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Li Y, Liu Y, Yang B, Li G, Chu H. Polarizable atomic multipole-based force field for cholesterol. J Biomol Struct Dyn 2024; 42:7747-7757. [PMID: 37565356 DOI: 10.1080/07391102.2023.2245045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023]
Abstract
Cholesterol is one of the essential component of lipid in membrane. We present a polarizable atomic multipole force field (FF) for the molecular dynamic simulation of cholesterol. The FF building process follows the computational framework as the atomic multipole optimized energetics for biomolecular applications (AMOEBA) model. In this framework, the electronics parameters, including atomic monopole moments, dipole moments, and quadrupole moments calculated from ab initio calculations in the gas phase, are applied to represent the charge distribution. Furthermore, the many-body polarization is modeled by following the same pattern of distributed atomic polarizabilities. Then, the bilayers composed of two typical phospholipid molecules, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), in a range of different cholesterol concentrations are built and implemented by molecular dynamics (MD) simulations based on the proposed polarizable FF. The simulation results are statistically analyzed to validate the feasibility of the proposed FF. The structural properties of the bilayers are calculated to compare with the related experimental values. The MD values show the same trend of experimental values changes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China
| | - Ye Liu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China
| | - Boya Yang
- Dalian Municipal Central Hospital, Liaoning, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China
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2
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Doktorova M, Khelashvili G, Ashkar R, Brown MF. Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics. Biophys J 2023; 122:984-1002. [PMID: 36474442 PMCID: PMC10111610 DOI: 10.1016/j.bpj.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 12/07/2022] Open
Abstract
Lipid bilayers form the main matrix of functional cell membranes, and their dynamics underlie a host of physical and biological processes. Here we show that elastic membrane properties and collective molecular dynamics (MD) are related by the mean-square amplitudes (order parameters) and relaxation rates (correlation times) of lipid acyl chain motions. We performed all-atom MD simulations of liquid-crystalline bilayers that allow direct comparison with carbon-hydrogen (CH) bond relaxations measured with NMR spectroscopy. Previous computational and theoretical approaches have assumed isotropic relaxation, which yields inaccurate description of lipid chain dynamics and incorrect data interpretation. Instead, the new framework includes a fixed bilayer normal (director axis) and restricted anisotropic motion of the CH bonds in accord with their segmental order parameters, enabling robust validation of lipid force fields. Simulated spectral densities of thermally excited CH bond fluctuations exhibited well-defined spin-lattice (Zeeman) relaxations analogous to those in NMR measurements. Their frequency signature could be fit to a simple power-law function, indicative of nematic-like collective dynamics. Moreover, calculated relaxation rates scaled as the squared order parameters yielding an apparent κC modulus for bilayer bending. Our results show a strong correlation with κC values obtained from solid-state NMR studies of bilayers without and with cholesterol as validated by neutron spin-echo measurements of membrane elasticity. The simulations uncover a critical role of interleaflet coupling in membrane mechanics and thus provide important insights into molecular sites of emerging elastic properties within lipid bilayers.
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Affiliation(s)
- Milka Doktorova
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, Virginia.
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York; Institute of Computational Biomedicine, Weill Cornell Medical College of Cornell University, New York, New York
| | - Rana Ashkar
- Department of Physics, Virginia Tech, Blacksburg, Virginia; Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virginia
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona; Department of Physics, University of Arizona, Tucson, Arizona; Program in Applied Mathematics, University of Arizona, Tucson, Arizona.
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3
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Doole FT, Gupta S, Kumarage T, Ashkar R, Brown MF. Biophysics of Membrane Stiffening by Cholesterol and Phosphatidylinositol 4,5-bisphosphate (PIP2). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1422:61-85. [PMID: 36988877 DOI: 10.1007/978-3-031-21547-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Cell membranes regulate a wide range of phenomena that are implicated in key cellular functions. Cholesterol, a critical component of eukaryotic cell membranes, is responsible for cellular organization, membrane elasticity, and other critical physicochemical parameters. Besides cholesterol, other lipid components such as phosphatidylinositol 4,5-bisphosphate (PIP2) are found in minor concentrations in cell membranes yet can also play a major regulatory role in various cell functions. In this chapter, we describe how solid-state deuterium nuclear magnetic resonance (2H NMR) spectroscopy together with neutron spin-echo (NSE) spectroscopy can inform synergetic changes to lipid molecular packing due to cholesterol and PIP2 that modulate the bending rigidity of lipid membranes. Fundamental structure-property relations of molecular self-assembly are illuminated and point toward a length and time-scale dependence of cell membrane mechanics, with significant implications for biological activity and membrane lipid-protein interactions.
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Affiliation(s)
- Fathima T Doole
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Sudipta Gupta
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, USA
| | - Teshani Kumarage
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, USA
| | - Rana Ashkar
- Department of Physics and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, USA.
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA.
- Department of Physics, University of Arizona, Tucson, AZ, USA.
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4
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Song ES, Oh Y, Sung BJ. Interdomain exchange and the flip-flop of cholesterol in ternary component lipid membranes and their effects on heterogeneous cholesterol diffusion. Phys Rev E 2021; 104:044402. [PMID: 34781553 DOI: 10.1103/physreve.104.044402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/17/2021] [Indexed: 11/07/2022]
Abstract
Cell membranes are heterogeneous with a variety of lipids, cholesterol, and proteins and are composed of domains of different compositions. Such heterogeneous environments make the transport of cholesterol complicated: cholesterol not only diffuses within a particular domain but also travels between domains. Cholesterol also flip-flops between upper and lower leaflets such that cholesterol may reside both within leaflets and in the central region between two leaflets. How the presence of multiple domains and the interdomain exchange of cholesterol would affect the cholesterol transport, however, remains elusive. In this study, therefore, we perform molecular dynamics simulations up to 100μs for ternary component lipid membranes, which consist of saturated lipids (dipalmitoylphosphatidylcholine, DPPC), unsaturated lipids (dilinoleylphosphatidylcholine, DIPC), and cholesterol. The ternary component membranes in our simulations form two domains readily: DPPC and DIPC domains. We find that the diffusion of cholesterol molecules is much more heterogeneous and non-Gaussian than expected for binary component lipid membranes of lipids and cholesterol. The non-Gaussian parameter of the cholesterol molecules is about four times larger in the ternary component lipid membranes than in the binary component lipid membranes. Such non-Gaussian and heterogeneous transport of cholesterol arises from the interplay among the interdomain kinetics, the different diffusivity of cholesterol in different domains, and the flip-flop of cholesterol. This suggests that in cell membranes that consist of various domains and proteins, the cholesterol transport can be very heterogeneous. We also find that the mechanism of the interdomain exchange differs for different domains: cholesterol tends to exit the DIPC domain along the central region of the membrane for the DIPC-to-DPPC transition, while the cholesterol is likely to exit the DPPC domain within the membrane leaflet for the DPPC-to-DIPC transition. Also, the interdomain exchange kinetics of cholesterol for the DPPC-to-DIPC transition is up to 7.9 times slower than the DIPC-to-DPPC transition.
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Affiliation(s)
- Eun Sub Song
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Younghoon Oh
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
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5
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Lu H, Martí J. Binding and dynamics of melatonin at the interface of phosphatidylcholine-cholesterol membranes. PLoS One 2019; 14:e0224624. [PMID: 31697738 PMCID: PMC6837308 DOI: 10.1371/journal.pone.0224624] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/17/2019] [Indexed: 12/18/2022] Open
Abstract
The characterization of interactions between melatonin, one main ingredient of medicines regulating sleeping rhythms, and basic components of cellular plasma membranes (phospholipids, cholesterol, metal ions and water) is very important to elucidate the main mechanisms for the introduction of melatonin into cells and also to identify its local structure and microscopic dynamics. Molecular dynamics simulations of melatonin inside mixtures of dimyristoylphosphatidylcholine and cholesterol in NaCl solution at physiological concentration have been performed at 303.15 K to systematically explore melatonin-cholesterol, melatonin-lipid and melatonin-water interactions. Properties such as the area per lipid and thickness of the membrane as well as selected radial distribution functions, binding free energies, angular distributions, atomic spectral densities and translational diffusion of melatonin are reported. The presence of cholesterol significantly affects the behavior of melatonin, which is mainly buried into the interfaces of membranes. Introducing cholesterol into the system helps melatonin change from folded to extended configurations more easily. Our results suggest that there exists a competition between the binding of melatonin to phospholipids and to cholesterol by means of hydrogen-bonds. Spectral densities of melatonin reported in this work, in overall good agreement with experimental data, revealed the participation of each atom of melatonin to its complete spectrum. Melatonin self-diffusion coefficients are of the order of 10-7 cm2/s and they significantly increase when cholesterol is addeed to the membrane.
