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Ramanthrikkovil Variyam A, Stolov M, Feng J, Amdursky N. Solid-State Molecular Protonics Devices of Solid-Supported Biological Membranes Reveal the Mechanism of Long-Range Lateral Proton Transport. ACS NANO 2024; 18:5101-5112. [PMID: 38314693 PMCID: PMC10867892 DOI: 10.1021/acsnano.3c11990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Lateral proton transport (PT) on the surface of biological membranes is a fundamental biochemical process in the bioenergetics of living cells, but a lack of available experimental techniques has resulted in a limited understanding of its mechanism. Here, we present a molecular protonics experimental approach to investigate lateral PT across membranes by measuring long-range (70 μm) lateral proton conduction via a few layers of lipid bilayers in a solid-state-like environment, i.e., without having bulk water surrounding the membrane. This configuration enables us to focus on lateral proton conduction across the surface of the membrane while decoupling it from bulk water. Hence, by controlling the relative humidity of the environment, we can directly explore the role of water in the lateral PT process. We show that proton conduction is dependent on the number of water molecules and their structure and on membrane composition, where we explore the role of the headgroup, the tail saturation, the membrane phase, and membrane fluidity. The measured PT as a function of temperature shows an inverse temperature dependency, which we explain by the desorption and adsorption of water molecules into the solid membrane platform. We explain our findings by discussing the role of percolating hydrogen bonding within the membrane structure in a Grotthuss-like mechanism.
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Affiliation(s)
| | - Mikhail Stolov
- Wolfson
Department of Chemical Engineering, Technion
− Israel Institute of Technology, Haifa 3200003, Israel
| | - Jiajun Feng
- Schulich
Faculty of Chemistry, Technion −
Israel Institute of Technology, Haifa 3200003, Israel
| | - Nadav Amdursky
- Schulich
Faculty of Chemistry, Technion −
Israel Institute of Technology, Haifa 3200003, Israel
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2
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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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3
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Nagao M, Seto H. Neutron scattering studies on dynamics of lipid membranes. BIOPHYSICS REVIEWS 2023; 4:021306. [PMID: 38504928 PMCID: PMC10903442 DOI: 10.1063/5.0144544] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/01/2023] [Indexed: 03/21/2024]
Abstract
Neutron scattering methods are powerful tools for the study of the structure and dynamics of lipid bilayers in length scales from sub Å to tens to hundreds nm and the time scales from sub ps to μs. These techniques also are nondestructive and, perhaps most importantly, require no additives to label samples. Because the neutron scattering intensities are very different for hydrogen- and deuterium-containing molecules, one can replace the hydrogen atoms in a molecule with deuterium to prepare on demand neutron scattering contrast without significantly altering the physical properties of the samples. Moreover, recent advances in neutron scattering techniques, membrane dynamics theories, analysis tools, and sample preparation technologies allow researchers to study various aspects of lipid bilayer dynamics. In this review, we focus on the dynamics of individual lipids and collective membrane dynamics as well as the dynamics of hydration water.
