1
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Punia R, Goel G. Free Energy Surface and Molecular Mechanism of Slow Structural Transitions in Lipid Bilayers. J Chem Theory Comput 2023; 19:8245-8257. [PMID: 37947833 DOI: 10.1021/acs.jctc.3c00856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Lipid membrane remodeling, crucial for many cellular processes, is governed by the coupling of membrane structure and shape fluctuations. Given the importance of the ∼ nm length scale, details of the transition intermediates for conformational change are not fully captured by a continuum-mechanical description. Slow dynamics and the lack of knowledge of reaction coordinates (RCs) for biasing methods pose a challenge for all-atom (AA) simulations. Here, we map system dynamics on Langevin dynamics in a normal mode space determined from an elastic network model representation for the lipid-water Hamiltonian. AA molecular dynamics (MD) simulations are used to determine model parameters, and Langevin dynamics predictions for bilayer structural, mechanical, and dynamic properties are validated against MD simulations and experiments. Transferability to describe the dynamics of a larger lipid bilayer and a heterogeneous membrane-protein system is assessed. A set of generic RCs for pore formation in two tensionless bilayers is obtained by coupling Langevin dynamics to the underlying energy landscape for membrane deformations. Structure evolution is carried out by AA MD, wherein the generic RCs are used in a path metadynamics or an umbrella sampling simulation to determine the thermodynamics of pore formation and its molecular determinants, such as the role of distinct bilayer motions, lipid solvation, and lipid packing.
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Affiliation(s)
- Rajat Punia
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi 110016, India
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2
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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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3
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Kinnun JJ, Scott HL, Bolmatov D, Collier CP, Charlton TR, Katsaras J. Biophysical studies of lipid nanodomains using different physical characterization techniques. Biophys J 2023; 122:931-949. [PMID: 36698312 PMCID: PMC10111277 DOI: 10.1016/j.bpj.2023.01.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
For the past 50 years, evidence for the existence of functional lipid domains has been steadily accumulating. Although the notion of functional lipid domains, also known as "lipid rafts," is now widely accepted, this was not always the case. This ambiguity surrounding lipid domains could be partly attributed to the fact that they are highly dynamic, nanoscopic structures. Since most commonly used techniques are sensitive to microscale structural features, it is therefore, not surprising that it took some time to reach a consensus regarding their existence. In this review article, we will discuss studies that have used techniques that are inherently sensitive to nanoscopic structural features (i.e., neutron scatting, nuclear magnetic resonance, and Förster resonance energy transfer). We will also mention techniques that may be of use in the future (i.e., cryoelectron microscopy, droplet interface bilayers, inelastic x-ray scattering, and neutron reflectometry), which can further our understanding of the different and unique physicochemical properties of nanoscopic lipid domains.
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Affiliation(s)
- Jacob J Kinnun
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
| | - Haden L Scott
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Dima Bolmatov
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Timothy R Charlton
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - John Katsaras
- Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Labs and Soft Matter Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
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4
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Luyet C, Elvati P, Vinh J, Violi A. Low-THz Vibrations of Biological Membranes. MEMBRANES 2023; 13:membranes13020139. [PMID: 36837641 PMCID: PMC9965665 DOI: 10.3390/membranes13020139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 05/12/2023]
Abstract
A growing body of work has linked key biological activities to the mechanical properties of cellular membranes, and as a means of identification. Here, we present a computational approach to simulate and compare the vibrational spectra in the low-THz region for mammalian and bacterial membranes, investigating the effect of membrane asymmetry and composition, as well as the conserved frequencies of a specific cell. We find that asymmetry does not impact the vibrational spectra, and the impact of sterols depends on the mobility of the components of the membrane. We demonstrate that vibrational spectra can be used to distinguish between membranes and, therefore, could be used in identification of different organisms. The method presented, here, can be immediately extended to other biological structures (e.g., amyloid fibers, polysaccharides, and protein-ligand structures) in order to fingerprint and understand vibrations of numerous biologically-relevant nanoscale structures.
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Affiliation(s)
- Chloe Luyet
- Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Paolo Elvati
- Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Jordan Vinh
- Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
| | - Angela Violi
- Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
- Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109-2125, USA
- Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109-2125, USA
- Correspondence:
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5
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Himbert S, Rheinstädter MC. Structural and mechanical properties of the red blood cell's cytoplasmic membrane seen through the lens of biophysics. Front Physiol 2022; 13:953257. [PMID: 36171967 PMCID: PMC9510598 DOI: 10.3389/fphys.2022.953257] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022] Open
Abstract
Red blood cells (RBCs) are the most abundant cell type in the human body and critical suppliers of oxygen. The cells are characterized by a simple structure with no internal organelles. Their two-layered outer shell is composed of a cytoplasmic membrane (RBC cm ) tethered to a spectrin cytoskeleton allowing the cell to be both flexible yet resistant against shear stress. These mechanical properties are intrinsically linked to the molecular composition and organization of their shell. The cytoplasmic membrane is expected to dominate the elastic behavior on small, nanometer length scales, which are most relevant for cellular processes that take place between the fibrils of the cytoskeleton. Several pathologies have been linked to structural and compositional changes within the RBC cm and the cell's mechanical properties. We review current findings in terms of RBC lipidomics, lipid organization and elastic properties with a focus on biophysical techniques, such as X-ray and neutron scattering, and Molecular Dynamics simulations, and their biological relevance. In our current understanding, the RBC cm 's structure is patchy, with nanometer sized liquid ordered and disordered lipid, and peptide domains. At the same time, it is surprisingly soft, with bending rigidities κ of 2-4 kBT. This is in strong contrast to the current belief that a high concentration of cholesterol results in stiff membranes. This extreme softness is likely the result of an interaction between polyunsaturated lipids and cholesterol, which may also occur in other biological membranes. There is strong evidence in the literature that there is no length scale dependence of κ of whole RBCs.
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Affiliation(s)
- Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada
- Origins Institute, McMaster University, Hamilton, ON, Canada
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada
- Origins Institute, McMaster University, Hamilton, ON, Canada
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6
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Surovtsev NV, Adichtchev SV. Dynamic response on a nanometer scale of binary phospholipid-cholesterol vesicles: Low-frequency Raman scattering insight. Phys Rev E 2021; 104:054406. [PMID: 34942765 DOI: 10.1103/physreve.104.054406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/18/2021] [Indexed: 11/07/2022]
Abstract
Low-frequency Raman spectroscopy was used to study the dynamic response on a nanometer scale of aqueous suspensions of two-component lipid vesicles. Binary mixtures of saturated phospholipid (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC) and cholesterol are interesting for possible coexistence of solidlike and liquid-ordered phases, while the phase coexistence was not reported for unsaturated phospholipid (1,2-dioleoyl-sn-glycero-3-phosphocholine, DOPC) and cholesterol mixtures. The DOPC-DPPC mixtures represent the well-documented case of coexisting domains of solidlike and liquid-disordered phases. These three series of lipid mixtures are studied here. A broad peak with the maximum in the range of 30-50cm^{-1} and a narrow peak near 10cm^{-1} are observed in the Raman susceptibility of the binary mixtures and attributed to the acousticlike vibrational density of states and layer modes, respectively. Parameters of the broad and narrow peaks are sensitive to lateral and conformational hydrocarbon chain ordering. It was also demonstrated that the low-frequency Raman susceptibility of multicomponent lipid bilayers allows one to determine the phase state of lipid bilayers and distinguish the homogeneous distribution of molecular complexes from coexisting domains with sizes above several nanometers. Thus, the low-frequency Raman spectroscopy provides unique information in studying phase coexistence in lipid bilayers.