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Affiliation(s)
- Huixia Lu
- Department of Physics, Technical University of Catalonia-Barcelona Tech. Barcelona, Catalonia, Spain
| | - Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech. Barcelona, Catalonia, Spain
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6
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Keyvanloo A, Shaghaghi M, Zuckermann MJ, Thewalt JL. The Phase Behavior and Organization of Sphingomyelin/Cholesterol Membranes: A Deuterium NMR Study. Biophys J 2019; 114:1344-1356. [PMID: 29590592 DOI: 10.1016/j.bpj.2018.01.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 01/10/2018] [Accepted: 01/18/2018] [Indexed: 10/17/2022] Open
Abstract
We have studied the dependence of the phase and domain characteristics of sphingomyelin (SM)/cholesterol model membranes on sterol content and temperature using deuterium nuclear magnetic resonance. NMR spectra of N-palmitoyl(D31)-D-erythro-sphingosylphosphorylcholine (PSM-d31) were taken for temperatures from 25 to 70°C and cholesterol concentrations of 0-40%. Analogous experiments were performed using 1-palmitoyl,2-palmitoyl(D31)-sn-glycero-3-phosphocholine (DPPC-d31)/cholesterol membranes to carefully compare the data obtained using palmitoyl chains that have similar "kinked" conformations. The constructed phase diagrams exhibit both solid-ordered (so) + liquid-ordered (lo) and liquid-disordered (ld) + lo phase-coexistence regions with a clear three-phase line. Macroscopic (micron-sized) coexistence of ld and lo phases was not observed; instead, line-broadening in the ld+lo region was characterized by intermediate exchange of lipids between the two types of domains. The length scales associated with the domains were estimated to be 75-150 nm for PSM-d31/cholesterol and DPPC-d31/cholesterol model membranes.
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Affiliation(s)
- Amir Keyvanloo
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Mehran Shaghaghi
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Martin J Zuckermann
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jenifer L Thewalt
- Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
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7
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Mallikarjunaiah KJ, Kinnun JJ, Petrache HI, Brown MF. Flexible lipid nanomaterials studied by NMR spectroscopy. Phys Chem Chem Phys 2019; 21:18422-18457. [DOI: 10.1039/c8cp06179c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in solid-state nuclear magnetic resonance spectroscopy inform the emergence of material properties from atomistic-level interactions in membrane lipid nanostructures.
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Affiliation(s)
- K. J. Mallikarjunaiah
- Department of Chemistry and Biochemistry
- University of Arizona
- Tucson
- USA
- Department of Physics
| | - Jacob J. Kinnun
- Department of Physics
- Indiana University-Purdue University
- Indianapolis
- USA
| | - Horia I. Petrache
- Department of Physics
- Indiana University-Purdue University
- Indianapolis
- USA
| | - Michael F. Brown
- Department of Chemistry and Biochemistry
- University of Arizona
- Tucson
- USA
- Department of Physics
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8
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Molugu TR, Brown MF. Cholesterol Effects on the Physical Properties of Lipid Membranes Viewed by Solid-state NMR Spectroscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1115:99-133. [PMID: 30649757 DOI: 10.1007/978-3-030-04278-3_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this chapter, we review the physical properties of lipid/cholesterol mixtures involving studies of model membranes using solid-state NMR spectroscopy. The approach allows one to quantify the average membrane structure, fluctuations, and elastic deformation upon cholesterol interaction. Emphasis is placed on understanding the membrane structural deformation and emergent fluctuations at an atomistic level. Lineshape measurements using solid-state NMR spectroscopy give equilibrium structural properties, while relaxation time measurements study the molecular dynamics over a wide timescale range. The equilibrium properties of glycerophospholipids, sphingolipids, and their binary and tertiary mixtures with cholesterol are accessible. Nonideal mixing of cholesterol with other lipids explains the occurrence of liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids, and may drive formation of lipid rafts. The functional dependence of 2H NMR spin-lattice relaxation (R 1Z) rates on segmental order parameters (S CD) for lipid membranes is indicative of emergent viscoelastic properties. Addition of cholesterol shows stiffening of the bilayer relative to the pure lipids and this effect is diminished for lanosterol. Opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale can potentially affect lipid raft formation in cellular membranes.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA. .,Department of Physics, University of Arizona, Tucson, AZ, USA.
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9
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Lu H, Martí J. Effects of cholesterol on the binding of the precursor neurotransmitter tryptophan to zwitterionic membranes. J Chem Phys 2018; 149:164906. [PMID: 30384712 DOI: 10.1063/1.5029430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The characterization of the microscopical forces between the essential α-amino-acid tryptophan, precursor of the neurotransmitter serotonin and of the hormone melatonin, and the basic components of cell membranes and their environments (phospholipids, cholesterol, ionic species, and water) is of central importance to elucidate their local structure and dynamics as well as the mechanisms responsible for the access of tryptophan to the interior of the cell. We have performed nanosecond molecular dynamics simulations of tryptophan embedded in model zwitterionic bilayer membranes made by di-palmitoyl-phosphatidyl-choline and cholesterol inside aqueous sodium-chloride solution in order to systematically examine tryptophan-lipid, tryptophan-cholesterol, and tryptophan-water interactions under liquid-crystalline phase conditions. Microscopic properties such as the area per lipid, lipid thickness, radial distribution functions, hydrogen-bonding lengths, atomic spectral densities, and self-diffusion coefficients have been evaluated. Our results show that the presence of tryptophan significantly affects the structure and dynamics of the membrane. Tryptophan spends long periods of time at the water-membrane interface, and it plays a central role by bridging a few lipids and cholesterol chains by means of hydrogen-bonds. The computed spectral densities, in excellent agreement with experimental infrared and Raman data, revealed the participation of each atomic site of tryptophan to the complete spectrum of the molecule. Tryptophan self-diffusion coefficients have been found to be in between 10-7 and 10-6 cm2/s and strongly depending of the concentration of cholesterol in the system.
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Affiliation(s)
- Huixia Lu
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B4-210 Northern Campus UPC, 08034 Barcelona, Catalonia, Spain
| | - Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B5-209 Northern Campus UPC, 08034 Barcelona, Catalonia, Spain
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10
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Oh Y, Sung BJ. Facilitated and Non-Gaussian Diffusion of Cholesterol in Liquid Ordered Phase Bilayers Depends on the Flip-Flop and Spatial Arrangement of Cholesterol. J Phys Chem Lett 2018; 9:6529-6535. [PMID: 30346769 DOI: 10.1021/acs.jpclett.8b02982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The diffusion of cholesterol in biological membranes is critical to cellular processes such as the formation of cholesterol-enriched domains. The cholesterol diffusion may be complicated especially when cholesterol flip-flops and/or stays at the membrane center. Understanding the diffusion mechanism of cholesterol at a molecular level should be, therefore, a topic of interest. We perform molecular dynamics simulations up to 100 μs for lipid bilayers with various concentrations of cholesterol. We find that cholesterol diffusion in the liquid ordered phase depends on whether it is within leaflets or at the bilayer center, is non-Gaussian for several microseconds, and is enhanced significantly compared to that of lipids. Cholesterol at the bilayer center diffuses fast, while cholesterol in the hydrocarbon region with upright orientation diffuses relatively slowly. Such position-dependent dynamics of cholesterol leads to facilitated and non-Gaussian diffusion.
