. Consequently, experiments and simulations together give a consistent picture of the structural and dynamical aspects of the main lipid transition and provide a basis for future, theoretical modelling of dynamics and phase behaviour in membranes. The need for more detailed analytical models is pointed out by the remaining variation of the dynamical amplitudes derived in two different ways from experiments on the one hand and simulations on the other.
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Affiliation(s)
- Bachir Aoun
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Eric Pellegrini
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Marcus Trapp
- Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120, Heidelberg, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie, Lise-Meitner Campus, Hahn-Meitner-Platz 1, 14109, Berlin, Germany
| | - Francesca Natali
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
- CNR-IOM-OGG, c/o Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Laura Cantù
- University of Milan, via F. lli Cervi 93, 20090, Segrate, Italy
| | - Paola Brocca
- University of Milan, via F. lli Cervi 93, 20090, Segrate, Italy
| | - Yuri Gerelli
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Bruno Demé
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Michael Marek Koza
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Mark Johnson
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France
| | - Judith Peters
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, 38042, Grenoble Cedex 9, France.
- LiPhy, UFR PhITEM, Univ. Grenoble Alpes, 71 avenue des Martyrs, CS 10090, 38044, Grenoble, France.
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30
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Tang J, Alsop RJ, Schmalzl K, Epand RM, Rheinstädter MC. Strong Static Magnetic Fields Increase the Gel Signal in Partially Hydrated DPPC/DMPC Membranes. MEMBRANES 2015; 5:532-52. [PMID: 26426063 PMCID: PMC4703998 DOI: 10.3390/membranes5040532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/17/2015] [Indexed: 11/16/2022]
Abstract
It was recently reported that static magnetic fields increase lipid order in the hydrophobic membrane core of dehydrated native plant plasma membranes [Poinapen, Soft Matter 9:6804-6813, 2013]. As plasma membranes are multicomponent, highly complex structures, in order to elucidate the origin of this effect, we prepared model membranes consisting of a lipid species with low and high melting temperature. By controlling the temperature, bilayers coexisting of small gel and fluid domains were prepared as a basic model for the plasma membrane core. We studied molecular order in mixed lipid membranes made of dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) using neutron diffraction in the presence of strong static magnetic fields up to 3.5 T. The contribution of the hydrophobic membrane core was highlighted through deuterium labeling the lipid acyl chains. There was no observable effect on lipid organization in fluid or gel domains at high hydration of the membranes. However, lipid order was found to be enhanced at a reduced relative humidity of 43%: a magnetic field of 3.5 T led to an increase of the gel signal in the diffraction patterns of 5%. While all biological materials have weak diamagnetic properties, the corresponding energy is too small to compete against thermal disorder or viscous effects in the case of lipid molecules. We tentatively propose that the interaction between the fatty acid chains’ electric moment and the external magnetic field is driving the lipid tails in the hydrophobic membrane core into a better ordered state.
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Affiliation(s)
- Jennifer Tang
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, L8S 4M1, Canada.
| | - Richard J Alsop
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, L8S 4M1, Canada.
| | - Karin Schmalzl
- JCNS, Forschungszentrum Jülich, Outstation at ILL, 38042 Grenoble, France.
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Maikel C Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, L8S 4M1, Canada.
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31
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Structural characterization of soft interfaces by standing-wave fluorescence with X-rays and neutrons. Curr Opin Colloid Interface Sci 2015. [DOI: 10.1016/j.cocis.2015.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Wanderlingh U, D'Angelo G, Branca C, Nibali VC, Trimarchi A, Rifici S, Finocchiaro D, Crupi C, Ollivier J, Middendorf HD. Multi-component modeling of quasielastic neutron scattering from phospholipid membranes. J Chem Phys 2015; 140:174901. [PMID: 24811662 DOI: 10.1063/1.4872167] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigated molecular motions in the 0.3-350 ps time range of D2O-hydrated bilayers of 1-palmitoyl-oleoyl-sn-glycero-phosphocholine and 1,2-dimyristoyl-sn-glycero-phosphocholine in the liquid phase by quasielastic neutron scattering. Model analysis of sets of spectra covering scale lengths from 4.8 to 30 Å revealed the presence of three types of motion taking place on well-separated time scales: (i) slow diffusion of the whole phospholipid molecules in a confined cylindrical region; (ii) conformational motion of the phospholipid chains; and (iii) fast uniaxial rotation of the hydrogen atoms around their carbon atoms. Based on theoretical models for the hydrogen dynamics in phospholipids, the spatial extent of these motions was analysed in detail and the results were compared with existing literature data. The complex dynamics of protons was described in terms of elemental dynamical processes involving different parts of the phospholipid chain on whose motions the hydrogen atoms ride.