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Affiliation(s)
| | - Hideki Seto
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan
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4
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Majcher MJ, Himbert S, Vito F, Campea MA, Dave R, Vetergaard Jensen G, Rheinstadter MC, Smeets NMB, Hoare T. Investigating the Kinetics and Structure of Network Formation in Ultraviolet-Photopolymerizable Starch Nanogel Network Hydrogels via Very Small-Angle Neutron Scattering and Small-Amplitude Oscillatory Shear Rheology. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael J. Majcher
- Department of Chemical Engineering, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4L8, Canada
| | - Sebastian Himbert
- Department of Physics & Astronomy, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4L8, Canada
| | - Francesco Vito
- Department of Chemical Engineering, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4L8, Canada
| | - Matthew A. Campea
- Department of Chemical Engineering, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4L8, Canada
| | - Ridhdhi Dave
- Department of Chemical Engineering, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4L8, Canada
| | - Grethe Vetergaard Jensen
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6100, United States
| | - Maikel C. Rheinstadter
- Department of Physics & Astronomy, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4L8, Canada
| | - Niels M. B. Smeets
- Department of Chemical Engineering, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4L8, Canada
| | - Todd Hoare
- Department of Chemical Engineering, McMaster University, 1280 Main St. W., Hamilton, Ontario L8S 4L8, Canada
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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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6
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Marques MPM, Santos IP, Batista de Carvalho ALM, Mamede AP, Martins CB, Figueiredo P, Sarter M, Sakai VG, Batista de Carvalho LAE. Water dynamics in human cancer and non-cancer tissues. Phys Chem Chem Phys 2022; 24:15406-15415. [PMID: 35704895 DOI: 10.1039/d2cp00621a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Normal-to-malignant transformation is a poorly understood process associated with cellular biomechanical properties. These are strongly dependent on the dynamical behaviour of water, known to play a fundamental role in normal cellular activity and in the maintenance of the three-dimensional architecture of the tissue and the functional state of biopolymers. In this study, quasi-elastic neutron scattering was used to probe the dynamical behaviour of water in human cancer specimens and their respective surrounding normal tissue from breast and tongue, as an innovative approach for identifying particular features of malignancy. This methodology has been successfully used by the authors in human cells and was the first study of human tissues by neutron scattering techniques. A larger flexibility was observed for breast versus tongue tissues. Additionally, different dynamics were found for malignant and non-malignant specimens, depending on the tissue: higher plasticity for breast invasive cancer versus the normal, and an opposite effect for tongue. The data were interpreted in the light of two different water populations within the samples: one displaying bulk-like dynamics (extracellular and intracellular/cytoplasmic) and another with constrained flexibility (extracellular/interstitial and intracellular/hydration layers).
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Affiliation(s)
- M P M Marques
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal. .,University of Coimbra, Department of Life Sciences, 3000-456 Coimbra, Portugal
| | - I P Santos
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - A L M Batista de Carvalho
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - A P Mamede
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - C B Martins
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - P Figueiredo
- Oncology Institute of Coimbra Francisco Gentil, 3000-075 Coimbra, Portugal
| | - M Sarter
- ISIS Neutron and Muon Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
| | - V García Sakai
- ISIS Neutron and Muon Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
| | - L A E Batista de Carvalho
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
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7
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Gonzalez MA, Zaragoza A, Lynch CI, Sansom MSP, Valeriani C. Influence of water models on water movement through AQP1. J Chem Phys 2021; 155:154502. [PMID: 34686053 DOI: 10.1063/5.0063986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are responsible for enabling water permeation through the cell membrane. AQPs are highly selective, allowing only water and relatively small polar molecules to cross the membrane. Experimentally, estimation of water flux through membrane proteins is still a challenge, and hence, accurate simulations of water permeation are of particular importance. We present a numerical study of water diffusion through AQP1 comparing three water models: TIP3P, OPC, and TIP4P/2005. Bulk diffusion, diffusion permeability, and osmotic permeability are computed and compared among all models. The results show that there are significant differences between TIP3P (a particularly widespread model for simulations of biological systems) and the more recently developed TIP4P/2005 and OPC models. We demonstrate that OPC and TIP4P/2005 reproduce protein-water interactions and dynamics in very good agreement with experimental data. From this study, we find that the choice of the water model has a significant effect on the computed water dynamics as well as its molecular behavior within a biological nanopore.