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Affiliation(s)
- Younghoon Oh
- Department of Chemistry and Research Institute for Basic Science , Sogang University , Seoul 04107 , Republic of Korea
| | - Bong June Sung
- Department of Chemistry and Research Institute for Basic Science , Sogang University , Seoul 04107 , Republic of Korea
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11
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Molugu TR, Lee S, Brown MF. Concepts and Methods of Solid-State NMR Spectroscopy Applied to Biomembranes. Chem Rev 2017; 117:12087-12132. [PMID: 28906107 DOI: 10.1021/acs.chemrev.6b00619] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Concepts of solid-state NMR spectroscopy and applications to fluid membranes are reviewed in this paper. Membrane lipids with 2H-labeled acyl chains or polar head groups are studied using 2H NMR to yield knowledge of their atomistic structures in relation to equilibrium properties. This review demonstrates the principles and applications of solid-state NMR by unifying dipolar and quadrupolar interactions and highlights the unique features offered by solid-state 2H NMR with experimental illustrations. For randomly oriented multilamellar lipids or aligned membranes, solid-state 2H NMR enables direct measurement of residual quadrupolar couplings (RQCs) due to individual C-2H-labeled segments. The distribution of RQC values gives nearly complete profiles of the segmental order parameters SCD(i) as a function of acyl segment position (i). Alternatively, one can measure residual dipolar couplings (RDCs) for natural abundance lipid samples to obtain segmental SCH order parameters. A theoretical mean-torque model provides acyl-packing profiles representing the cumulative chain extension along the normal to the aqueous interface. Equilibrium structural properties of fluid bilayers and various thermodynamic quantities can then be calculated, which describe the interactions with cholesterol, detergents, peptides, and integral membrane proteins and formation of lipid rafts. One can also obtain direct information for membrane-bound peptides or proteins by measuring RDCs using magic-angle spinning (MAS) in combination with dipolar recoupling methods. Solid-state NMR methods have been extensively applied to characterize model membranes and membrane-bound peptides and proteins, giving unique information on their conformations, orientations, and interactions in the natural liquid-crystalline state.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Soohyun Lee
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
| | - Michael F Brown
- Department of Chemistry & Biochemistry and ‡Department of Physics, University of Arizona , Tucson, Arizona 85721, United States
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12
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Fu R, Miao Y, Qin H, Cross TA. Probing Hydronium Ion Histidine NH Exchange Rate Constants in the M2 Channel via Indirect Observation of Dipolar-Dephased 15N Signals in Magic-Angle-Spinning NMR. J Am Chem Soc 2016; 138:15801-15804. [PMID: 27960325 PMCID: PMC5368641 DOI: 10.1021/jacs.6b08376] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Water-protein chemical exchange in membrane-bound proteins is an important parameter for understanding how proteins interact with their aqueous environment, but has been difficult to observe in membrane-bound biological systems. Here, we demonstrate the feasibility of probing specific water-protein chemical exchange in membrane-bound proteins in solid-state MAS NMR. By spin-locking the 1H magnetization along the magic angle, the 1H spin diffusion is suppressed such that a water-protein chemical exchange process can be monitored indirectly by dipolar-dephased 15N signals through polarization transfer from 1H. In the example of the Influenza A full length M2 protein, the buildup of dipolar-dephased 15N signals from the tetrad of His37 side chains have been observed as a function of spin-lock time. This confirms that hydronium ions are in exchange with protons in the His37 NH bonds at the heart of the M2 proton conduction mechanism, with an exchange rate constant of ∼1750 s-1 for pH 6.2 at -10 °C.
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Affiliation(s)
- Riqiang Fu
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Yimin Miao
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Huajun Qin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
| | - Timothy A. Cross
- National High Magnet Field Lab, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, United States
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13
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Measurement of the bending elastic modulus in unilamellar vesicles membranes by fast field cycling NMR relaxometry. Chem Phys Lipids 2016; 201:21-27. [DOI: 10.1016/j.chemphyslip.2016.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/22/2016] [Accepted: 10/31/2016] [Indexed: 01/01/2023]
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14
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Molugu TR, Brown MF. Cholesterol-induced suppression of membrane elastic fluctuations at the atomistic level. Chem Phys Lipids 2016; 199:39-51. [PMID: 27154600 DOI: 10.1016/j.chemphyslip.2016.05.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/29/2016] [Accepted: 05/02/2016] [Indexed: 12/14/2022]
Abstract
Applications of solid-state NMR spectroscopy for investigating the influences of lipid-cholesterol interactions on membrane fluctuations are reviewed in this paper. Emphasis is placed on understanding the energy landscapes and fluctuations at an emergent atomistic level. Solid-state (2)H NMR spectroscopy directly measures residual quadrupolar couplings (RQCs) due to individual C-(2)H labeled segments of the lipid molecules. Moreover, residual dipolar couplings (RDCs) of (13)C-(1)H bonds are obtained in separated local-field NMR spectroscopy. The distributions of RQC or RDC values give nearly complete profiles of the order parameters as a function of acyl segment position. Measured equilibrium properties of glycerophospholipids and sphingolipids including their binary and tertiary mixtures with cholesterol show unequal mixing associated with liquid-ordered domains. The entropic loss upon addition of cholesterol to sphingolipids is less than for glycerophospholipids and may drive the formation of lipid rafts. In addition relaxation time measurements enable one to study the molecular dynamics over a wide time-scale range. For (2)H NMR the experimental spin-lattice (R1Z) relaxation rates follow a theoretical square-law dependence on segmental order parameters (SCD) due to collective slow dynamics over mesoscopic length scales. The functional dependence for the liquid-crystalline lipid membranes is indicative of viscoelastic properties as they emerge from atomistic-level interactions. A striking decrease in square-law slope upon addition of cholesterol denotes stiffening relative to the pure lipid bilayers that is diminished in the case of lanosterol. Measured equilibrium properties and relaxation rates infer opposite influences of cholesterol and detergents on collective dynamics and elasticity at an atomistic scale that potentially affects lipid raft formation in cellular membranes.
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Affiliation(s)
- Trivikram R Molugu
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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15
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Swanson SD, Malyarenko DI, Fabiilli ML, Welsh RC, Nielsen JF, Srinivasan A. Molecular, dynamic, and structural origin of inhomogeneous magnetization transfer in lipid membranes. Magn Reson Med 2016; 77:1318-1328. [PMID: 27029318 DOI: 10.1002/mrm.26210] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 02/06/2016] [Accepted: 02/18/2016] [Indexed: 02/04/2023]
Abstract
PURPOSE To elucidate the dynamic, structural, and molecular properties that create inhomogeneous magnetization transfer (ihMT) contrast. METHODS Amphiphilic lipids, lamellar phospholipids with cholesterol, and bovine spinal cord (BSC) specimens were examined along with nonlipid systems. Magnetization transfer (MT), enhanced MT (eMT, obtained with double-sided radiofrequency saturation), ihMT (MT - eMT), and dipolar relaxation, T1D , were measured at 2.0 and 11.7 T. RESULTS The amplitude of ihMT ratio (ihMTR) is positively correlated with T1D values. Both ihMTR and T1D increase with increasing temperature in BSC white matter and in phospholipids and decrease with temperature in other lipids. Changes in ihMTR with temperature arise primarily from alterations in MT rather than eMT. Spectral width of MT, eMT, and ihMT increases with increasing carbon chain length. CONCLUSIONS Concerted motions of phospholipids in white matter decrease proton spin diffusion leading to increased proton T1D times and increased ihMT amplitudes, consistent with decoupling of Zeeman and dipolar spin reservoirs. Molecular specificity and dynamic sensitivity of ihMT contrast make it a suitable candidate for probing myelin membrane disorders. Magn Reson Med 77:1318-1328, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Scott D Swanson
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Mario L Fabiilli
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert C Welsh
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jon-Fredrik Nielsen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Ashok Srinivasan
- Department of Radiology, University of Michigan, Ann Arbor, Michigan, USA
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16
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Yasuda T, Matsumori N, Tsuchikawa H, Lönnfors M, Nyholm TKM, Slotte JP, Murata M. Formation of Gel-like Nanodomains in Cholesterol-Containing Sphingomyelin or Phosphatidylcholine Binary Membrane As Examined by Fluorescence Lifetimes and (2)H NMR Spectra. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13783-13792. [PMID: 26639840 DOI: 10.1021/acs.langmuir.5b03566] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
In this study, we measured the time-resolved fluorescence of trans-parinaric acid (tPA), steady-state fluorescence anisotropy of diphenylhexatriene (DPH), and (2)H NMR of 10,10-d2-stearoyl lipids in stearoyl sphingomyelin with cholesterol (SSM/Chol) and l-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholine with Chol (PSPC/Chol) binary membranes. The results suggest that the membrane order obtained from the fluorescence experiments shows a similar temperature dependency as those of the (2)H NMR data. More importantly, the time-resolved fluorescence data implied the presence of at least two types of domains, cholesterol-poor gel-like domains (CPGLD) and cholesterol-enriched liquid-ordered (Lo) domains. These domains appear on a nano-to-micro second time scale for both SSM-Chol and PSPC-Chol membranes. The relative size of the gel-like domain was also estimated from the temperature-dependent lifetime measurements and (2)H NMR spectral changes. The results imply that the size of the gel-like domains is very small, probably on the nanometer scale, and smaller in SSM-Chol membrane than those in PSPC-Chol bilayers, which could account for the higher thermal stability of SM-Chol membranes. The present study demonstrates that gel-like nanodomains occur in SM-Chol binary membrane even with Chol content of over 33 mol %, which has been thought to consist exclusively of Lo phase, implying that not only Lo domains but also gel-like nanodomains are important for formation of lipid-ordered phase in SM-Chol and PC-Chol membranes.