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Affiliation(s)
- U Wanderlingh
- Dipartimento di Fisica e Scienze della Terra, University of Messina, I-98166 Messina, Italy
| | - G D'Angelo
- Dipartimento di Fisica e Scienze della Terra, University of Messina, I-98166 Messina, Italy
| | - C Branca
- Dipartimento di Fisica e Scienze della Terra, University of Messina, I-98166 Messina, Italy
| | - V Conti Nibali
- Institute for Physical Chemistry II, Ruhr-University Bochum, Bochum, Germany
| | - A Trimarchi
- Dipartimento di Fisica e Scienze della Terra, University of Messina, I-98166 Messina, Italy
| | - S Rifici
- Dipartimento di Fisica e Scienze della Terra, University of Messina, I-98166 Messina, Italy
| | - D Finocchiaro
- Dipartimento di Fisica e Scienze della Terra, University of Messina, I-98166 Messina, Italy
| | - C Crupi
- IPCF-V.le F. Stagno D'Alcontres, n. 37, Messina 98158, Italy
| | - J Ollivier
- Institut Laue-Langevin, 6 rue J. Horowitz, BP 156, F-38042 Grenoble, France
| | - H D Middendorf
- Clarendon Laboratory, University of Oxford, Oxford, United Kingdom
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33
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Sharma VK, Mamontov E, Anunciado DB, O’Neill H, Urban V. Nanoscopic Dynamics of Phospholipid in Unilamellar Vesicles: Effect of Gel to Fluid Phase Transition. J Phys Chem B 2015; 119:4460-70. [DOI: 10.1021/acs.jpcb.5b00220] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- V. K. Sharma
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Solid
State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - E. Mamontov
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - D. B. Anunciado
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - H. O’Neill
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - V. Urban
- Biology
and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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34
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Control and role of pH in peptide–lipid interactions in oriented membrane samples. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:833-41. [DOI: 10.1016/j.bbamem.2014.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/01/2014] [Accepted: 12/04/2014] [Indexed: 12/22/2022]
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35
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Gerelli Y, de Ghellinck A, Jouhet J, Laux V, Haertlein M, Fragneto G. Multi-lamellar organization of fully deuterated lipid extracts of yeast membranes. ACTA ACUST UNITED AC 2014; 70:3167-76. [PMID: 25478835 DOI: 10.1107/s1399004714022913] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 10/18/2014] [Indexed: 05/28/2023]
Abstract
Neutron scattering studies on mimetic biomembranes are currently limited by the low availability of deuterated unsaturated lipid species. In the present work, results from the first neutron diffraction experiments on fully deuterated lipid extracts from the yeast Pichia pastoris are presented. The structural features of these fully deuterated lipid stacks are compared with those of their hydrogenous analogues and with other similar synthetic systems. The influence of temperature and humidity on the samples has been investigated by means of small momentum-transfer neutron diffraction. All of the lipid extracts investigated self-assemble into multi-lamellar stacks having different structural periodicities; the stacking distances are affected by temperature and humidity without altering the basic underlying arrangement. At high relative humidity the deuterated and hydrogenous samples are similar in their multi-lamellar arrangement, being characterized by two main periodicities of ∼75 and ∼110 Å reflecting the presence of a large number of polar phospholipid molecules. Larger differences are found at lower relative humidity, where hydrogenous lipids are characterized by a larger single lamellar structure than that observed in the deuterated samples. In both cases the heterogeneity in composition is reflected in a wide structural complexity. The different behaviour upon dehydration can be related to compositional differences in the molecular composition of the two samples, which is attributed to metabolic effects related to the use of perdeuterated growth media.