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Affiliation(s)
| | - Alberto Zaragoza
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Charlotte I Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Chantal Valeriani
- Universidad Complutense de Madrid, Facultad de Ciencias Fícias, Departamento de Estructura de la Materia, Física Térmica y Electrónica, 28040 Madrid, Spain
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8
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Khairy Y, Alvarez F, Arbe A, Colmenero J. Disentangling Self-Atomic Motions in Polyisobutylene by Molecular Dynamics Simulations. Polymers (Basel) 2021; 13:polym13040670. [PMID: 33672368 PMCID: PMC7927061 DOI: 10.3390/polym13040670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/08/2021] [Accepted: 02/17/2021] [Indexed: 01/16/2023] Open
Abstract
We present fully atomistic molecular dynamics simulations on polyisobutylene (PIB) in a wide temperature range above the glass transition. The cell is validated by direct comparison of magnitudes computed from the simulation and measured by neutron scattering on protonated samples reported in previous works. Once the reliability of the simulation is assured, we exploit the information in the atomic trajectories to characterize the dynamics of the different kinds of atoms in PIB. All of them, including main-chain carbons, show a crossover from Gaussian to non-Gaussian behavior in the intermediate scattering function that can be described in terms of the anomalous jump diffusion model. The full characterization of the methyl-group hydrogen motions requires accounting for rotational motions. We show that the usually assumed statistically independence of rotational and segmental motions fails in this case. We apply the rotational rate distribution model to correlation functions calculated for the relative positions of methyl-group hydrogens with respect to the carbon atom at which they are linked. The contributions to the vibrational density of states are also discussed. We conclude that methyl-group rotations are coupled with the main-chain dynamics. Finally, we revise in the light of the simulations the hypothesis and conclusions made in previously reported neutron scattering investigations on protonated samples trying to address the origin of the dielectric β-process.
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Affiliation(s)
- Yasmin Khairy
- Physics Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt;
- Centro de Física de Materiales (CSIC, UPV/EHU), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (F.A.); (A.A.)
| | - Fernando Alvarez
- Centro de Física de Materiales (CSIC, UPV/EHU), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (F.A.); (A.A.)
- Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Departamento de Polímeros y Materiales Avanzados: Física, Química y Tecnología (UPV/EHU), Apartado 1072, E-20080 San Sebastián, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CSIC, UPV/EHU), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (F.A.); (A.A.)
- Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - Juan Colmenero
- Centro de Física de Materiales (CSIC, UPV/EHU), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain; (F.A.); (A.A.)
- Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Departamento de Polímeros y Materiales Avanzados: Física, Química y Tecnología (UPV/EHU), Apartado 1072, E-20080 San Sebastián, Spain
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
- Correspondence:
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9
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Himbert S, Zhang L, Alsop RJ, Cristiglio V, Fragneto G, Rheinstädter MC. Anesthetics significantly increase the amount of intramembrane water in lipid membranes. SOFT MATTER 2020; 16:9674-9682. [PMID: 32869047 DOI: 10.1039/d0sm01271h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The potency of anesthesia was directly linked to the partitioning of the drug molecules in cell membranes by Meyer and Overton. Many molecules interact with lipid bilayers and lead to structural and functional changes. It remains an open question which change in membrane properties is responsible for a potential anesthetic effect or if anesthetics act by binding to direct targets. We studied the effect of ethanol, diethyl ether and isoflurane on the water distribution in lipid bilayers by combining all-atom molecular dynamics simulations and neutron diffraction experiments. The simulations show strong membrane-drug interactions with partitioning coefficients of 38%, 92% and 100% for ethanol, diethyl ether and isoflurane, respectively, and provide evidence for an increased water partitioning in the membrane core. The amount of intramembrane water molecules was experimentally determined by selectively deuterium labeling lipids, anesthetic drug and water molecules in neutron diffraction experiments. Four additional water molecules per lipid were observed in the presence of ethanol. Diethyl ether and isoflurane were found to significantly increase the amount of intramembrane water by 25% (8 water molecules). This increase in intramembrane water may contribute to the non-specific interactions between anesthetics and lipid membranes.
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Affiliation(s)
- Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, ABB-241, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada.
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10
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Affiliation(s)
- Nadav Amdursky
- Schulich Faculty of ChemistryTechnion – Israel Institute of Technology Haifa 3200003 Israel
| | - Yiyang Lin
- State Key Laboratory of Organic-Inorganic Composites Beijing Laboratory of Biomedical MaterialsBeijing University of Chemical Technology Beijing 100029 China
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11
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Yamada T, Seto H. Quasi-Elastic Neutron Scattering Studies on Hydration Water in Phospholipid Membranes. Front Chem 2020; 8:8. [PMID: 32039163 PMCID: PMC6993101 DOI: 10.3389/fchem.2020.00008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/07/2020] [Indexed: 11/20/2022] Open
Abstract
The dynamic behavior of hydration water in phospholipid membranes has been investigated to understand the relationship between water and biological molecules using various experimental techniques. Quasi-elastic neutron scattering (QENS) is an effective method for this purpose because the dynamic behaviors of both water and lipid molecules could be identified by using selective deuteration. In addition, the measurable ranges from the 10−12 to 10−9 s time scale and the 10−11 to 10−8 m length scale are suitable to investigate the slowing down of water molecules due to their interaction with lipid membranes. In this mini-review, QENS experiments on the dynamic behavior of hydration water molecules in neighboring phospholipid membranes are summarized.