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Affiliation(s)
- Tomokazu Yasuda
- Department of Chemistry, Graduate School of Science, Osaka University , Toyonaka, Osaka 560-0043, Japan
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Toyonaka, Osaka 560-0043, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University , Toyonaka, Osaka 560-0043, Japan
- Department of Chemistry, Graduate School of Sciences, Kyushu University , Higashi-ku, Fukuoka 812-8581, Japan
| | - Hiroshi Tsuchikawa
- Department of Chemistry, Graduate School of Science, Osaka University , Toyonaka, Osaka 560-0043, Japan
| | - Max Lönnfors
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University , Tykistökatu 6A, FIN-20520 Turku, Finland
| | - Thomas K M Nyholm
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University , Tykistökatu 6A, FIN-20520 Turku, Finland
| | - J Peter Slotte
- Biochemistry, Faculty of Science and Engineering, Åbo Akademi University , Tykistökatu 6A, FIN-20520 Turku, Finland
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University , Toyonaka, Osaka 560-0043, Japan
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Toyonaka, Osaka 560-0043, Japan
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17
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Madej BD, Gould IR, Walker RC. A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field. J Phys Chem B 2015; 119:12424-35. [PMID: 26359797 DOI: 10.1021/acs.jpcb.5b04924] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Amber Lipid14 force field is expanded to include cholesterol parameters for all-atom cholesterol and lipid bilayer molecular dynamics simulations. The General Amber and Lipid14 force fields are used as a basis for assigning atom types and basic parameters. A new RESP charge derivation for cholesterol is presented, and tail parameters are adapted from Lipid14 alkane tails. 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers are simulated at a range of cholesterol contents. Experimental bilayer structural properties are compared with bilayer simulations and are found to be in good agreement. With this parameterization, another component of complex membranes is available for molecular dynamics with the Amber Lipid14 force field.
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Affiliation(s)
- Benjamin D Madej
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States.,San Diego Supercomputer Center , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States
| | - Ian R Gould
- Department of Chemistry and Institute of Chemical Biology, Imperial College London , South Kensington SW7 2AZ, United Kingdom
| | - Ross C Walker
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States.,San Diego Supercomputer Center , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States
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18
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Yang J, Calero C, Martí J. Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes. J Chem Phys 2014; 140:104901. [PMID: 24628199 DOI: 10.1063/1.4867385] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10(-5) cm(2)/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10(-8) cm(2)/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2-8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a "wagging of the tails" frequency around 30 cm(-1), which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.
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Affiliation(s)
- J Yang
- Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
| | - C Calero
- Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
| | - J Martí
- Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
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19
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Yasuda T, Kinoshita M, Murata M, Matsumori N. Detailed comparison of deuterium quadrupole profiles between sphingomyelin and phosphatidylcholine bilayers. Biophys J 2014; 106:631-8. [PMID: 24507603 DOI: 10.1016/j.bpj.2013.12.034] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/25/2013] [Accepted: 12/26/2013] [Indexed: 11/25/2022] Open
Abstract
Lipid rafts are microdomains rich in sphingomyelin (SM) and cholesterol (Chol). The essential question is why natural lipid rafts prefer SM rather than saturated diacyl glycerophosphocholine, although both form ordered membranes with Chol in model systems. Hence in this study, we synthesized site-specifically deuterated 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholines that match the acyl chain length of stearoyl-SM (SSM), and compared their deuterium quadrupole coupling profiles in detail. The results suggest a deeper distribution of Chol in the SSM membranes, a lower entropic penalty upon accommodation of Chol in SSM membranes, and a higher thermal stability of acyl-chain orders in the SSM-Chol bilayers than in the 1-palmitoyl-2-stearoyl-sn-glycero-3-phosphocholine-Chol system at various Chol concentrations. The entropy effect and thermal stability should render SM a more preferred raft constituent than saturated diacyl glycerophosphocholine. Our data also demonstrate that the selective and comprehensive deuteration strategy is indispensable for accurate comparison of order profiles.
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Affiliation(s)
- Tomokazu Yasuda
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan; Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Toyonaka, Osaka, Japan
| | - Masanao Kinoshita
- Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Toyonaka, Osaka, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan; Japan Science and Technology Agency, ERATO, Lipid Active Structure Project, Toyonaka, Osaka, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
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20
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Mouret L, Da Costa G, Bondon A. Sterols associated with small unilamellar vesicles (SUVs): intrinsic mobility role for 1H NMR detection. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2014; 52:339-344. [PMID: 24691941 DOI: 10.1002/mrc.4069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/27/2014] [Accepted: 03/11/2014] [Indexed: 06/03/2023]
Abstract
Small unilamellar vesicles (SUVs) of phospholipids are often used as a membrane model system for studying the interaction of molecules. When using NMR under the standard liquid-state conditions, SUV phospholipid proton spectra can be recorded, exhibiting sharp signals. This is not only because of the fast vesicular tumbling but also because of the combination of this tumbling with the individual motion of the lipids inside the bilayer. This appears evident because addition of cholesterol is responsible of broader resonances because of the slowing down of the lipid motion. On the other hand, no (1)H signal is detected for cholesterol in the bilayer. This lack of detection of the inserted molecules explains why generally SUVs are not considered as a good model for NMR studies under the standard liquid-state conditions. Here, we use two other sterols in order to demonstrate that an increase of the molecular mobility inside the bilayer could allow the detection of their proton resonances. For desmosterol and lanosterol, which show higher mobility inside the bilayer, with increasing lateral diffusion rates, (1)H sterol signals are detected in contrast to cholesterol. For the fast diffusing lanosterol, no significant improvement in detection is observed using deuterated lipids, demonstrating that homonuclear dipolar coupling is fully averaged out. Furthermore, in the case of low mobility such as for cholesterol, the use of a fast magic angle spinning probe is shown to be efficient to recover the full proton spectrum.
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Affiliation(s)
- Liza Mouret
- Université de Rennes 1, UMR CNRS 6226, ICMV, PRISM Biosit, Campus de Villejean, 35043, Rennes Cedex, France
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21
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Fraenza CC, Meledandri CJ, Anoardo E, Brougham DF. The effect of cholesterol on membrane dynamics on different timescales in lipid bilayers from fast field-cycling NMR relaxometry studies of unilamellar vesicles. Chemphyschem 2014; 15:425-35. [PMID: 24482248 DOI: 10.1002/cphc.201301051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Indexed: 01/16/2023]
Abstract
The general applicability of fast field-cycling nuclear magnetic resonance relaxometry in the study of dynamics in lipid bilayers is demonstrated through analysis of binary unilamellar liposomes composed of 1,2-dioleoyl-sn-glycero-3-posphocholine (DOPC) and cholesterol. We extend an evidence-based method to simulating the NMR relaxation response, previously validated for single-component membranes, to evaluate the effect of the sterol molecule on local ordering and dynamics over multiple timescales. The relaxometric results are found to be most consistent with the partitioning of the lipid molecules into affected and unaffected portions, rather than a single averaged phase. Our analysis suggests that up to 25 mol%, each cholesterol molecule orders three DOPC molecules, providing experimental backup to the findings of many molecular dynamics studies. A methodology is established for studying dynamics on multiple timescales in unilamellar membranes of more complex compositions.
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Affiliation(s)
- Carla C Fraenza
- Laboratorio de Relaxometría y Técnicas Especiales, Grupo de Resonancia Magnética Nuclear, Facultad de Matemática, Astronomía y Física, Universidad Nacional de Córdoba and IFEG (CONICET), Córdoba (Argentina)
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22
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Huster D. Solid-state NMR spectroscopy to study protein-lipid interactions. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:1146-60. [PMID: 24333800 DOI: 10.1016/j.bbalip.2013.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/04/2013] [Indexed: 12/22/2022]
Abstract
The appropriate lipid environment is crucial for the proper function of membrane proteins. There is a tremendous variety of lipid molecules in the membrane and so far it is often unclear which component of the lipid matrix is essential for the function of a respective protein. Lipid molecules and proteins mutually influence each other; parameters such as acyl chain order, membrane thickness, membrane elasticity, permeability, lipid-domain and annulus formation are strongly modulated by proteins. More recent data also indicates that the influence of proteins goes beyond a single annulus of next-neighbor boundary lipids. Therefore, a mesoscopic approach to membrane lipid-protein interactions in terms of elastic membrane deformations has been developed. Solid-state NMR has greatly contributed to the understanding of lipid-protein interactions and the modern view of biological membranes. Methods that detect the influence of proteins on the membrane as well as direct lipid-protein interactions have been developed and are reviewed here. Examples for solid-state NMR studies on the interaction of Ras proteins, the antimicrobial peptide protegrin-1, the G protein-coupled receptor rhodopsin, and the K(+) channel KcsA are discussed. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany.