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Affiliation(s)
- Yuri Gerelli
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | | | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire and Végétale (LPCV), CNRS (UMR5168)/Université Grenoble Alpes/INRA (USC1359)/CEA Grenoble, Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), 17 Rue des Martyrs, 38054 Grenoble CEDEX 9, France
| | - Valérie Laux
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Michael Haertlein
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Giovanna Fragneto
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
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36
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Thermal Fluctuations in Amphipol A8-35 Particles: A Neutron Scattering and Molecular Dynamics Study. J Membr Biol 2014; 247:897-908. [DOI: 10.1007/s00232-014-9725-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/26/2014] [Indexed: 01/03/2023]
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37
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Grosse W, Psakis G, Mertins B, Reiss P, Windisch D, Brademann F, Bürck J, Ulrich A, Koert U, Essen LO. Structure-based engineering of a minimal porin reveals loop-independent channel closure. Biochemistry 2014; 53:4826-38. [PMID: 24988371 DOI: 10.1021/bi500660q] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Porins, like outer membrane protein G (OmpG) of Escherichia coli, are ideal templates among ion channels for protein and chemical engineering because of their robustness and simple architecture. OmpG shows fast transitions between open and closed states, which were attributed to loop 6 (L6). As flickering limits single-channel-based applications, we pruned L6 by either 8 or 12 amino acids. While the open probabilities of both L6 variants resemble that of native OmpG, their gating frequencies were reduced by 63 and 81%, respectively. Using the 3.2 Å structure of the shorter L6 variant in the open state, we engineered a minimal porin (220 amino acids), where all remaining extramembranous loops were truncated. Unexpectedly, this minimized porin still exhibited gating, but it was 5-fold less frequent than in OmpG. The residual gating of the minimal pore is hence independent of L6 rearrangements and involves narrowing of the ion conductance pathway most probably driven by global stretching-flexing deformations of the membrane-embedded β-barrel.
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Affiliation(s)
- Wolfgang Grosse
- Department of Chemistry, Philipps-University Marburg , Hans-Meerwein-Straße, 35032 Marburg, Germany
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38
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Trapp M, Marion J, Tehei M, Demé B, Gutberlet T, Peters J. High hydrostatic pressure effects investigated by neutron scattering on lipid multilamellar vesicles. Phys Chem Chem Phys 2014; 15:20951-6. [PMID: 24201561 DOI: 10.1039/c3cp52762j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effects of high hydrostatic pressure on the structure and dynamics of model membrane systems were investigated using neutron scattering. Diffraction experiments show shifts of the pre- and main-phase transitions of multilamellar vesicles of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) to higher temperatures with increased pressure which are close to results observed previously by other techniques, namely (10.4 ± 1.0) K kbar(-1) and (20.0 ± 0.5) K kbar(-1) for the two transitions. Backscattering spectroscopy reveals that the mean square displacements in the liquid phase are about 10% smaller at 300 bar and about 20% smaller at 600 bar compared to atmospheric pressure, whereas in the gel phase below the main phase transition the mean square displacements show a smaller difference in the dynamics of the three pressure values within the studied pressure range.
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Affiliation(s)
- Marcus Trapp
- Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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39
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Stadler AM, Unruh T, Namba K, Samatey F, Zaccai G. Correlation between supercoiling and conformational motions of the bacterial flagellar filament. Biophys J 2014; 105:2157-65. [PMID: 24209861 DOI: 10.1016/j.bpj.2013.09.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 09/02/2013] [Accepted: 09/23/2013] [Indexed: 10/26/2022] Open
Abstract
The bacterial flagellar filament is a very large macromolecular assembly of a single protein, flagellin. Various supercoiled states of the filament exist, which are formed by two structurally different conformations of flagellin in different ratios. We investigated the correlation between supercoiling of the protofilaments and molecular dynamics in the flagellar filament using quasielastic and elastic incoherent neutron scattering on the picosecond and nanosecond timescales. Thermal fluctuations in the straight L- and R-type filaments were measured and compared to the resting state of the wild-type filament. Amplitudes of motion on the picosecond timescale were found to be similar in the different conformational states. Mean-square displacements and protein resilience on the 0.1 ns timescale demonstrate that the L-type state is more flexible and less resilient than the R-type, whereas the wild-type state lies in between. Our results provide strong support that supercoiling of the protofilaments in the flagellar filament is determined by the strength of molecular forces in and between the flagellin subunits.
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Affiliation(s)
- Andreas M Stadler
- Jülich Centre for Neutron Science JCNS (JCNS-1) and Institute for Complex Systems (ICS-1), Forschungszentrum Jülich, Jülich, Germany.