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Affiliation(s)
- N V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - S V Adichtchev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
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7
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Mondal D, Malik S, Banerjee P, Kundu N, Debnath A, Sarkar N. Modulation of Membrane Fluidity to Control Interfacial Water Structure and Dynamics in Saturated and Unsaturated Phospholipid Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12423-12434. [PMID: 33035065 DOI: 10.1021/acs.langmuir.0c02736] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The structure and dynamics of interfacial water in biological systems regulate the biochemical reactions. But, it is still enigmatic how the behavior of the interfacial water molecule is controlled. Here, we have investigated the effect of membrane fluidity on the structure and dynamics of interfacial water molecules in biologically relevant phopholipid vesicles. This study delineates that modulation of membrane fluidity through interlipid separation and unsaturation not only mitigate membrane rigidity but also disrupt the strong hydrogen bond (H-bond) network around the lipid bilayer interface. As a result, a disorder in H-bonding between water molecules arises several layers beyond the first hydration shell of the polar headgroup, which essentially modifies the interfacial water structure and dynamics. Furthermore, we have also provided evidence of increasing transportation through these modulated membranes, which enhance the membrane mediated isomerization reaction rate.
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Affiliation(s)
- Dipankar Mondal
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
| | - Sheeba Malik
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Pavel Banerjee
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
| | - Niloy Kundu
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
- Environment Research Group, R&D and Scientific Services Department, Tata Steel Ltd., Jamshedpur 831007, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, Rajasthan, India
| | - Nilmoni Sarkar
- Department of Chemistry, Indian Institute of Technology Kharagpur Kharagpur 721302, West Bengal, India
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8
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Morisaku T, Sunada M, Miyazaki A, Sakai T, Matsuo K, Yui H. Dynamic Light Scattering Measurements for Soft Materials on Solid Substrates: Employing Evanescent-wave Illumination and Dark-field Collection with a High Numerical Aperture Microscope Objective. ANAL SCI 2020; 36:1211-1215. [PMID: 32418932 DOI: 10.2116/analsci.20p068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We developed an instrument that allows us to measure dynamic light scattering from soft materials on solid substrates by avoiding strong background due to the reflection light from substrates. In the instrument, samples on substrates are illuminated by evanescent-light field and the resultant scattered light from the samples is collected with a dark-field optical configuration by employing a high numerical aperture microscope objective. We applied the instrument to measure the dynamic properties of supported lipid bilayers (SLBs), which have been widely utilized in industries as functional materials such as biosensors. From the time course of the scattered light from the SLBs, the power spectrum with the broad peak ranging from 10 to 20 kHz is observed. The use of the microscope objectives enables us to apply the instrument to future light scattering imaging for dynamic properties of soft materials supported on various substrates by combining with conventional microscope systems.
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Affiliation(s)
- Toshinori Morisaku
- Water Frontier Science & Technology Research Center, Research Institute for Science & Technology, Tokyo University of Science
| | - Miki Sunada
- Department of Chemistry, Graduate School of Science, Tokyo University of Science
| | | | | | | | - Hiroharu Yui
- Water Frontier Science & Technology Research Center, Research Institute for Science & Technology, Tokyo University of Science.,Department of Chemistry, Graduate School of Science, Tokyo University of Science.,Department of Chemistry, Faculty of Science, Tokyo University of Science
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9
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Bolmatov D, Soloviov D, Zhernenkov M, Zav'yalov D, Mamontov E, Suvorov A, Cai YQ, Katsaras J. Molecular Picture of the Transient Nature of Lipid Rafts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4887-4896. [PMID: 32259453 DOI: 10.1021/acs.langmuir.0c00125] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In biological membranes, lipid rafts are now thought to be transient and nanoscopic. However, the mechanism responsible for these nanoscopic assemblies remains poorly understood, even in the case of model membranes. As a result, it has proven extremely challenging to probe the physicochemical properties of lipid rafts at the molecular level. Here, we use all-atom molecular dynamics (MD) simulations and inelastic X-ray scattering (IXS), an intrinsically nanoscale technique, to directly probe the energy transfer and collective short-wavelength dynamics (phonons) of biologically relevant model membranes. We show that the nanoscale propagation of stress in lipid rafts takes place in the form of collective motions made up of longitudinal (compression waves) and transverse (shear waves) molecular vibrations. Importantly, we provide a molecular picture for the so-called van der Waals mediated "force from lipid" [Anishkin, A. et al. Proc. Natl. Acad. Sci. U.S.A. 2014, 111, 7898], a key parameter for the ionic channel mechano-transduction and the mechanism for the lipid transfer of molecular level stress [Aponte-Santamarı́a, C. et al. J. Am. Chem. Soc. 2017, 139, 13588]. Specifically, we describe how lipid rafts are formed and maintained through the propagation of molecular stress, lipid raft rattling dynamics, and a relaxation process. Eventually, the rafts dissipate through the self-diffusion of lipids making up the rafts. We also show that the molecular stress and viscoelastic properties of transient lipid rafts can be modulated through the use of hydrophobic biomolecules such as melatonin and tryptophan. Ultimately, the herein proposed mechanism describing the molecular interactions for the formation and dissolution of lipid rafts may offer insights as to how lipid rafts enable biological function.
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Affiliation(s)
- Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dmytro Soloviov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia
- Institute for Safety Problems of Nuclear Power Plants, NAS of Ukraine, Kyiv 03680, Ukraine
| | - Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | | | - Eugene Mamontov
- Spectroscopy Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Alexey Suvorov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - John Katsaras
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, United States
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10
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Soloviov D, Cai YQ, Bolmatov D, Suvorov A, Zhernenkov K, Zav'yalov D, Bosak A, Uchiyama H, Zhernenkov M. Functional lipid pairs as building blocks of phase-separated membranes. Proc Natl Acad Sci U S A 2020; 117:4749-4757. [PMID: 32071249 PMCID: PMC7060688 DOI: 10.1073/pnas.1919264117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Biological membranes exhibit a great deal of compositional and phase heterogeneity due to hundreds of chemically distinct components. As a result, phase separation processes in cell membranes are extremely difficult to study, especially at the molecular level. It is currently believed that the lateral membrane heterogeneity and the formation of domains, or rafts, are driven by lipid-lipid and lipid-protein interactions. Nevertheless, the underlying mechanisms regulating membrane heterogeneity remain poorly understood. In the present work, we combine inelastic X-ray scattering with molecular dynamics simulations to provide direct evidence for the existence of strongly coupled transient lipid pairs. These lipid pairs manifest themselves experimentally through optical vibrational (a.k.a. phononic) modes observed in binary (1,2-dipalmitoyl-sn-glycero-3-phosphocholine [DPPC]-cholesterol) and ternary (DPPC-1,2-dioleoyl-sn-glycero-3-phosphocholine/1-palmitoyl-2-oleoyl-glycero-3-phosphocholine [DOPC/POPC]-cholesterol) systems. The existence of a phononic gap in these vibrational modes is a direct result of the finite size of patches formed by these lipid pairs. The observation of lipid pairs provides a spatial (subnanometer) and temporal (subnanosecond) window into the lipid-lipid interactions in complex mixtures of saturated/unsaturated lipids and cholesterol. Our findings represent a step toward understanding the lateral organization and dynamics of membrane domains using a well-validated probe with a high spatial and temporal resolution.