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23
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Lee CC, Petersen NO. The Triple Layer Model: A Different Perspective on Lipid Bilayers. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200400174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Domonkos I, Kis M, Gombos Z, Ughy B. Carotenoids, versatile components of oxygenic photosynthesis. Prog Lipid Res 2013; 52:539-61. [PMID: 23896007 DOI: 10.1016/j.plipres.2013.07.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 07/19/2013] [Accepted: 07/19/2013] [Indexed: 12/13/2022]
Abstract
Carotenoids (CARs) are a group of pigments that perform several important physiological functions in all kingdoms of living organisms. CARs serve as protective agents, which are essential structural components of photosynthetic complexes and membranes, and they play an important role in the light harvesting mechanism of photosynthesizing plants and cyanobacteria. The protection against reactive oxygen species, realized by quenching of singlet oxygen and the excited states of photosensitizing molecules, as well as by the scavenging of free radicals, is one of the main biological functions of CARs. X-ray crystallographic localization of CARs revealed that they are present at functionally and structurally important sites of both the PSI and PSII reaction centers. Characterization of a CAR-less cyanobacterial mutant revealed that while the absence of CARs prevents the formation of PSII complexes, it does not abolish the assembly and function of PSI. CAR molecules assist in the formation of protein subunits of the photosynthetic complexes by gluing together their protein components. In addition to their aforementioned indispensable functions, CARs have a substantial role in the formation and maintenance of proper cellular architecture, and potentially also in the protection of the translational machinery under stress conditions.
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Affiliation(s)
- Ildikó Domonkos
- Institute of Plant Biology, Biological Research Centre of Hungarian Academy of Sciences, P.O. Box 521, H-6701 Szeged, Hungary
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25
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Qiu C, Blanchard GJ. Phospholipid vesicle stability and temporal variations in acyl chain organization. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 110:383-390. [PMID: 23583873 DOI: 10.1016/j.saa.2013.03.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 06/02/2023]
Abstract
We report on our investigation of the long-term dimensional stability and acyl chain organization of unilamellar vesicles containing 1,2-dimyristoyl-sn-phosphatidylcholine (DMPC) and DMPC with cholesterol. Vesicles of 100% DMPC, 80% DMPC/20% cholesterol and 70% DMPC/30% cholesterol, formed by extrusion in aqueous buffer solution (pH 8) were shown to remain dimensionally stable for periods in excess of 600 h by dynamic light scattering (DLS) measurements. The rotational diffusion dynamics of perylene confined in the vesicle acyl chain region revealed structural evolution that was dependent on vesicle composition. Re-extrusion of the vesicles caused no changes in the average diameter or size distribution, but did give rise to diminished organization in the lipid acyl chain region for DMPC vesicles. Cholesterol-containing vesicles exhibited somewhat less pronounced change in organization on re-extrusion, suggesting a structurally mediating role for cholesterol.
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Affiliation(s)
- Chen Qiu
- Michigan State University, Department of Chemistry, East Lansing, MI 48824-1322, USA
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26
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Jämbeck JPM, Lyubartsev AP. Another Piece of the Membrane Puzzle: Extending Slipids Further. J Chem Theory Comput 2012; 9:774-84. [PMID: 26589070 DOI: 10.1021/ct300777p] [Citation(s) in RCA: 210] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To be able to model complex biological membranes in a more realistic manner, the force field Slipids (Stockholm lipids) has been extended to include parameters for sphingomyelin (SM), phosphatidylglycerol (PG), phosphatidylserine (PS) lipids, and cholesterol. Since the parametrization scheme was faithful to the scheme used in previous editions of Slipids, all parameters are consistent and fully compatible. The results of careful validation of a number of key structural properties for one and two component lipid bilayers are in excellent agreement with experiments. Potentials of mean force for transferring water across binary mixtures of lipids and cholesterol were also computed in order to compare water permeability rates to experiments. In agreement with experimental and simulation studies, it was found that the permeability and partitioning of water is affected by cholesterol in lipid bilayers made of saturated lipids to the largest extent. With the extensions of Slipids presented here, it is now possible to study complex systems containing many different lipids and proteins in a fully atomistic resolution in the isothermic-isobaric (NPT) ensemble, which is the proper ensemble for membrane simulations.
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Affiliation(s)
- Joakim P M Jämbeck
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
| | - Alexander P Lyubartsev
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, SE-10691, Sweden
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27
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Manickam Achari V, Nguan HS, Heidelberg T, Bryce RA, Hashim R. Molecular Dynamics Study of Anhydrous Lamellar Structures of Synthetic Glycolipids: Effects of Chain Branching and Disaccharide Headgroup. J Phys Chem B 2012; 116:11626-34. [DOI: 10.1021/jp302292s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Hock Seng Nguan
- Department
of Chemistry, University of Malaya, 50603
Kuala Lumpur, Malaysia
| | | | - Richard A. Bryce
- School of Pharmacy and Pharmaceutical
Sciences, University of Manchester, Manchester,
M13 9PT, U.K
| | - Rauzah Hashim
- Department
of Chemistry, University of Malaya, 50603
Kuala Lumpur, Malaysia
- Kavli Institute
of Theoretical
Physics China, Chinese Academy of Sciences, Beijing 100190, China
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28
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Schrader W, Behrends R, Kaatze U. Cholesterol-Induced Variations in the Domain Structure Fluctuations and Microdynamics of Lipid Membranes. J Phys Chem B 2012; 116:2446-54. [DOI: 10.1021/jp2106007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- W. Schrader
- Drittes Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen,
Germany
| | - R. Behrends
- Drittes Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen,
Germany
| | - U. Kaatze
- Drittes Physikalisches Institut, Georg-August-Universität Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen,
Germany
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29
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Lucas TR, Bauer BA, Davis JE, Patel S. Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields. J Comput Chem 2012; 33:141-52. [PMID: 21997857 PMCID: PMC3488352 DOI: 10.1002/jcc.21927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 06/24/2011] [Accepted: 07/30/2011] [Indexed: 12/21/2022]
Abstract
We present results of molecular dynamics simulations of a model DPPC-water monolayer using charge equilibration (CHEQ) force fields, which explicitly account for electronic polarization in a classical treatment of intermolecular interactions. The surface pressure, determined as the difference between the monolayer and pure water surface tensions at 323 K, is predicted to be 22.92 ±1.29 dyne/cm, just slightly below the broad range of experimental values reported for this system. The surface tension for the DPPC-water monolayer is predicted to be 42.35 ±1.16 dyne/cm, in close agreement with the experimentally determined value of 40.9 dyne/cm. This surface tension is also consistent with the value obtained from DPPC monolayer simulations using state-of-the-art nonpolarizable force fields. The current results of simulations predict a monolayer-water potential difference relative to the pure water-air interface of 0.64 ±0.02 Volts, an improved prediction compared to the fixed-charge CHARMM27 force field, yet still overestimating the experimental range of 0.3 to 0.45 Volts. As the charge equilibration model is a purely charge-based model for polarization, the current results suggest that explicitly modeled polarization effects can offer improvements in describing interfacial electrostatics in such systems.
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Affiliation(s)
- Timothy R. Lucas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Joseph E. Davis
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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30
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O’Connor JW, Klauda JB. Lipid Membranes with a Majority of Cholesterol: Applications to the Ocular Lens and Aquaporin 0. J Phys Chem B 2011; 115:6455-64. [DOI: 10.1021/jp108650u] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joseph W. O’Connor
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, United States
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31
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Mosca M, Ceglie A, Ambrosone L. Effect of membrane composition on lipid oxidation in liposomes. Chem Phys Lipids 2011; 164:158-65. [DOI: 10.1016/j.chemphyslip.2010.12.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 12/15/2010] [Accepted: 12/16/2010] [Indexed: 10/18/2022]
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32
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Leftin A, Brown MF. An NMR database for simulations of membrane dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:818-39. [PMID: 21134351 DOI: 10.1016/j.bbamem.2010.11.027] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 11/18/2010] [Accepted: 11/22/2010] [Indexed: 10/18/2022]
Abstract
Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations.