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Affiliation(s)
- Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, Tokai, Japan
| | - Hideki Seto
- Institute of Materials Structure Science/J-PARC Center, High Energy Accelerator Research Organization, Tsukuba, Japan
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12
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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13
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Exploring fast proton transfer events associated with lateral proton diffusion on the surface of membranes. Proc Natl Acad Sci U S A 2019; 116:2443-2451. [PMID: 30679274 DOI: 10.1073/pnas.1812351116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proton diffusion (PD) across biological membranes is a fundamental process in many biological systems, and much experimental and theoretical effort has been employed for deciphering it. Here, we report on a spectroscopic probe, which can be tightly tethered to the membrane, for following fast (nanosecond) proton transfer events on the surface of membranes. Our probe is composed of a photoacid that serves as our light-induced proton source for the initiation of the PD process. We use our probe to follow PD, and its pH dependence, on the surface of lipid vesicles composed of a zwitterionic headgroup, a negative headgroup, a headgroup that is composed only from the negative phosphate group, or a positive headgroup without the phosphate group. We reveal that the PD kinetic parameters are highly sensitive to the nature of the lipid headgroup, ranging from a fast lateral diffusion at some membranes to the escape of protons from surface to bulk (and vice versa) at others. By referring to existing theoretical models for membrane PD, we found that while some of our results confirm the quasi-equilibrium model, other results are in line with the nonequilibrium model.
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14
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Ashkar R, Bilheux HZ, Bordallo H, Briber R, Callaway DJE, Cheng X, Chu XQ, Curtis JE, Dadmun M, Fenimore P, Fushman D, Gabel F, Gupta K, Herberle F, Heinrich F, Hong L, Katsaras J, Kelman Z, Kharlampieva E, Kneller GR, Kovalevsky A, Krueger S, Langan P, Lieberman R, Liu Y, Losche M, Lyman E, Mao Y, Marino J, Mattos C, Meilleur F, Moody P, Nickels JD, O'Dell WB, O'Neill H, Perez-Salas U, Peters J, Petridis L, Sokolov AP, Stanley C, Wagner N, Weinrich M, Weiss K, Wymore T, Zhang Y, Smith JC. Neutron scattering in the biological sciences: progress and prospects. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1129-1168. [PMID: 30605130 DOI: 10.1107/s2059798318017503] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
The scattering of neutrons can be used to provide information on the structure and dynamics of biological systems on multiple length and time scales. Pursuant to a National Science Foundation-funded workshop in February 2018, recent developments in this field are reviewed here, as well as future prospects that can be expected given recent advances in sources, instrumentation and computational power and methods. Crystallography, solution scattering, dynamics, membranes, labeling and imaging are examined. For the extraction of maximum information, the incorporation of judicious specific deuterium labeling, the integration of several types of experiment, and interpretation using high-performance computer simulation models are often found to be particularly powerful.