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Affiliation(s)
- Dmytro Soloviov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Frank Laboratory for Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia
- Department of Physics, Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
- Nuclear Facility Safety Department, Institute for Safety Problems of Nuclear Power Plants of National Academy of Science of Ukraine, Chornobyl 07270, Ukraine
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973
| | - Dima Bolmatov
- Large Scale Structures Group, Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996
| | - Alexey Suvorov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973
| | - Kirill Zhernenkov
- Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Forschungszentrum Jülich GmbH, 85748 Garching, Germany
- Frank Laboratory for Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - Dmitry Zav'yalov
- Department of Physics, Volgograd State Technical University, Volgograd 400005, Russia
| | - Alexey Bosak
- Experiments Division, European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Hiroshi Uchiyama
- Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo 679-5198, Japan
| | - Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973;
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11
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Zakhvataev VE. Dynamic structure factor of a lipid bilayer in the presence of a high electric field. J Chem Phys 2019; 151:234902. [PMID: 31864280 DOI: 10.1063/1.5123786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The influence of a high average electric field (∼1 V/nm) in the hydrophobic interior of a bilayer lipid membrane on short-wavelength in-plane phononic motions of lipid chains is considered. The average electric field is assumed to be nearly constant on a picosecond time scale and a nanometer length scale. This field may be induced, for instance, by externally applied subnanosecond electric pulses or the membrane dipole potential. Using a generalized hydrodynamic approach, we derive a corresponding electrohydrodynamic model generalized to high wave numbers. In the considered approximation, all electric field effects are reduced only to a constant contribution to the generalized isothermal compressibility modulus. The corresponding dynamic structure factor for a lipid bilayer is derived. We show that due to polarization effects, the high field can critically impact the dynamics of longitudinal acousticlike modes at wave numbers near the major peak of the static structure factor. We estimate quantitatively that for typical lipid bilayers, transverse high electric fields can cause strong phonon energy softening, enhancement of phonon population, and formation of a gap in the dispersion of excitation frequency. The results obtained agree with simulations of the initiation of lipid bilayer electropores, suggesting that the proposed model reproduces the essential features of the field's impact on atomic density fluctuations. The proposed mechanism may have significant implications for the understanding of electroporation, passive molecular transport, and spontaneous pore formation in lipid bilayers.
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Affiliation(s)
- V E Zakhvataev
- Federal Research Center "Krasnoyarsk Scientific Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036 Russia and Siberian Federal University, Krasnoyarsk 660041 Russia
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12
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Kheyfets B, Galimzyanov T, Mukhin S. Lipid lateral self-diffusion drop at liquid-gel phase transition. Phys Rev E 2019; 99:012414. [PMID: 30780230 DOI: 10.1103/physreve.99.012414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 11/06/2022]
Abstract
A drop of lipid lateral self-diffusion coefficient at the liquid-gel phase transition in lipid membranes is calculated. So far this drop was missing theoretical description. Our microscopic model captures so-called subdiffusion regime, which takes place on 1 ps-100 ns timescale and reveals a jump of self-diffusion coefficient. Calculation of the jump is based on our recent study of liquid-gel phase transition. Subdiffusive regime is described within the free volume theory. Calculated values of self-diffusion coefficient are in agreement with quasielastic neutron scattering measurements. Self-diffusion coefficient is found to be composed of two factors: one is related to an area per lipid change at the phase transition, and the other one is due to an order of magnitude change in the stiffness of entropic repulsive potential.
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Affiliation(s)
- Boris Kheyfets
- National University of Science and Technology MISIS, Moscow, Russia
| | - Timur Galimzyanov
- A. N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Moscow, Russia
| | - Sergei Mukhin
- National University of Science and Technology MISIS, Moscow, Russia
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13
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Päslack C, Schäfer LV, Heyden M. Atomistic characterization of collective protein–water–membrane dynamics. Phys Chem Chem Phys 2019; 21:15958-15965. [DOI: 10.1039/c9cp00725c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water mediates correlated vibrations of atoms of protein and membrane bilayer surfaces.
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Affiliation(s)
- Christopher Päslack
- Center for Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Lars V. Schäfer
- Center for Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Matthias Heyden
- School of Molecular Sciences
- Arizona State University
- Tempe
- USA
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14
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Päslack C, Smith JC, Heyden M, Schäfer LV. Hydration-mediated stiffening of collective membrane dynamics by cholesterol. Phys Chem Chem Phys 2019; 21:10370-10376. [DOI: 10.1039/c9cp01431d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration water governs the cholesterol-induced changes in collective headgroup dynamics in lipid bilayers.
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Affiliation(s)
- Christopher Päslack
- Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- D-44780 Bochum
- Germany
| | - Jeremy C. Smith
- Center for Molecular Biophysics
- Oak Ridge National Laboratory
- Oak Ridge
- USA
- Department of Biochemistry and Cellular and Molecular Biology
| | - Matthias Heyden
- School of Molecular Sciences
- Arizona State University
- Tempe
- USA
| | - Lars V. Schäfer
- Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr University Bochum
- D-44780 Bochum
- Germany
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15
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Leonov DV, Dzuba SA, Surovtsev NV. Normal vibrations of ternary DOPC/DPPC/cholesterol lipid bilayers by low-frequency Raman spectroscopy. RSC Adv 2019; 9:34451-34456. [PMID: 35530012 PMCID: PMC9073921 DOI: 10.1039/c9ra06114b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/20/2019] [Indexed: 11/23/2022] Open
Abstract
A lipid bilayer containing a ternary mixture of low- and high-melting lipids and cholesterol (Chol) can give rise to domain formation, referred to as lipid rafts. Low-frequency Raman spectroscopy at reduced temperatures allows detection of normal membrane mechanical vibrations. In this work, Raman spectra were obtained in the spectral range between 5 and 90 cm−1 for bilayers prepared from dioleoyl-glycero-phosphocholine (DOPC), dipalmitoyl-glycero-phosphocholine (DPPC) and Chol. A narrow peak detected between 13 and 16 cm−1 was attributed to the vibrational eigenmode of a lipid monolayer (a leaflet). For the equimolar DOPC/DPPC ratio, the Chol concentration dependence for the peak position, width and amplitude may be divided into three distinct ranges: below 9 mol%, the intermediate range between 9 mol% and 38 mol%, and above 38 mol%. In the intermediate range the peak position attains its minimum, and the peak width drops approximately by a factor of two as compared with the Chol-free bilayers. Meanwhile, this range is known for raft formation in a fluid state. The obtained results may be interpreted as evidence that bilayer structures in the raft-containing fluid state may be frozen at low temperatures. The drop of peak width indicates that at the spatial scale of the experiment (∼2.5 nm) the intermolecular bilayer structure with raft formation becomes more homogeneous and more cohesive. Upon lipid raft formation, the Raman peak corresponding to monolayer normal mechanical vibrations drops remarkably in position and width.![]()
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Affiliation(s)
- Dmitry V. Leonov
- Department of Physics
- Novosibirsk State University
- Novosibirsk
- Russia
| | - Sergei A. Dzuba
- Department of Physics
- Novosibirsk State University
- Novosibirsk
- Russia
- Voevodsky Institute of Chemical Kinetics and Combustion
| | - Nikolay V. Surovtsev
- Department of Physics
- Novosibirsk State University
- Novosibirsk
- Russia
- Institute of Automation and Electrometry
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16
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Zakhvataev VE. Nonequilibrium dynamic structure factor of a lipid bilayer in the presence of an in-plane temperature gradient. Phys Rev E 2018; 98:022404. [PMID: 30253585 DOI: 10.1103/physreve.98.022404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Indexed: 01/02/2023]
Abstract
There is rapidly increasing evidence that nanoscale temperature heterogeneities are involved in important biological processes. Combining nanoheating and nanoscale thermosensors forms the basis of emerging unique methods of cell therapy, tissue engineering, and regenerative medicine. Understanding corresponding phenomena seems to require a mesoscopic nonequilibrium hydrodynamic theory. In this paper, a Langevin-type model of dynamics of phonon modes propagating along a bilayer lipid membrane in the presence of an in-plane temperature gradient is proposed. Corresponding quantitative estimates for the Brillouin components of the nonequilibrium dynamic structure factor and the equal-time longitudinal momentum-density correlation function for a lipid bilayer are obtained. The analysis reveals that for typical values of parameters of lipid bilayer, the longitudinal temperature gradient of the order of 5qK for wave numbers q from 0.01 to 1nm^{-1} induces significant asymmetry of the Brillouin components of the dynamic structure factor and long-range spatial correlations in the plane of the bilayer. The corresponding membrane temperature gradients seem to be typical or achievable for cellular processes responsible for intracellular temperature variations and such external physical impacts as high-intensity electromagnetic pulses or heating of membrane-associated nanoparticles.