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Affiliation(s)
- Avigdor Leftin
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA
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33
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Raudino A, Pannuzzo M. Adhesion Kinetics between a Membrane and a Flat Substrate. An Ideal Upper Bound to the Spreading Rate of an Adhesive Patch. J Phys Chem B 2010; 114:15495-505. [DOI: 10.1021/jp106722w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Antonio Raudino
- Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 6-95125, Catania, Italy
| | - Martina Pannuzzo
- Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 6-95125, Catania, Italy
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Neumann A, Czub J, Baginski M. On the possibility of the amphotericin B-sterol complex formation in cholesterol- and ergosterol-containing lipid bilayers: a molecular dynamics study. J Phys Chem B 2010; 113:15875-85. [PMID: 19929013 DOI: 10.1021/jp905133f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amphotericin B (AmB) is a well-known membrane-active antibiotic that has been used to treat systemic fungal infections for more than 45 years. Therapeutic application of AmB is based on the fact that it is more active against ergosterol-containing membranes of fungal cells than against mammalian membranes with cholesterol. In this paper, we examine the hypothesis according to which the selectivity of the AmB's membrane action originates from its different ability to form the binary complexes with the relevant sterols. To this end, molecular dynamics simulations were performed for systems containing the preformed models of AmB/sterol complexes embedded in lipid bilayers containing either cholesterol or ergosterol. The initial structures of the studied binary associates were selected on the basis of a systematic scan of all possible mutual positions and orientations of the two molecules. The results obtained demonstrate that in general the complexes with ergosterol are more stable on the 100 ns time scale. Furthermore, on the basis of motional correlation analysis, taking into account the effects of lipid environment, we propose that, within the sterol-enriched liquid-ordered membrane phases, AmB molecules exhibit a greater tendency to bind ergosterol than cholesterol. The analysis of the interactions suggests that this affinity difference is of enthalpic origin and may arise from the considerable difference in the energy of the van der Waals interactions between AmB and the two types of sterols. Thus, our current results: (i) support the hypothesis that binary AmB/sterol complexes form within a lipid membrane and (ii) suggest that the higher toxicity may at least partly be attributed to the higher affinity of AmB for ergosterol than for cholesterol within a lipid membrane environment.
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Affiliation(s)
- Anna Neumann
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Narutowicza St. 11/12, 80-233 Gdansk, Poland
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35
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Raudino A, Pannuzzo M. Nucleation theory with delayed interactions: An application to the early stages of the receptor-mediated adhesion/fusion kinetics of lipid vesicles. J Chem Phys 2010; 132:045103. [DOI: 10.1063/1.3290823] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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36
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Seemann H, Winter R. Volumetric Properties, Compressibilities and Volume Fluctuations in Phospholipid-Cholesterol Bilayers. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zpch.217.7.831.20388] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
We conducted detailed measurements of the apparent specific volume of dipalmitoylphosphatidylcholine (DPPC)–cholesterol mixtures in excess water as a function of pressure up to 70MPa (700bar) at 20, 38 and 50°C. The volumetric properties and the isothermal compressibility κ
T of the lipid vesicles were determined at cholesterol concentrations, χchol, ranging up to 50 mol. The thermodynamic data are compared with other physico-chemical properties of phospholipid–cholesterol mixtures. Furthermore, the thermodynamic properties of the system are discussed in the light of the various T, χchol–phase diagrams and computer simulation studies published in the literature.
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Brown MF, Salgado GFJ, Struts AV. Retinal dynamics during light activation of rhodopsin revealed by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:177-93. [PMID: 19716801 DOI: 10.1016/j.bbamem.2009.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/25/2009] [Accepted: 08/12/2009] [Indexed: 11/28/2022]
Abstract
Rhodopsin is a canonical member of class A of the G protein-coupled receptors (GPCRs) that are implicated in many of the drug interventions in humans and are of great pharmaceutical interest. The molecular mechanism of rhodopsin activation remains unknown as atomistic structural information for the active metarhodopsin II state is currently lacking. Solid-state (2)H NMR constitutes a powerful approach to study atomic-level dynamics of membrane proteins. In the present application, we describe how information is obtained about interactions of the retinal cofactor with rhodopsin that change with light activation of the photoreceptor. The retinal methyl groups play an important role in rhodopsin function by directing conformational changes upon transition into the active state. Site-specific (2)H labels have been introduced into the methyl groups of retinal and solid-state (2)H NMR methods applied to obtain order parameters and correlation times that quantify the mobility of the cofactor in the inactive dark state, as well as the cryotrapped metarhodopsin I and metarhodopsin II states. Analysis of the angular-dependent (2)H NMR line shapes for selectively deuterated methyl groups of rhodopsin in aligned membranes enables determination of the average ligand conformation within the binding pocket. The relaxation data suggest that the beta-ionone ring is not expelled from its hydrophobic pocket in the transition from the pre-activated metarhodopsin I to the active metarhodopsin II state. Rather, the major structural changes of the retinal cofactor occur already at the metarhodopsin I state in the activation process. The metarhodopsin I to metarhodopsin II transition involves mainly conformational changes of the protein within the membrane lipid bilayer rather than the ligand. The dynamics of the retinylidene methyl groups upon isomerization are explained by an activation mechanism involving cooperative rearrangements of extracellular loop E2 together with transmembrane helices H5 and H6. These activating movements are triggered by steric clashes of the isomerized all-trans retinal with the beta4 strand of the E2 loop and the side chains of Glu(122) and Trp(265) within the binding pocket. The solid-state (2)H NMR data are discussed with regard to the pathway of the energy flow in the receptor activation mechanism.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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38
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Davis JE, Patel S. Charge equilibration force fields for lipid environments: applications to fully hydrated DPPC bilayers and DMPC-embedded gramicidin A. J Phys Chem B 2009; 113:9183-96. [PMID: 19526999 PMCID: PMC2746983 DOI: 10.1021/jp901088g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polarizable force fields for lipid and solvent environments are used for molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer and gramicidin A (gA) dimer embedded in a dimyristoylphosphatidylcholine (DMPC) bilayer. The lipid bilayer is modeled using the CHARMM charge equilibration (CHEQ) polarizable force field for lipids and the TIP4P-FQ force field to represent solvent. For the DPPC bilayer system, results are compared to the same system simulated using the nonpolarizable CHARMM27r (C27r) force field and TIP3P water. Calculated atomic and electron density profiles, head group orientations as measured by the phosphorus-nitrogen vector orientation, and deuterium order parameters are found to be consistent with previous simulations and with experiment. The CHEQ model exhibits greater water penetration into the bilayer interior, as demonstrated by the potential of mean force calculated from the water density profile. This is a result of the variation of the water molecular dipole from 2.55 D in the bulk to 1.88 D in the interior. We discuss this finding in the context of previous studies (both simulation and experiment) that have investigated the extent of penetration of water into DPPC bilayers. We also discuss the effects of including explicit polarization on the water dipole moment variation as a function of distance from the bilayer. We show distributions of atomic charges over the course of the simulation since the CHEQ model allows the charges to fluctuate. We have calculated the interfacial dipole potential, which the CHEQ model predicts to be 0.95 V compared to 0.86 V as predicted by the C27r model. We also discuss dielectric permittivity profiles and the differences arising between the two models. We obtain bulk values of 72.77 for the CHEQ model (TIP4P-FQ water) and 91.22 for C27r (TIP3P), and values approaching unity in the membrane interior. Finally, we present results of simulations of gA embedded in a DMPC bilayer using the CHEQ model and discuss structural properties.