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40
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Knoll W, Peters J, Kursula P, Gerelli Y, Ollivier J, Demé B, Telling M, Kemner E, Natali F. Structural and dynamical properties of reconstituted myelin sheaths in the presence of myelin proteins MBP and P2 studied by neutron scattering. SOFT MATTER 2014; 10:519-529. [PMID: 24651633 DOI: 10.1039/c3sm51393a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The myelin sheath is a tightly packed, multilayered membrane structure wrapped around selected nerve axons in the central and the peripheral nervous system. Because of its electrical insulation of the axons, which allows fast, saltatory nerve impulse conduction, myelin is crucial for the proper functioning of the vertebrate nervous system. A subset of myelin-specific proteins is well-defined, but their influence on membrane dynamics, i.e. myelin stability, has not yet been explored in detail. We investigated the structure and the dynamics of reconstituted myelin membranes on a pico- to nanosecond timescale, influenced by myelin basic protein (MBP) and myelin protein 2 (P2), using neutron diffraction and quasi-elastic neutron scattering. A model for the scattering function describing molecular lipid motions is suggested. Although dynamical properties are not affected significantly by MBP and P2 proteins, they act in a highly synergistic manner influencing the membrane structure.
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Affiliation(s)
- Wiebke Knoll
- University Joseph Fourier UFR PhITEM, Grenoble, France
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41
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Peters J, Giudici-Orticoni MT, Zaccai G, Guiral M. Dynamics measured by neutron scattering correlates with the organization of bioenergetics complexes in natural membranes from hyperthermophile and mesophile bacteria. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:78. [PMID: 23880731 DOI: 10.1140/epje/i2013-13078-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 02/01/2013] [Accepted: 02/26/2013] [Indexed: 06/02/2023]
Abstract
Various models on membrane structure and organization of proteins and complexes in natural membranes emerged during the last years. However, the lack of systematic dynamical studies to complement structural investigations hindered the establishment of a more complete picture of these systems. Elastic incoherent neutron scattering gives access to the dynamics on a molecular level and was applied to natural membranes extracted from the hyperthermophile Aquifex aeolicus and the mesophile Wolinella succinogenes bacteria. The results permitted to extract a hierarchy of dynamic flexibility and atomic resilience within the samples, which correlated with the organization of proteins in bioenergetics complexes and the functionality of the membranes.
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Affiliation(s)
- J Peters
- Institut Laue Langevin, 6 rue J. Horowitz, BP 156, F-38042 Grenoble Cedex 9, France.
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42
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Choi DH, Son H, Jung S, Park J, Park WY, Kwon OS, Park GS. Dielectric relaxation change of water upon phase transition of a lipid bilayer probed by terahertz time domain spectroscopy. J Chem Phys 2013; 137:175101. [PMID: 23145747 DOI: 10.1063/1.4764304] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We investigate the influence of the 1, 2-ditetradecanoyl-sn-glycero-3-phosphocholine lipid bilayer phases on the water reorientation dynamics with terahertz time domain spectroscopy. The phase of the lipids was controlled by the temperature in the range of 14-35 °C. During the gel-to-fluid phase transition, the hydration water ratio drastically changed from 0.3 to 0.6. The absorption coefficient of the hydration water increased with the temperature in the gel phase and then decreased in the fluid phase. The dielectric relaxation time of the lipid solution decreased initially but then increased after the phase transition. This indicates that the hydration water reorientation dynamics are restricted by lipids and that this phenomenon is pronounced in a biologically relevant fluid phase.