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Affiliation(s)
- V E Zakhvataev
- Federal Research Center, "Krasnoyarsk Scientific Center of the Siberian Branch of the Russian Academy of Sciences," Krasnoyarsk 660036, Russia and Siberian Federal University, Krasnoyarsk 660041, Russia
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17
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D'Angelo G, Nibali VC, Wanderlingh U, Branca C, De Francesco A, Sacchetti F, Petrillo C, Paciaroni A. Multiple Interacting Collective Modes and Phonon Gap in Phospholipid Membranes. J Phys Chem Lett 2018; 9:4367-4372. [PMID: 30024172 DOI: 10.1021/acs.jpclett.8b01658] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We combine Brillouin neutron scattering measurements with recent inelastic X-ray scattering [ Zhernenkov et al. Nat. Commun. 2016 , 7 , 11575 ] to propose a model for the collective dynamics of phospholipid bilayers. Neutron and X-ray spectra were fitted by the model response function associated with the Hamiltonian of an interacting-phonon system. This approach allows for a comprehensive and unprecedented picture of the vibrational collective features of phospholipids. At low wavevectors Q, the dispersion relations can be interpreted in terms of two acoustic-like modes, one longitudinal and one transverse, plus a dispersionless optic-like mode. The transverse mode of the liquid phase shows a phonon gap that can be linked to a passive transport mechanism through membranes, an interpretation that was proposed in Zhernenkov et al. At higher Q values, the interaction of the longitudinal acoustic excitation with the dispersionless mode gives rise to a pattern that is consistent with avoided-crossing behavior. Evidence is found for a slow- to fast-sound transition, similar to bulk water and other biomolecules.
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Affiliation(s)
- Giovanna D'Angelo
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra , Universitá degli Studi di Messina , Viale F. Stagno d'Alcontres 31 , 98166 Messina , Italy
| | - Valeria Conti Nibali
- Lehrstuhl fur Physikalische Chemie II , Ruhr Universitat , 44801 Bochum , Germany
| | - Ulderico Wanderlingh
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra , Universitá degli Studi di Messina , Viale F. Stagno d'Alcontres 31 , 98166 Messina , Italy
| | - Caterina Branca
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra , Universitá degli Studi di Messina , Viale F. Stagno d'Alcontres 31 , 98166 Messina , Italy
| | - Alessio De Francesco
- Consiglio Nazionale delle Ricerche , Istituto Officina dei Materiali OGG, c/o Institut Laue Langevin , 71 Ave. des Martyrs , BP 156 F-38042 Grenoble Cedex , France
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia , Universitá degli Studi di Perugia , Via Pascoli , 06123 Perugia , Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia , Universitá degli Studi di Perugia , Via Pascoli , 06123 Perugia , Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia , Universitá degli Studi di Perugia , Via Pascoli , 06123 Perugia , Italy
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18
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Bolmatov D, Cai YQ, Zav'yalov D, Zhernenkov M. Crossover from picosecond collective to single particle dynamics defines the mechanism of lateral lipid diffusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2446-2455. [PMID: 30031781 DOI: 10.1016/j.bbamem.2018.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/04/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
It has been widely accepted that the thermally excited motions of the molecules in a cell membrane is the prerequisite for a cell to carry its biological functions. On the other hand, the detailed mapping of the ultrafast picosecond single-molecule and the collective lipid dynamics in a cell membrane remains rather elusive. Here, we report all-atom molecular dynamics simulations of a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine bilayer over a wide range of temperature. We elucidate a molecular mechanism underlying the lateral lipid diffusion in a cell membrane across the gel, rippled, and liquid phases using an analysis of the longitudinal and transverse current correlation spectra, the velocity auto-correlation functions, and the molecules mean square displacements. The molecular mechanism is based on the anomalous ultrafast vibrational properties of lipid molecules at the viscous-to-elastic crossover. The macroscopic lipid diffusion coefficients predicted by the proposed diffusion model are in a good agreement with experimentally observed values. Furthermore, we unveil the role of water confined at the water-lipid interface in triggering collective vibrations in a lipid bilayer.
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Affiliation(s)
- Dima Bolmatov
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996, USA.
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | | | - Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA.
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19
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Alsop RJ, Himbert S, Dhaliwal A, Schmalzl K, Rheinstädter MC. Aspirin locally disrupts the liquid-ordered phase. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171710. [PMID: 29515878 PMCID: PMC5830767 DOI: 10.1098/rsos.171710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/23/2018] [Indexed: 06/12/2023]
Abstract
Local structure and dynamics of lipid membranes play an important role in membrane function. The diffusion of small molecules, the curvature of lipids around a protein and the existence of cholesterol-rich lipid domains (rafts) are examples for the membrane to serve as a functional interface. The collective fluctuations of lipid tails, in particular, are relevant for diffusion of membrane constituents and small molecules in and across membranes, and for structure and formation of membrane domains. We studied the effect of aspirin (acetylsalicylic acid, ASA) on local structure and dynamics of membranes composed of dimyristoylphosphocholine (DMPC) and cholesterol. Aspirin is a common analgesic, but is also used in the treatment of cholesterol. Using coherent inelastic neutron scattering experiments and molecular dynamics (MD) simulations, we present evidence that ASA binds to liquid-ordered, raft-like domains and disturbs domain organization and dampens collective fluctuations. By hydrogen-bonding to lipid molecules, ASA forms 'superfluid' complexes with lipid molecules that can organize laterally in superlattices and suppress cholesterol's ordering effect.