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Affiliation(s)
- Rana Ashkar
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - Hassina Z Bilheux
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Robert Briber
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - David J E Callaway
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Xiaolin Cheng
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
| | - Xiang Qiang Chu
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mark Dadmun
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Paul Fenimore
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Frank Gabel
- Institut Laue-Langevin, Université Grenoble Alpes, CEA, CNRS, IBS, 38042 Grenoble, France
| | - Kushol Gupta
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederick Herberle
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Frank Heinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Liang Hong
- Department of Physics and Astronomy, Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - John Katsaras
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zvi Kelman
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Eugenia Kharlampieva
- Department of Chemistry, University of Alabama at Birmingham, 901 14th Street South, Birmingham, AL 35294, USA
| | - Gerald R Kneller
- Centre de Biophysique Moléculaire, CNRS, Université d'Orléans, Chateau de la Source, Avenue du Parc Floral, Orléans, France
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Susan Krueger
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Paul Langan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Raquel Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Yun Liu
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Mathias Losche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, DE 19716, USA
| | - Yimin Mao
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - John Marino
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Carla Mattos
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Flora Meilleur
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Peter Moody
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, England
| | - Jonathan D Nickels
- Department of Physics, Virginia Polytechnic Institute and State University, 850 West Campus Drive, Blacksburg, VA 24061, USA
| | - William B O'Dell
- Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, MD 20850, USA
| | - Hugh O'Neill
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Ursula Perez-Salas
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | | | - Loukas Petridis
- Materials Science and Engineeering, University of Maryland, 1109 Chemical and Nuclear Engineering Building, College Park, MD 20742, USA
| | - Alexei P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| | - Christopher Stanley
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Norman Wagner
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
| | - Michael Weinrich
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Kevin Weiss
- Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Troy Wymore
- Graduate School of China Academy of Engineering Physics, Beijing, 100193, People's Republic of China
| | - Yang Zhang
- NIST Center for Neutron Research, National Institutes of Standard and Technology, 100 Bureau Drive, Mail Stop 6102, Gaithersburg, MD 20899, USA
| | - Jeremy C Smith
- Department of Medicinal Chemistry and Pharmacognosy, Ohio State University College of Pharmacy, 642 Riffe Building, Columbus, OH 43210, USA
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15
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Bi H, Wang X, Han X, Voïtchovsky K. Impact of Electric Fields on the Nanoscale Behavior of Lipid Monolayers at the Surface of Graphite in Solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9561-9571. [PMID: 30028144 DOI: 10.1021/acs.langmuir.8b01631] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The nanoscale organization and dynamics of lipid molecules in self-assembled membranes is central to the biological function of cells and in the technological development of synthetic lipid structures as well as in devices such as biosensors. Here, we explore the nanoscale molecular arrangement and dynamics of lipids assembled in monolayers at the surface of highly ordered pyrolytic graphite (HOPG), in different ionic solutions, and under electrical potentials. Using a combination of atomic force microscopy and fluorescence recovery after photobleaching, we show that HOPG is able to support fully formed and fluid lipid membranes, but mesoscale order and corrugations can be observed depending on the type of the lipid considered (1,2-dioleoyl- sn-glycero-3-phosphocholine, 1,2-dioleoyl- sn-glycero-3-phospho-l-serine (DOPS), and 1,2-dioleoyl-3-trimethylammoniumpropane) and the ion present (Na+, Ca2+, Cl-). Interfacial solvation forces and ion-specific effects dominate over the electrostatic changes induced by moderate electric fields (±1.0 V vs Ag/AgCl reference electrode) with particularly marked effects in the presence of calcium, and for DOPS. Our results provide insights into the interplay between the molecular, ionic, and electrostatic interactions and the formation of dynamical ordered structures in fluid lipid membranes.
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Affiliation(s)
- Hongmei Bi
- College of Science , Heilongjiang Bayi Agricultural University , Daqing 163319 , China
| | - Xuejing Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin 150001 , China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering , Harbin Institute of Technology , Harbin 150001 , China
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16
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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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17
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Elola MD, Rodriguez J. Influence of Cholesterol on the Dynamics of Hydration in Phospholipid Bilayers. J Phys Chem B 2018; 122:5897-5907. [PMID: 29742895 DOI: 10.1021/acs.jpcb.8b00360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the dynamics of interfacial waters in dipalmitoylphosphatidylcholine (DPPC) bilayers upon the addition of cholesterol, by molecular dynamics simulations. Our data reveal that the inclusion of cholesterol modifies the membrane aqueous interfacial dynamics: waters diffuse faster, their rotational decay time is shorter, and the DPPC/water hydrogen bond dynamics relaxes faster than in the pure DPPC membrane. The observed acceleration of the translational water dynamics agrees with recent experimental results, in which, by means of NMR techniques, an increment of the surface water diffusivity is measured upon the addition of cholesterol. A microscopic analysis of the lipid/water hydrogen bond network at the interfacial region suggests that the mechanism underlying the observed water mobility enhancement is given by the rupture of a fraction of interlipid water bridge hydrogen bonds connecting two different DPPC molecules, concomitant to the formation of new lipid/solvent bonds, whose dynamics is faster than that of the former. The consideration of a simple two-state model for the decay of the hydrogen bond correlation function yielded excellent results, obtaining two well-separated characteristic time scales: a slow one (∼250 ps) associated with bonds linking two DPPC molecules, and a fast one (∼15 ps), related to DPPC/solvent bonds.