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Affiliation(s)
- Joseph E. Davis
- 238 Brown Laboratory, Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- 238 Brown Laboratory, Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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39
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Wan S, Coveney PV. A comparative study of the COX-1 and COX-2 isozymes bound to lipid membranes. J Comput Chem 2009; 30:1038-50. [PMID: 18942723 DOI: 10.1002/jcc.21130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The monotopic proteins COX-1 and -2 in dimeric form bound to lipid bilayer membranes are studied using molecular dynamics simulations within an aqueous environment. The 25-ns simulations are performed for both isozymes with arachidonic acid bound in the cyclooxygenase sites. The interactions between the enzymes and the lipids are analyzed, providing insight into the attachment mechanism of monotopic proteins to membranes. Our study reveals some key differences between the two isozymes that include the orientations at which they sit on the surface of the membranes and the depths to which they embed within the membranes. The differences in membrane association of the isozymes indicate that they may integrate distinctively with the same membrane, and/or with different membranes or their lipid components. Our results indicate that arachidonic acid can be bound in the cyclooxygenase active site in distinct catalytically competent conformations that lead to certain hydroperoxy acids; and the arachidonic acid and/or cyclooxygenase sites undergo a conformational change which makes only one subunit of each homodimer catalytically active.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London WC1A 0HE, United Kingdom
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40
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Skaug MJ, Longo ML, Faller R. Computational Studies of Texas Red−1,2-Dihexadecanoyl-sn-glycero-3-phosphoethanolamine—Model Building and Applications. J Phys Chem B 2009; 113:8758-66. [DOI: 10.1021/jp902877y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael J. Skaug
- Department of Chemical Engineering and Materials Science, 3112 Bainer Hall, One Shields Ave, University of California—Davis, Davis, California 95616
| | - Marjorie L. Longo
- Department of Chemical Engineering and Materials Science, 3112 Bainer Hall, One Shields Ave, University of California—Davis, Davis, California 95616
| | - Roland Faller
- Department of Chemical Engineering and Materials Science, 3112 Bainer Hall, One Shields Ave, University of California—Davis, Davis, California 95616
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41
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Davis JE, Rahaman O, Patel S. Molecular dynamics simulations of a DMPC bilayer using nonadditive interaction models. Biophys J 2009; 96:385-402. [PMID: 19167291 DOI: 10.1016/j.bpj.2008.09.048] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022] Open
Abstract
We present a polarizable force field based on the charge-equilibration formalism for molecular dynamics simulations of phospholipid bilayers. We discuss refinement of headgroup dihedral potential parameters to reproduce ab initio conformational energies of dimethylphosphate calculated at the MP2/cc-pVTZ level of theory. We also address the refinement of electrostatic and Lennard-Jones (van der Waals) parameters to reproduce ab initio polarizabilities and water interaction energies of dimethylphosphate and tetramethylammonium. We present results of molecular dynamics simulations of a solvated dimyristoylphosphatidylcholine bilayer using this polarizable force field as well as the nonpolarizable, fixed-charge CHARMM27 and CHARMM27r force fields for comparison. Calculated atomic and electron-density profiles, deuterium order parameters, and headgroup orientations are found to be consistent with previous simulations and with experiment. Polarizable interaction models for solvent and lipid exhibit greater water penetration into the lipid interior; this is due to the variation of water molecular dipole moment from a bulk value of 2.6 Debye to a value of 1.9 Debye in the membrane interior. The reduction in the electrostatic component of the desolvation free-energy penalty allows for greater water density. The surface dipole potential predicted by the polarizable model is 0.95 V compared to the value of 0.8 V based on nonpolarizable force-field calculations. Effects of inclusion of explicit polarization are discussed in relation to water dipole moment and varying charge distributions. Dielectric permittivity profiles for polarizable and nonpolarizable interactions exhibit subtle differences arising from the nature of the individual component parameterizations; for the polarizable force field, we obtain a bulk dielectric permittivity of 79, whereas the nonpolarizable force field plateaus at 97 (the value for pure TIP3P water). In the membrane interior, both models predict unit permittivities, with the polarizable models contributing from one to two more units due to the optical dielectric (high-frequency dipole fluctuations). This contribution is a step toward the continuing development of a CHARMM (Chemistry at Harvard Molecular Mechanics) polarizable force field for simulations of biomacromolecular systems.
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Affiliation(s)
- Joseph E Davis
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
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42
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Davis JH, Clair JJ, Juhasz J. Phase equilibria in DOPC/DPPC-d62/cholesterol mixtures. Biophys J 2009; 96:521-39. [PMID: 19167302 DOI: 10.1016/j.bpj.2008.09.042] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2008] [Accepted: 09/30/2008] [Indexed: 01/18/2023] Open
Abstract
There is broad interest in the question of fluid-fluid phase coexistence in membranes, in particular, whether evidence for liquid-disordered (l(d))-liquid-ordered (l(o)) two-phase regions or membrane "rafts" can be found in natural membranes. In model membrane systems, such phase behavior is observed, and we have used deuterium nuclear magnetic resonance spectroscopy to map the phase boundaries of ternary mixtures containing 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), chain-perdeuterated 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC-d(62)), and cholesterol. For both this ternary model system and the binary DPPC-d(62)/cholesterol system, we present clear evidence for l(d)-l(o) two-phase coexistence. We have selected sample compositions to focus on this region of fluid-fluid phase coexistence and to determine its temperature and composition ranges. The deuterium nuclear magnetic resonance spectra for compositions near the l(d)-l(o) phase boundary at high cholesterol concentrations show evidence of exchange broadening or critical fluctuations in composition, similar to that reported by Vist and Davis. There appears to be a line of critical compositions ranging from 48 degrees C for a DOPC/DPPC-d(62)/cholesterol composition of 0:75:25, to approximately -8 degrees C for the composition 57:14:29. At temperatures below this two-phase region, there is a region of three-phase coexistence (l(d)-l(o)-gel). These results are collected and presented in terms of a partial ternary phase diagram that is consistent with previously reported results of Vist and Davis.
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Affiliation(s)
- James H Davis
- Department of Physics, University of Guelph, Guelph, Ontario, Canada.
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43
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Efrat R, Kesselman E, Aserin A, Garti N, Danino D. Solubilization of hydrophobic guest molecules in the monoolein discontinuous QL cubic mesophase and its soft nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:1316-1326. [PMID: 18781793 DOI: 10.1021/la8016084] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Hydrophobic bioactive guest molecules were solubilized in the discontinuous cubic mesophase (QL) of monoolein. Their effects on the mesophase structure and thermal behavior, and on the formation of soft nanoparticles upon dispersion of the bulk mesophase were studied. Four additives were analyzed. They were classified into two types based on their presumed location within the lipid bilayer and their influence on the phase behavior and structure. Differential scanning calorimetry (DSC), small-angle X-ray scattering (SAXS), polarized light microscopy, cryogenic-transmission electron microscopy (cryo-TEM), and dynamic light scattering (DLS) were used for the analysis. We found that carbamazepine and cholesterol (type I molecules) likely localize in the hydrophobic domains, but close to the hydrophobic-hydrophilic region. They induce strong perturbation to the mesophase packing by influencing both the order of the lipid acyl chains and interactions between lipid headgroups. This results in significant reduction of the phase transition enthalpy, and phase separation into lamellar and cubic mesophases above the maximum loading capacity. The inclusion of type I molecules in the mesophase also prevents the formation of soft nanoparticles with long-range internal order upon dispersion. In their presence, only vesicles or sponge-like nanoparticles form. Phytosterols and coenzyme Q10 (type II molecules) present only moderate effects. These molecules reside in the hydrophobic domains, where they cannot alter the lipid curvature or transform the QL mesophase into another phase. Therefore, above maximum loading, excess solubilizate precipitates in crystal forms. Moreover, when type II-loaded QL is dispersed, nanoparticles with long-range order and cubic symmetry (i.e., cubosomes) do form. A model for the growth of the ordered nanoparticles was developed from a series of intermediate structures identified by cryo-TEM. It proposes the development of the internal structure by fusion events between bilayer segments.
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Affiliation(s)
- Rivka Efrat
- Casali Institute of Applied Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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44
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Ordering effects of cholesterol and its analogues. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:97-121. [DOI: 10.1016/j.bbamem.2008.08.022] [Citation(s) in RCA: 450] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 08/27/2008] [Accepted: 08/31/2008] [Indexed: 12/12/2022]
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45
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Brunsveld L, Waldmann H, Huster D. Membrane binding of lipidated Ras peptides and proteins--the structural point of view. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1788:273-88. [PMID: 18771652 DOI: 10.1016/j.bbamem.2008.08.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 08/01/2008] [Accepted: 08/06/2008] [Indexed: 10/21/2022]
Abstract
Biological membranes are interesting interfaces, at which important biological processes occur. In addition to integral membrane proteins, a number of proteins bind to the membrane surface and associate with it. Posttranslational lipid modification is one important mechanism, by which soluble molecules develop a propensity towards the membrane and reversibly bind to it. Membrane binding by insertion of hydrophobic lipid moieties is relevant for up to 10% of all cellular proteins. A particular interesting lipid-modified protein is the small GTPase Ras, which plays a key role in cellular signal transduction. Until recently, the structural basis for membrane binding of Ras was not well-defined. However, with the advent of new synthesis techniques and the advancement of several biophysical methods, a number of structural and dynamical features about membrane binding of Ras proteins have been revealed. This review will summarize the chemical biology of Ras and discuss in more detail the biophysical and structural features of the membrane bound C-terminus of the protein.