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Affiliation(s)
- Richard J. Alsop
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Alexander Dhaliwal
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
| | - Karin Schmalzl
- JCNS, Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at ILL, Grenoble, France
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20
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Bolmatov D, Zhernenkov M, Sharpnack L, Agra-Kooijman DM, Kumar S, Suvorov A, Pindak R, Cai YQ, Cunsolo A. Emergent Optical Phononic Modes upon Nanoscale Mesogenic Phase Transitions. NANO LETTERS 2017; 17:3870-3876. [PMID: 28548861 DOI: 10.1021/acs.nanolett.7b01324] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The investigation of phononic collective excitations in soft matter systems at the molecular scale has always been challenging due to limitations of experimental techniques in resolving low-energy modes. Recent advances in inelastic X-ray scattering (IXS) enabled the study of such systems with unprecedented spectral contrast at meV excitation energies. In particular, it has become possible to shed light on the low-energy collective motions in materials whose morphology and phase behavior can easily be manipulated, such as mesogenic systems. The understanding of collective mode behavior with a Q-dependence is the key to implement heat management based on the control of a sample structure. The latter has great potential for a large number of energy-inspired innovations. As a first step toward this goal, we carried out high contrast IXS measurements on a liquid crystal sample, D7AOB, which exhibits solid-like dynamic features, such as the coexistence of longitudinal and transverse phononic modes. For the first time, we found that these terahertz phononic excitations persist in the crystal, smectic A, and isotropic phases. Furthermore, the intermediate smectic A phase is shown to support a van der Waals-mediated nonhydrodynamic mode with an optical-like phononic behavior. The tunability of the collective excitations at nanometer-terahertz scales via selection of the sample mesogenic phase represents a new opportunity to manipulate optomechanical properties of soft metamaterials.
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Affiliation(s)
- Dima Bolmatov
- National Synchrotron Light Source II, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Lewis Sharpnack
- Department of Physics, Kent State University , Kent, Ohio 44242, United States
| | | | - Satyendra Kumar
- Department of Physics, Kent State University , Kent, Ohio 44242, United States
- Division of Research and Department of Physics, University at Albany , Albany, New York 12222, United States
| | - Alexey Suvorov
- National Synchrotron Light Source II, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Ronald Pindak
- National Synchrotron Light Source II, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory , Upton, New York 11973, United States
| | - Alessandro Cunsolo
- National Synchrotron Light Source II, Brookhaven National Laboratory , Upton, New York 11973, United States
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21
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Zakhvataev VE. Localized density pulses in lipid membranes on the piсosecond time scale. Biophysics (Nagoya-shi) 2017. [DOI: 10.1134/s0006350917030253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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22
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D'Angelo G, Conti Nibali V, Crupi C, Rifici S, Wanderlingh U, Paciaroni A, Sacchetti F, Branca C. Probing Intermolecular Interactions in Phospholipid Bilayers by Far-Infrared Spectroscopy. J Phys Chem B 2017; 121:1204-1210. [PMID: 28118017 DOI: 10.1021/acs.jpcb.6b10323] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fast thermal fluctuations and low frequency phonon modes are thought to play a part in the dynamic mechanisms of many important biological functions in cell membranes. Here we report a detailed far-infrared study of the molecular subpicosecond motions of phospholipid bilayers at various hydrations. We show that these systems sustain several low frequency collective modes and deduce that they arise from vibrations of different lipids interacting through intermolecular van der Waals forces. Furthermore, we observe that the low frequency vibrations of lipid membrane have strong similarities with the subpicosecond motions of liquid water and suggest that resonance mechanisms are an important element to the dynamics coupling between membranes and their hydration water.
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Affiliation(s)
- Giovanna D'Angelo
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
| | - Valeria Conti Nibali
- Institute for Physical Chemistry II, Ruhr-University Bochum , 44801 Bochum, Germany
| | - Cristina Crupi
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
| | - Simona Rifici
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
| | - Ulderico Wanderlingh
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica, Università degli Studi di Perugia , 06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica, Università degli Studi di Perugia , 06123 Perugia, Italy
| | - Caterina Branca
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Messina , 98122 Messina, Italy
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23
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The Molecular Structure of Human Red Blood Cell Membranes from Highly Oriented, Solid Supported Multi-Lamellar Membranes. Sci Rep 2017; 7:39661. [PMID: 28045119 PMCID: PMC5206716 DOI: 10.1038/srep39661] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/24/2016] [Indexed: 12/30/2022] Open
Abstract
We prepared highly oriented, multi-lamellar stacks of human red blood cell (RBC) membranes applied on silicon wafers. RBC ghosts were prepared by hemolysis and applied onto functionalized silicon chips and annealed into multi-lamellar RBC membranes. High resolution X-ray diffraction was used to determine the molecular structure of the stacked membranes. We present direct experimental evidence that these RBC membranes consist of nanometer sized domains of integral coiled-coil peptides, as well as liquid ordered (lo) and liquid disordered (ld) lipids. Lamellar spacings, membrane and hydration water layer thicknesses, areas per lipid tail and domain sizes were determined. The common drug aspirin was added to the RBC membranes and found to interact with RBC membranes and preferably partition in the head group region of the lo domain leading to a fluidification of the membranes, i.e., a thinning of the bilayers and an increase in lipid tail spacing. Our results further support current models of RBC membranes as patchy structures and provide unprecedented structural details of the molecular organization in the different domains.
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24
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Zhernenkov M, Bolmatov D, Soloviov D, Zhernenkov K, Toperverg BP, Cunsolo A, Bosak A, Cai YQ. Revealing the mechanism of passive transport in lipid bilayers via phonon-mediated nanometre-scale density fluctuations. Nat Commun 2016; 7:11575. [PMID: 27175859 PMCID: PMC4865866 DOI: 10.1038/ncomms11575] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/10/2016] [Indexed: 12/21/2022] Open
Abstract
The passive transport of molecules through a cell membrane relies on thermal motions of the lipids. However, the nature of transmembrane transport and the precise mechanism remain elusive and call for a comprehensive study of phonon excitations. Here we report a high resolution inelastic X-ray scattering study of the in-plane phonon excitations in 1,2-dipalmitoyl-sn-glycero-3-phosphocholine above and below the main transition temperature. In the gel phase, for the first time, we observe low-frequency transverse modes, which exhibit a phonon gap when the lipid transitions into the fluid phase. We argue that the phonon gap signifies the formation of short-lived nanometre-scale lipid clusters and transient pores, which facilitate the passive molecular transport across the bilayer plane. Our findings suggest that the phononic motion of the hydrocarbon tails provides an effective mechanism of passive transport, and illustrate the importance of the collective dynamics of biomembranes. The molecular transport through bio-membranes of cells heavily relies on the dynamics of lipids, but the related mechanism remains unknown. Here, Zhernenkov et al. observe the propagating transverse phonon mode with a finite band gap and suggest its connection to short-lived local lipid clustering.