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Affiliation(s)
- M Dolores Elola
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina
| | - Javier Rodriguez
- Departamento de Física , Comisión Nacional de Energía Atómica , Av Libertador 8250, 1429 Buenos Aires , Argentina.,ECyT , UNSAM , Martín de Irigoyen 3100, 1650 San Martín, Provincia de Buenos Aires , Argentina
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18
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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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19
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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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20
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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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21
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Perticaroli S, Ehlers G, Stanley CB, Mamontov E, O'Neill H, Zhang Q, Cheng X, Myles DAA, Katsaras J, Nickels JD. Description of Hydration Water in Protein (Green Fluorescent Protein) Solution. J Am Chem Soc 2016; 139:1098-1105. [PMID: 27783480 DOI: 10.1021/jacs.6b08845] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structurally and dynamically perturbed hydration shells that surround proteins and biomolecules have a substantial influence upon their function and stability. This makes the extent and degree of water perturbation of practical interest for general biological study and industrial formulation. We present an experimental description of the dynamical perturbation of hydration water around green fluorescent protein in solution. Less than two shells (∼5.5 Å) were perturbed, with dynamics a factor of 2-10 times slower than bulk water, depending on their distance from the protein surface and the probe length of the measurement. This dependence on probe length demonstrates that hydration water undergoes subdiffusive motions (τ ∝ q-2.5 for the first hydration shell, τ ∝ q-2.3 for perturbed water in the second shell), an important difference with neat water, which demonstrates diffusive behavior (τ ∝ q-2). These results help clarify the seemingly conflicting range of values reported for hydration water retardation as a logical consequence of the different length scales probed by the analytical techniques used.
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Affiliation(s)
- Stefania Perticaroli
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Georg Ehlers
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Christopher B Stanley
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Eugene Mamontov
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Hugh O'Neill
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Qiu Zhang
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Xiaolin Cheng
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Dean A A Myles
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - John Katsaras
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jonathan D Nickels
- Shull Wollan Center, a Joint Institute for Neutron Sciences, ‡Quantum Condensed Matter Division, §Biology and Soft Matter Division, ∥Chemical and Engineering Materials Division, and ⊥Center for Molecular Biophysics, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology and ∇Department of Physics and Astronomy, University of Tennessee , Knoxville, Tennessee 37996, United States
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22
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Roosen-Runge F, Bicout DJ, Barrat JL. Analytical correlation functions for motion through diffusivity landscapes. J Chem Phys 2016; 144:204109. [DOI: 10.1063/1.4950889] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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23
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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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24
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Tang J, Alsop RJ, Backholm M, Dies H, Shi AC, Rheinstädter MC. Amyloid-β(25-35) peptides aggregate into cross-β sheets in unsaturated anionic lipid membranes at high peptide concentrations. SOFT MATTER 2016; 12:3165-3176. [PMID: 26934592 DOI: 10.1039/c5sm02619a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
One of the hallmarks of Alzheimer's disease is the formation of protein plaques in the brain, which mainly consist of amyloid-β peptides of different lengths. While the role of these plaques in the pathology of the disease is not clear, the mechanism behind peptide aggregation is a topic of intense research and discussion. Because of their simplicity, synthetic membranes are promising model systems to identify the elementary processes involved. We prepared unsaturated zwitterionic/anionic lipid membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-phosphocholine (POPC) and 1,2-dimyristoyl-sn-glycero-3-phospho-l-serine (DMPS) at concentrations of POPC/3 mol% DMPS containing 0 mol%, 3 mol%, 10 mol%, and 20 mol% amyloid-β25-35 peptides. Membrane-embedded peptide clusters were observed at peptide concentrations of 10 and 20 mol% with a typical cluster size of ∼11 μm. Cluster density increased with peptide concentration from 59 (±3) clusters per mm(2) to 920 (±64) clusters per mm(2), respectively. While monomeric peptides take an α-helical state when embedded in lipid bilayers at low peptide concentrations, the peptides in peptide clusters were found to form cross-β sheets and showed the characteristic pattern in X-ray experiments. The presence of the peptides was accompanied by an elastic distortion of the bilayers, which can induce a long range interaction between the peptides. The experimentally observed cluster patterns agree well with Monte Carlo simulations of long-range interacting peptides. This interaction may be the fundamental process behind cross-β sheet formation in membranes and these sheets may serve as seeds for further growth into amyloid fibrils.