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Affiliation(s)
- Da-Hye Choi
- Center for THz-Bio Application Systems, Department of Physics and Astronomy, Seoul National University, Seoul 151-747, South Korea
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43
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Sharma VK, Mitra S, Garcia Sakai V, Mukhopadhyay R. Dynamical features in cationic micelles of varied chain length. J Phys Chem B 2012; 116:9007-15. [PMID: 22775756 DOI: 10.1021/jp304841a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chain length is one of the parameters controlling the structural arrangement of micelle monomers, such that one can tailor the monomers for different applications, but the effect of chain length on the dynamical behavior of micelles is unknown. In this article, we report a study on the effect of varying chain length on the dynamical behavior of alkyltrimethylammonium bromide (C(n)TAB) micelles (n = 10, 12, 14, and 16) using incoherent quasielastic neutron scattering (QENS). The data analysis clearly shows the presence of two distinct motions: global motion of whole micelles and faster internal motions of the C(n)TAB monomers. The global diffusion is Fickian in nature, whereas the internal motions can be described with a model that considers the motions of the headgroup and the hydrophobic alkyl chain separately. Methyl groups in the headgroup undergo 3-fold jump rotations, and the hydrogen atoms belonging to the alkyl chain undergo localized translational diffusion. The hydrogen atoms belonging to the alkyl chain are confined within spherical volumes that increase linearly along the C(n)TAB chain: the hydrogen atoms closer to the headgroup move within smaller spheres with lower diffusion coefficients than those farther from the headgroup. The main result is that, with increasing chain length, the dynamics of the C(n)TAB monomer is greatly affected: diffusion is reduced and occurs in smaller spheres, and residence times are increased. Global motion is also hindered with increased chain length.
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Affiliation(s)
- V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
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44
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Pieper J, Trapp M, Skomorokhov A, Natkaniec I, Peters J, Renger G. Temperature-dependent vibrational and conformational dynamics of photosystem II membrane fragments from spinach investigated by elastic and inelastic neutron scattering. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1213-9. [PMID: 22465855 DOI: 10.1016/j.bbabio.2012.03.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/07/2012] [Accepted: 03/16/2012] [Indexed: 11/27/2022]
Abstract
Vibrational and conformational protein dynamics of photosystem II (PS II) membrane fragments from spinach were investigated by elastic and inelastic incoherent neutron scattering (EINS and IINS). As to the EINS experiments, the average atomic mean square displacement values of PS II membrane fragments hydrated at a relative humidity of 57% exhibit a dynamical transition at ~230K. In contrast, the dynamical transition was absent at a relative humidity of 44%. These findings are in agreement with previous studies which reported a "freezing" of protein mobility due to dehydration (Pieper et al. (2008) Eur. Biophys. J. 37: 657-663) and its correlation with an inhibition of electron transfer from Q(A)(-) to Q(B) (Kaminskaya et al. (2003) Biochemistry 42, 8119-8132). IINS spectra of a sample hydrated at a relative humidity of 57% show a distinct Boson peak at ~7.5meV at 20K, which shifts towards lower energy values upon temperature increase to 250K. This unexpected effect is interpreted in terms of a "softening" of the protein matrix along with the onset of conformational protein dynamics as revealed by the EINS experiments. Information on the density of vibrational states of pigment-protein complexes is important for a realistic calculation of excitation energy transfer kinetics and spectral lineshapes and is often routinely obtained by optical line-narrowing spectroscopy at liquid helium temperature. The data presented here demonstrate that IINS is a valuable experimental tool in determining the density of vibrational states not only at cryogenic, but also at nearly physiological temperatures up to 250K. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
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Affiliation(s)
- Jörg Pieper
- Institute of Physics, University of Tartu, Tartu, Estonia.
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45
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Nagy G, Pieper J, Krumova SB, Kovács L, Trapp M, Garab G, Peters J. Dynamic properties of photosystem II membranes at physiological temperatures characterized by elastic incoherent neutron scattering. Increased flexibility associated with the inactivation of the oxygen evolving complex. PHOTOSYNTHESIS RESEARCH 2012; 111:113-24. [PMID: 22052408 DOI: 10.1007/s11120-011-9701-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 10/13/2011] [Indexed: 05/02/2023]
Abstract
Elastic incoherent neutron scattering (EINS), a non-invasive technique which is capable of measuring the mean square displacement of atoms in the sample, has been widely used in biology for exploring the dynamics of proteins and lipid membranes but studies on photosynthetic systems are scarce. In this study we investigated the dynamic characteristics of Photosystem II (PSII) membrane fragments between 280 and 340 K, i.e., in the physiological temperature range and in the range of thermal denaturation of some of the protein complexes. The mean square displacement values revealed the presence of a hydration-sensitive transition in the sample between 310 and 320 K, suggesting that the oxygen evolving complex (OEC) plays an important role in the transition. Indeed, in samples in which the OEC had been removed by TRIS- or heat-treatments (323 and 333 K) no such transition was found. Further support on the main role of OEC in these reorganizations is provided by data obtained from differential scanning calorimetry experiments, showing marked differences between the untreated and TRIS-treated samples. In contrast, circular dichroism spectra exhibited only minor changes in the excitonic interactions below 323 K, showing that the molecular organization of the pigment-protein complexes remains essentially unaffected. Our data, along with earlier incoherent neutron scattering data on PSII membranes at cryogenic temperatures (Pieper et al., Biochemistry 46:11398-11409, 2007), demonstrate that this technique can be applied to characterize the dynamic features of PSII membranes, and can be used to investigate photosynthetic membranes under physiologically relevant experimental conditions.