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Affiliation(s)
- Mikhail Zhernenkov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Dima Bolmatov
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Dmitry Soloviov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Kirill Zhernenkov
- Institut Nanosciences et Cryogénie, Commissariat à l'Energie Atomique, Grenoble 38054, France
| | - Boris P Toperverg
- Petersburg Nuclear Physics Institute, Gatchina 188300, Russia.,Institut Laue Langevin, 6, rue Jules Horowitz, Grenoble 38042, France
| | - Alessandro Cunsolo
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
| | - Alexey Bosak
- European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Yong Q Cai
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, USA
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25
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Marquardt D, Heberle FA, Nickels JD, Pabst G, Katsaras J. On scattered waves and lipid domains: detecting membrane rafts with X-rays and neutrons. SOFT MATTER 2015; 11:9055-72. [PMID: 26428538 PMCID: PMC4719199 DOI: 10.1039/c5sm01807b] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/21/2015] [Indexed: 05/28/2023]
Abstract
In order to understand the biological role of lipids in cell membranes, it is necessary to determine the mesoscopic structure of well-defined model membrane systems. Neutron and X-ray scattering are non-invasive, probe-free techniques that have been used extensively in such systems to probe length scales ranging from angstroms to microns, and dynamics occurring over picosecond to millisecond time scales. Recent developments in the area of phase separated lipid systems mimicking membrane rafts will be presented, and the underlying concepts of the different scattering techniques used to study them will be discussed in detail.
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Affiliation(s)
- Drew Marquardt
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Humboldtstr. 50/III, Graz, Austria. and BioTechMed-Graz, Graz, Austria
| | - Frederick A Heberle
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. and Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, USA
| | - Jonathan D Nickels
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. and Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, USA
| | - Georg Pabst
- University of Graz, Institute of Molecular Biosciences, Biophysics Division, NAWI Graz, Humboldtstr. 50/III, Graz, Austria. and BioTechMed-Graz, Graz, Austria
| | - John Katsaras
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. and Joint Institute for Neutron Sciences, Oak Ridge, Tennessee 37831, USA
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26
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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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27
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Abstract
Water is crucial to the structure and function of biological membranes. In fact, the membrane's basic structural unit, i.e. the lipid bilayer, is self-assembled and stabilized by the so-called hydrophobic effect, whereby lipid molecules unable to hydrogen bond with water aggregate in order to prevent their hydrophobic portions from being exposed to water. However, this is just the beginning of the lipid-bilayer-water relationship. This mutual interaction defines vesicle stability in solution, controls small molecule permeation, and defines the spacing between lamella in multi-lamellar systems, to name a few examples. This chapter will describe the structural and dynamical properties central to these, and other water- lipid bilayer interactions.
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Affiliation(s)
- Jonathan D Nickels
- Joint Institute for Neutron Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - John Katsaras
- Biology & Soft Matter and Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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28
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Wang Z, Chiang WS, Le P, Fratini E, Li M, Alatas A, Baglioni P, Chen SH. One role of hydration water in proteins: key to the "softening" of short time intraprotein collective vibrations of a specific length scale. SOFT MATTER 2014; 10:4298-4303. [PMID: 24789017 DOI: 10.1039/c4sm00257a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
High resolution inelastic X-ray scattering (IXS) experiments show that the "phonon energy softening" and "phonon population enhancement" observed in a hydrated native protein when increasing the temperature from 200 K to physiological temperature are not directly related to the protein structure. Such phenomena were also observed in a denatured sample without a defined tertiary structure and with a limited residual secondary structure. However, in a dry sample, such "softening" is strongly suppressed. These facts suggest that the above-mentioned protein "softening" phenomenon is water-induced. In addition, increasing the hydration level can also induce "phonon energy softening" at room temperature, but not at 200 K. This change may be due to a qualitative difference in the dynamics of hydration water at 200 K and at room temperature.
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Affiliation(s)
- Zhe Wang
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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29
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Conti Nibali V, D'Angelo G, Tarek M. Molecular dynamics simulation of short-wavelength collective dynamics of phospholipid membranes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:050301. [PMID: 25353727 DOI: 10.1103/physreve.89.050301] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Indexed: 06/04/2023]
Abstract
We investigated the short-wavelength longitudinal and transverse collective dynamics of the fluid and gel phases of phospholipid bilayers by means of molecular dynamics simulation. Similarly to a crystal, the spectrum of collective excitations in a bilayer consists of longitudinal and transverse acoustic modes, though modified by disorder. Beside acoustic modes, a series of broad dispersionless excitations are revealed. The dispersion curves of the observed excitations may be represented in a pseudo-Brillouin zone scheme centered around the spatial correlation peak of the acyl chains. The study provides evidence for a resonant interaction between the lowest frequency optical phonon and the longitudinal acoustic mode.
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Affiliation(s)
| | - Giovanna D'Angelo
- Dipartimento di Fisica, Università degli Studi di Messina, Messina, Italy
| | - Mounir Tarek
- UMR Structure et Réactivité des Systèmes Moléculaires Complexes, Nancy University, CNRS, Nancy, France
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Armstrong CL, Häussler W, Seydel T, Katsaras J, Rheinstädter MC. Nanosecond lipid dynamics in membranes containing cholesterol. SOFT MATTER 2014; 10:2600-2611. [PMID: 24647350 DOI: 10.1039/c3sm51757h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Lipid dynamics in the cholesterol-rich (40 mol%) liquid-ordered (lo) phase of dimyristoylphosphatidylcholine membranes were studied using neutron spin-echo and neutron backscattering. Recent theoretical and experimental evidence supports the notion of the liquid-ordered phase in phospholipid membranes as a locally structured liquid, with small ordered 'domains' of a highly dynamic nature in equilibrium with a disordered matrix [S. Meinhardt, R. L. C. Vink and F. Schmid, Proc. Natl. Acad. Sci. U. S. A., 2013, 110(12), 4476-4481, C. L. Armstrong et al., PLoS One, 2013, 8(6), e66162]. This local structure was found to have a pronounced impact on the membranes' dynamical properties. We found that the long-wavelength dynamics in the liquid-ordered phase, associated with the elastic properties of the membranes, were faster by two orders of magnitude as compared to the liquid disordered phase. At the same time, collective nanoscale diffusion was significantly slower. The presence of a soft-mode (a slowing down) in the long-wavelength dispersion relationship suggests an upper size limit for the ordered lipid domain of ≈220 Å. Moreover, from the relaxation rate of the collective lipid diffusion of lipid-lipid distances, the lifetime of these domains was estimated to be about 100 nanoseconds.
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Affiliation(s)
- Clare L Armstrong
- Department of Physics and Astronomy, McMaster University, Hamilton, ON, Canada.