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Affiliation(s)
- Jennifer Tang
- Department of Physics and Astronomy, McMaster University, ABB-241, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada.
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25
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Nickels JD, Atkinson J, Papp-Szabo E, Stanley C, Diallo SO, Perticaroli S, Baylis B, Mahon P, Ehlers G, Katsaras J, Dutcher JR. Structure and Hydration of Highly-Branched, Monodisperse Phytoglycogen Nanoparticles. Biomacromolecules 2016; 17:735-43. [DOI: 10.1021/acs.biomac.5b01393] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Jonathan D. Nickels
- Joint
Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Physics, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - John Atkinson
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Erzsebet Papp-Szabo
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Christopher Stanley
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Souleymane O. Diallo
- Chemical
and Engineering Materials Division, Oak Ridge National Laboratory, Oak
Ridge, Tennessee 37831, United States
| | | | - Benjamin Baylis
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Perry Mahon
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Georg Ehlers
- Quantum Condensed
Matter Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - John Katsaras
- Joint
Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Physics, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biology
and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - John R. Dutcher
- Department
of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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26
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Metzler R, Jeon JH, Cherstvy AG. Non-Brownian diffusion in lipid membranes: Experiments and simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2451-2467. [PMID: 26826272 DOI: 10.1016/j.bbamem.2016.01.022] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/21/2016] [Accepted: 01/23/2016] [Indexed: 12/14/2022]
Abstract
The dynamics of constituents and the surface response of cellular membranes-also in connection to the binding of various particles and macromolecules to the membrane-are still a matter of controversy in the membrane biophysics community, particularly with respect to crowded membranes of living biological cells. We here put into perspective recent single particle tracking experiments in the plasma membranes of living cells and supercomputing studies of lipid bilayer model membranes with and without protein crowding. Special emphasis is put on the observation of anomalous, non-Brownian diffusion of both lipid molecules and proteins embedded in the lipid bilayer. While single component, pure lipid bilayers in simulations exhibit only transient anomalous diffusion of lipid molecules on nanosecond time scales, the persistence of anomalous diffusion becomes significantly longer ranged on the addition of disorder-through the addition of cholesterol or proteins-and on passing of the membrane lipids to the gel phase. Concurrently, experiments demonstrate the anomalous diffusion of membrane embedded proteins up to macroscopic time scales in the minute time range. Particular emphasis will be put on the physical character of the anomalous diffusion, in particular, the occurrence of ageing observed in the experiments-the effective diffusivity of the measured particles is a decreasing function of time. Moreover, we present results for the time dependent local scaling exponent of the mean squared displacement of the monitored particles. Recent results finding deviations from the commonly assumed Gaussian diffusion patterns in protein crowded membranes are reported. The properties of the displacement autocorrelation function of the lipid molecules are discussed in the light of their appropriate physical anomalous diffusion models, both for non-crowded and crowded membranes. In the last part of this review we address the upcoming field of membrane distortion by elongated membrane-binding particles. We discuss how membrane compartmentalisation and the particle-membrane binding energy may impact the dynamics and response of lipid membranes. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- R Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany; Department of Physics, Tampere University of Technology, 33101 Tampere, Finland.
| | - J-H Jeon
- Korea Institute for Advanced Study (KIAS), Seoul, Republic of Korea
| | - A G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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