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Affiliation(s)
- Luc Brunsveld
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
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46
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Fluid mechanical matching of H+-ATP synthase subunit c-ring with lipid membranes revealed by 2H solid-state NMR. Biophys J 2008; 94:4339-47. [PMID: 18310246 DOI: 10.1529/biophysj.107.123745] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The F(1)F(o)-ATP synthase utilizes the transmembrane H(+) gradient for the synthesis of ATP. F(o) subunit c-ring plays a key role in transporting H(+) through F(o) in the membrane. We investigated the interactions of Escherichia coli subunit c with dimyristoylphosphatidylcholine (DMPC-d(54)) at lipid/protein ratios of 50:1 and 20:1 by means of (2)H-solid-state NMR. In the liquid-crystalline state of DMPC, the (2)H-NMR moment values and the order parameter (S(CD)) profile were little affected by the presence of subunit c, suggesting that the bilayer thickness in the liquid-crystalline state is matched to the transmembrane hydrophobic surface of subunit c. On the other hand, hydrophobic mismatch of subunit c with the lipid bilayer was observed in the gel state of DMPC. Moreover, the viscoelasticity represented by a square-law function of the (2)H-NMR relaxation was also little influenced by subunit c in the fluid phase, in contrast with flexible nonionic detergents or rigid additives. Thus, the hydrophobic matching of the lipid bilayer to subunit c involves at least two factors, the hydrophobic length and the fluid mechanical property. These findings may be important for the torque generation in the rotary catalytic mechanism of the F(1)F(o)-ATPse molecular motor.
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47
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Giordani C, Wakai C, Yoshida K, Okamura E, Matubayasi N, Nakahara M. Cholesterol Location and Orientation in Aqueous Suspension of Large Unilamellar Vesicles of Phospholipid Revealed by Intermolecular Nuclear Overhauser Effect. J Phys Chem B 2008; 112:2622-8. [DOI: 10.1021/jp0760713] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cristiano Giordani
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Chihiro Wakai
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Ken Yoshida
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Emiko Okamura
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Nobuyuki Matubayasi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masaru Nakahara
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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48
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Brown MF, Heyn MP, Job C, Kim S, Moltke S, Nakanishi K, Nevzorov AA, Struts AV, Salgado GFJ, Wallat I. Solid-state 2H NMR spectroscopy of retinal proteins in aligned membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1768:2979-3000. [PMID: 18021739 PMCID: PMC5233718 DOI: 10.1016/j.bbamem.2007.10.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 10/10/2007] [Accepted: 10/10/2007] [Indexed: 11/21/2022]
Abstract
Solid-state 2H NMR spectroscopy gives a powerful avenue to investigating the structures of ligands and cofactors bound to integral membrane proteins. For bacteriorhodopsin (bR) and rhodopsin, retinal was site-specifically labeled by deuteration of the methyl groups followed by regeneration of the apoprotein. 2H NMR studies of aligned membrane samples were conducted under conditions where rotational and translational diffusion of the protein were absent on the NMR time scale. The theoretical lineshape treatment involved a static axial distribution of rotating C-C2H3 groups about the local membrane frame, together with the static axial distribution of the local normal relative to the average normal. Simulation of solid-state 2H NMR lineshapes gave both the methyl group orientations and the alignment disorder (mosaic spread) of the membrane stack. The methyl bond orientations provided the angular restraints for structural analysis. In the case of bR the retinal chromophore is nearly planar in the dark- and all-trans light-adapted states, as well upon isomerization to 13-cis in the M state. The C13-methyl group at the "business end" of the chromophore changes its orientation to the membrane upon photon absorption, moving towards W182 and thus driving the proton pump in energy conservation. Moreover, rhodopsin was studied as a prototype for G protein-coupled receptors (GPCRs) implicated in many biological responses in humans. In contrast to bR, the retinal chromophore of rhodopsin has an 11-cis conformation and is highly twisted in the dark state. Three sites of interaction affect the torsional deformation of retinal, viz. the protonated Schiff base with its carboxylate counterion; the C9-methyl group of the polyene; and the beta-ionone ring within its hydrophobic pocket. For rhodopsin, the strain energy and dynamics of retinal as established by 2H NMR are implicated in substituent control of activation. Retinal is locked in a conformation that is twisted in the direction of the photoisomerization, which explains the dark stability of rhodopsin and allows for ultra-fast isomerization upon absorption of a photon. Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state 2H NMR is thus illuminating in terms of their different biological functions.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA.
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49
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Leermakers FAM, Rabinovich AL. Interaction of cholesterol-like molecules in polyunsaturated phosphatidylcholine lipid bilayers as revealed by a self-consistent field theory. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:031904. [PMID: 17930268 DOI: 10.1103/physreve.76.031904] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Revised: 07/31/2007] [Indexed: 05/25/2023]
Abstract
Cholesterol is one of the most abundant components in biological membranes. In this paper we apply a detailed state-of-the-art self-consistent field (SCF) theory to predict the influence of cholesterol-look-alikes in the bilayer composed of 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphatidylcholine (18:022:6omega3cis PC) lipids with a polyunsaturated 22:6 and a fully saturated 18:0 tail. The cholesterol-like molecule is composed of a hydroxyl group, a rigid chain fragment with length n segments and a branched semiflexible moiety with methylene side groups. We vary both the length of the rigid fragment in the cholesterol-look-alikes and their mole fraction in the tensionless bilayers. We find that these additives significantly increase the order of the saturated tails, but influence the conformational properties of the unsaturated tail much less. With increasing loading the bilayer thickness and the area available per PC head group increase. The hydroxyl group anchors close to the membrane-water interface, but with increasing loading the distribution of this polar group widens. The orientational order of the rigid part is high and we conclude that the cholesterol has significant mobility in the normal direction in the hydrophobic region of the bilayer indicating that one singly hydroxyl group is giving only a weak anchoring to the water-interface. Cholesterol-look-alikes increase the fluctuation of the tail ends and decrease the interdigitation of the tails. Several of our predictions correspond to molecular dynamics (MD) simulation results, but there are also important differences. Most notably the cholesterol-look-alikes can visit the membrane symmetry-plane more easily in SCF than in MD. Possible reasons for this are discussed.
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Affiliation(s)
- F A M Leermakers
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, the Netherlands
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50
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Matyszewska D, Tappura K, Orädd G, Bilewicz R. Influence of Perfluorinated Compounds on the Properties of Model Lipid Membranes. J Phys Chem B 2007; 111:9908-18. [PMID: 17672485 DOI: 10.1021/jp068874g] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of selected perfluorinated compounds (PFCs), perfluorooctanoic acid (PFOA) or perfluorooctanesulfonic acid (PFOS), on the structure and organization of lipid membranes was investigated using model membranes-lipid monolayers and bilayers. The simplest model--a lipid monolayer--was studied at the air-water interface using the Langmuir-Blodgett technique with surface pressure and surface potential measurements. Lipid bilayers were characterized by NMR techniques and molecular dynamics simulations. Two phospholipids, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), characterized by different surface properties have been chosen as components of the model membranes. For a DPPC monolayer, a phase transition from the liquid-expanded state to the liquid-condensed state can be observed upon compression at room temperature, while a DMPC monolayer under the same conditions remains in the liquid-expanded state. For each of the two lipids, the presence of both PFOA and PFOS leads to the formation of a more fluidic layer at the air-water interface. Pulsed field gradient NMR measurements of the lateral diffusion coefficient (DL) of DMPC and PFOA in oriented bilayers reveal that, upon addition of PFOA to DMPC bilayers, DL of DMPC decreases for small amounts of PFOA, while larger additions produce an increased DL. The DL values of PFOA were found to be slightly larger than those for DMPC, probably as a consequence of the water solubility of PFOA. Furthermore, 31P and 2H NMR showed that the gel-liquid crystalline phase transition temperature decreased by the addition of PFOA for concentrations of 5 mol % and above, indicating a destabilizing effect of PFOA on the membranes. Deuterium order parameters of deuterated DMPC were found to increase slightly upon increasing the PFOA concentration. The monolayer experiments reveal that PFOS also penetrates slowly into already preformed lipid layers, leading to a change of their properties with time. These experimental observations are in qualitative agreement with the computational results obtained from the molecular dynamics simulations showing a slow migration of PFCs from the surrounding water phase into DPPC and DMPC bilayers.
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Affiliation(s)
- Dorota Matyszewska
- Department of Chemistry, University of Warsaw, ul. Pasteura 1, 02093 Warsaw, Poland
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