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31
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Rheinstädter MC, Mouritsen OG. Small-scale structure in fluid cholesterol–lipid bilayers. Curr Opin Colloid Interface Sci 2013. [DOI: 10.1016/j.cocis.2013.07.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Paciaroni A, Orecchini A, Goracci G, Cornicchi E, Petrillo C, Sacchetti F. Glassy Character of DNA Hydration Water. J Phys Chem B 2013; 117:2026-31. [DOI: 10.1021/jp3105437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alessandro Paciaroni
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
- Istituto Officina dei Materiali,
Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
| | - Andrea Orecchini
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
- Istituto Officina dei Materiali,
Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
- Institut Laue Langevin, 6 rue J. Horowitz F-38042 Grenoble, France
| | - Guido Goracci
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
| | - Elena Cornicchi
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
- Istituto Officina dei Materiali,
Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli
I-06123 Perugia, Italy
- Istituto Officina dei Materiali,
Unità di Perugia, c/o Dipartimento di Fisica, Università di Perugia, I-06123 Perugia, Italy
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33
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Wang Z, Bertrand CE, Chiang WS, Fratini E, Baglioni P, Alatas A, Alp EE, Chen SH. Inelastic X-ray Scattering Studies of the Short-Time Collective Vibrational Motions in Hydrated Lysozyme Powders and Their Possible Relation to Enzymatic Function. J Phys Chem B 2013; 117:1186-95. [DOI: 10.1021/jp312842m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhe Wang
- Department of Nuclear Science and
Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Christopher E. Bertrand
- Department of Nuclear Science and
Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wei-Shan Chiang
- Department of Nuclear Science and
Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Emiliano Fratini
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Florence,
I-50019, Italy
| | - Piero Baglioni
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Florence,
I-50019, Italy
| | - Ahmet Alatas
- Advanced Photon
Source, Argonne National Lab, Argonne,
Illinois, 60439, United States
| | - E. Ercan Alp
- Advanced Photon
Source, Argonne National Lab, Argonne,
Illinois, 60439, United States
| | - Sow-Hsin Chen
- Department of Nuclear Science and
Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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34
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Effect of cholesterol on the lateral nanoscale dynamics of fluid membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2012; 41:901-13. [DOI: 10.1007/s00249-012-0826-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/03/2012] [Accepted: 05/07/2012] [Indexed: 12/17/2022]
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35
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36
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Antoniou D, Schwartz SD. Low-Frequency Collective Motions in Proteins. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633603000458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
There are several kinds of low-frequency collective motions in proteins, which are believed to have a significant effect on their properties. We propose that a new kind of global collective motion in proteins are density fluctuations, which are slowly-varying, long-lived, propagating disturbances. These can be studied using the linear response formalism, which is a dynamical approximation that uses the full anharmonic interatomic potential. We have performed a molecular dynamics simulation of a realistic protein and have found results that are consistent with the theoretical predictions of linear response theory.
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Affiliation(s)
- Dimitri Antoniou
- Department of Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Steven D. Schwartz
- Department of Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
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37
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PABST GEORG. GLOBAL PROPERTIES OF BIOMIMETIC MEMBRANES: PERSPECTIVES ON MOLECULAR FEATURES. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s1793048006000069] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Global properties of biological model membranes such as, e.g., structure or elasticity, are known to be closely related to their local features. If a membrane active compound interacts with the membrane assembly, the membrane will primarily be affected on the local, molecular level. The local perturbation may than, through some coupling, translate into a global adjustment of the membrane. In order to address this coupling x-ray and neutron diffraction data analysis techniques have been developed that allow accurate monitoring of changes in global properties. This offers new perspectives on molecular membrane features that in combination with complementary techniques, such as differential scanning calorimetry, spectroscopy or dynamic scattering lead to a better understanding of biomimetic membranes. The present article reviews these aspects giving application examples for single- and multicomponent membranes, respectively.
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Affiliation(s)
- GEORG PABST
- Institute of Biophysics and X-ray Structure Research, Austrian Academy of Sciences, Schmiedlstraße 6, Graz, 8042, Austria
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38
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Cornicchi E, Sebastiani F, De Francesco A, Orecchini A, Paciaroni A, Petrillo C, Sacchetti F. Collective density fluctuations of DNA hydration water in the time-window below 1 ps. J Chem Phys 2011; 135:025101. [PMID: 21766968 DOI: 10.1063/1.3609101] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The coherent density fluctuations propagating through DNA hydration water were studied by neutron scattering spectroscopy. Two collective modes were found to be sustained by the aqueous solvent: a propagating excitation, characterised by a speed of about 3500 m/s, and another one placed at about 6 meV. These results globally agree with those previously found for the coherent excitations in bulk water, although in DNA hydration water the speed of propagating modes is definitely higher than that of the pure solvent. The short-wavelength collective excitations of DNA hydration water are reminiscent of those observed in protein hydration water and in the amorphous forms of ice.
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Affiliation(s)
- Elena Cornicchi
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli, I-06123 Perugia, Italy.
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39
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Kaye MD, Schmalzl K, Nibali VC, Tarek M, Rheinstädter MC. Ethanol enhances collective dynamics of lipid membranes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:050907. [PMID: 21728483 DOI: 10.1103/physreve.83.050907] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Indexed: 05/31/2023]
Abstract
From inelastic neutron-scattering experiments and all atom molecular dynamics simulations we present evidence for a low-energy dynamical mode in the fluid phase of a 1,2-dimyristoyl-sn-glycero-3-phoshatidylcholine (DMPC) bilayer immersed in a 5% water/ethanol solution. In addition to the well-known phonon that shows a liquidlike dispersion with energies up to 4.5 meV, we observe an additional mode at smaller energies of 0.8 meV, which shows little or no dispersion. Both modes show transverse properties and might be related to molecular motion perpendicular to the bilayer.
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Affiliation(s)
- Martin D Kaye
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario, Canada
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40
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Trapp M, Gutberlet T, Juranyi F, Unruh T, Demé B, Tehei M, Peters J. Hydration dependent studies of highly aligned multilayer lipid membranes by neutron scattering. J Chem Phys 2010; 133:164505. [DOI: 10.1063/1.3495973] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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41
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Yoshida K, Hosokawa S, Baron AQR, Yamaguchi T. Collective dynamics of hydrated β-lactogloblin by inelastic x-ray scattering. J Chem Phys 2010; 133:134501. [DOI: 10.1063/1.3484238] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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42
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Abstract
Highly aligned, substrate supported membranes have made it possible for physical techniques to extract unambiguous structural information previously not accessible from commonly available membrane dispersions, or so-called powder samples. This review will highlight some of the major breakthroughs in model membrane research that have taken place as a result of substrate supported samples.
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43
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Brüning B, Rheinstädter MC, Hiess A, Weinhausen B, Reusch T, Aeffner S, Salditt T. Influence of cholesterol on the collective dynamics of the phospholipid acyl chains in model membranes. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2010; 31:419-428. [PMID: 20405158 DOI: 10.1140/epje/i2010-10574-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Revised: 02/18/2010] [Accepted: 03/12/2010] [Indexed: 05/29/2023]
Abstract
We have studied the packing and collective dynamics of the phospholipid acyl chains in a model membrane composed of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) and cholesterol in varied phase state. After a structural characterization of this two-component model bilayer using X-ray reflectivity, we have carried out coherent inelastic neutron scattering to investigate the chain dynamics. Both DMPC/cholesterol membranes exhibited much sharper and more pronounced low-energy inelastic excitations than a pure DMPC membrane. In the high-energy regime above 10 meV, the insertion of cholesterol into the membrane was found to shift the position of the inelastic excitation towards values otherwise found in the pure lipids gel phase. Thus, the dissipative collective short-range dynamics of the acyl chains is strongly influenced by the presence of cholesterol.
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Affiliation(s)
- B Brüning
- Institut Laue-Langevin, B.P. 156, 38042, Grenoble, France.