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Affiliation(s)
- Gergely Nagy
- Institut Laue-Langevin, P.O. Box 156, 38042, Grenoble Cedex 9, France
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46
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Nafday OA, Lenhert S. High-throughput optical quality control of lipid multilayers fabricated by dip-pen nanolithography. NANOTECHNOLOGY 2011; 22:225301. [PMID: 21464525 DOI: 10.1088/0957-4484/22/22/225301] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Surface supported phospholipid multilayers are promising materials for nanotechnology because of their tendency to self-organize, their innate biocompatibility, the possibility to encapsulate other materials within the multilayers, and the ability to control the multilayer thickness between ∼ 2 and 100 nm during fabrication. Dip-pen nanolithography (DPN) is an atomic force microscopy (AFM) based fabrication method that allows high-throughput fabrication and integration of a variety of micro- and nanostructured materials including lipid multilayers, with areal throughputs on the scale of cm(2) min(-1). Although multilayer thickness is a critical feature that determines the functionality of the lipid multilayer structures (for instance as carriers for other materials as well as optical scattering properties), reliable height characterization by AFM is slow (on the order of µm(2) min(-1)) and a bottleneck in the lithographic process. Here we describe a novel optical method to reliably measure the height of fluorescent multilayers with thicknesses above 10 nm, and widths above the optical diffraction limit based on calibrating the fluorescence intensity using one-time AFM height measurements. This allows large surface areas to be rapidly and quantitatively characterized using a standard fluorescence microscope. Importantly, different pattern dimensions (0D dots, 1D lines or 2D squares) require different calibration parameters, indicating that shape influences the optical properties of the structured lipid multilayers. This method has general implications in the systematic and high-throughput optical characterization of nanostructure-function relationships.
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Affiliation(s)
- Omkar A Nafday
- Department of Biological Science and Integrative Nanoscience Institute, Florida State University, Tallahassee, FL 32306-4370, USA
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47
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Berntsen P, Svanberg C, Swenson J. Interplay between hydration water and headgroup dynamics in lipid bilayers. J Phys Chem B 2011; 115:1825-32. [PMID: 21302948 DOI: 10.1021/jp110899j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, the interplay between water and lipid dynamics has been investigated by broadband dielectric spectroscopy and modulated differential scanning calorimetry (MDSC). The multilamellar lipid bilayer system 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) has been studied over a broad temperature range at three different water contents: about 3, 6, and 9 water molecules per lipid molecule. The results from the dielectric relaxation measurements show that at temperatures <250 K the lipid headgroup rotation is described by a super-Arrhenius temperature dependence at the lowest hydration level and by the Arrhenius law at the highest hydration level. This difference in the temperature dependence of the lipid headgroup rotation can be explained by the increasing interaction between the headgroups with decreasing water content, which causes their rotational motion to be more cooperative in character. The main water relaxation shows an anomalous dependence on the water content in the supercooled and glassy regime. In contrast to the general behavior of interfacial water, the water dynamics is fastest in the driest sample and its temperature dependence is best described by a super-Arrhenius temperature dependence. The best explanation for this anomalous behavior is that the water relaxation becomes more determined by fast local lipid motions than by the intrinsic water dynamics at low water contents. In support for this interpretation is the finding that the relaxation time of the main water process is faster than that in most other host systems at temperatures below 180 K. Thus, the dielectric relaxation data show clearly the strong interplay between water and lipid dynamics; the water influences the lipid dynamics and vice versa. In the MDSC data, we observe a weak enthalpy relaxation at 203 K for the driest sample and at 179 K for the most hydrated sample, attributed to the freezing-in of the lipid headgroup rotation observed in the dielectric data, since this motion reaches a time scale of about 100 s at about the same temperatures.
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Affiliation(s)
- P Berntsen
- Department of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg, Sweden.
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