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44
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Pabst G, Kucerka N, Nieh MP, Rheinstädter MC, Katsaras J. Applications of neutron and X-ray scattering to the study of biologically relevant model membranes. Chem Phys Lipids 2010; 163:460-79. [PMID: 20361949 DOI: 10.1016/j.chemphyslip.2010.03.010] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/23/2010] [Accepted: 03/24/2010] [Indexed: 11/19/2022]
Abstract
Scattering techniques, in particular electron, neutron and X-ray scattering have played a major role in elucidating the static and dynamic structure of biologically relevant membranes. Importantly, neutron and X-ray scattering have evolved to address new sample preparations that better mimic biological membranes. In this review, we will report on some of the latest model membrane results, and the neutron and X-ray techniques that were used to obtain them.
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Affiliation(s)
- G Pabst
- Institute of Biophysics and Nanosystems Research, Austrian Academy of Sciences, A-8042 Graz, Austria
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45
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Abbamonte P, Wong GCL, Cahill DG, Reed JP, Coridan RH, Schmidt NW, Lai GH, Joe YI, Casa D. Ultrafast imaging and the phase problem for inelastic X-ray scattering. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2010; 22:1141-1147. [PMID: 20401938 DOI: 10.1002/adma.200904098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A new method for imaging ultrafast dynamics in condensed matter using inelastic X-ray scattering (IXS) is described. Using the concepts of causality and irreversibility a general solution to the inverse scattering problem (or "phase problem") for IXS is illustrated, which enables direct imaging of dynamics of the electron density with resolutions of approximately 1 attosecond (10(-18) s) in time and <1 A in space. This method is not just Fourier transformation of the IXS data, but a means to impose causality on the data and reconstruct the charge propagator. The method can also be applied to inelastic electron or neutron scattering. A general outline of phenomena that can and cannot be studied with this technique and an outlook for the future is provided.
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Affiliation(s)
- Peter Abbamonte
- Frederick Seitz Materials Research Laboratory University of Illinois Urbana, IL 61801, USA.
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46
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Coridan RH, Schmidt NW, Lai GH, Wong GCL. Hydration structures near finite-sized nanoscopic objects reconstructed using inelastic x-ray scattering measurements. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:424115. [PMID: 21715850 DOI: 10.1088/0953-8984/21/42/424115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent work has shown that it is possible to use high resolution dynamical structure factor S(q,ω) data measured with inelastic x-ray scattering to reconstruct the Green's function of water, which describes its dynamical density response to a point charge. Here, we generalize this approach and describe a strategy for reconstructing hydration behavior near simple charge distributions with excluded volumes, with the long term goal of engaging hydration processes in complex molecular systems. We use this Green's function based imaging of dynamics method to generate hydration structures and show that they are consistent with those of well-studied model systems.
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Affiliation(s)
- Robert H Coridan
- Department of Physics, University of Illinois at Urbana-Champaign, IL 61801, USA
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47
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Orecchini A, Paciaroni A, De Francesco A, Petrillo C, Sacchetti F. Collective dynamics of protein hydration water by brillouin neutron spectroscopy. J Am Chem Soc 2009; 131:4664-9. [PMID: 19284757 DOI: 10.1021/ja807957p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By a detailed experimental study of THz dynamics in the ribonuclease protein, we could detect the propagation of coherent collective density fluctuations within the protein hydration shell. The emerging picture indicates the presence of both a dispersing mode, traveling with a speed greater than 3000 m/s, and a nondispersing one, characterized by an almost constant energy of 6-7 meV. In agreement with molecular dynamics simulations [Phys. Rev. Lett. 2002, 89, 275501], the features of the dispersion curves closely resemble those observed in pure liquid water [Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2004, 69, 061203]. On the contrary, the observed damping factors are much larger than in bulk water, with the dispersing mode becoming overdamped at Q = 0.6 A(-1) already. Such novel experimental findings are discussed as a dynamic signature of the disordering effect induced by the protein surface on the local structure of water.
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Affiliation(s)
- Andrea Orecchini
- Dipartimento di Fisica, Università degli Studi di Perugia, Via Pascoli I-06123 Perugia, Italy.
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48
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Yang YT, Liao JD, Lee YL, Chang CW, Tsai HJ. Ultra-thin phospholipid layers physically adsorbed upon glass characterized by nano-indentation at the surface contact level. NANOTECHNOLOGY 2009; 20:195702. [PMID: 19420646 DOI: 10.1088/0957-4484/20/19/195702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Dipalmitoylphosphatic acid was chosen as a model to interpret how molecules physically adsorbed upon glass responded to an infinitesimal oscillation force at the surface contact level. Oscillation of a nano-indentation tip toward the phospholipid layers was driven by a dynamic contact module at a constant harmonic frequency; the phase angle of the oscillation frequency was exponentially relaxed along the nano-scale displacement. The tip-on-molecule contact was thereafter identified and influenced by the characteristic of the physically adsorbed phospholipids. By applying the harmonic displacement of the nano-indentation tip and making a distinction between full contact displacements, the thickness of the phospholipid layers was thereafter estimated. Moreover, the additional force required to penetrate through the physically adsorbed molecules was minor compared to the analogous process for the chemically adsorbed ones. The importance of recognizing the physically adsorbed molecules is relevant to applications of contact mechanics for the distinction of various phospholipids. Furthermore it is very promising to interpret the mechanism by which cells convert mechanical stimuli into biochemical responses on the channels of phospholipids.
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Affiliation(s)
- Yun-Ta Yang
- Department of Materials Science and Engineering, National Cheng Kung University, Tainan, Taiwan
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49
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Rheinstädter MC, Das J, Flenner EJ, Brüning B, Seydel T, Kosztin I. Motional coherence in fluid phospholipid membranes. PHYSICAL REVIEW LETTERS 2008; 101:248106. [PMID: 19113677 DOI: 10.1103/physrevlett.101.248106] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Indexed: 05/08/2023]
Abstract
We report a high energy-resolution neutron backscattering study, combined with in situ diffraction, to investigate slow molecular motions on nanosecond time scales in the fluid phase of phospholipid bilayers of 1,2-dimyristoyl-sn-glycero-3-phoshatidylcholine. A cooperative structural relaxation process was observed. From the in-plane scattering vector dependence of the relaxation rates in hydrogenated and deuterated samples, combined with results from a 0.1 micros long all-atom molecular dynamics simulation, it is concluded that correlated dynamics in lipid membranes occurs over several lipid distances, spanning a time interval from pico- to nanoseconds.
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Affiliation(s)
- Maikel C Rheinstädter
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, Missouri 65211, USA.
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50
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Liu D, Chu XQ, Lagi M, Zhang Y, Fratini E, Baglioni P, Alatas A, Said A, Alp E, Chen SH. Studies of phononlike low-energy excitations of protein molecules by inelastic x-ray scattering. PHYSICAL REVIEW LETTERS 2008; 101:135501. [PMID: 18851459 DOI: 10.1103/physrevlett.101.135501] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Revised: 07/25/2008] [Indexed: 05/26/2023]
Abstract
Molecular dynamics simulations and neutron scattering experiments have shown that many hydrated globular proteins exhibit a universal dynamic transition at TD = 220 K, below which the biological activity of a protein sharply diminishes. We studied the phononlike low-energy excitations of two structurally very different proteins, lysozyme and bovine serum albumin, using inelastic x-ray scattering above and below TD. We found that the excitation energies of the high-Q phonons show a marked softening above TD. This suggests that the large amplitude motions of wavelengths corresponding to this specific Q range are intimately correlated with the increase of biological activities of the proteins.
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Affiliation(s)
- Dazhi Liu
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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