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Doktorova M, Kučerka N, Kinnun JJ, Pan J, Marquardt D, Scott HL, Venable RM, Pastor RW, Wassall SR, Katsaras J, Heberle FA. Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data. J Phys Chem B 2020; 124:5186-5200. [PMID: 32468822 DOI: 10.1021/acs.jpcb.0c03389] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have determined the fluid bilayer structure of palmitoyl sphingomyelin (PSM) and stearoyl sphingomyelin (SSM) by simultaneously analyzing small-angle neutron and X-ray scattering data. Using a newly developed scattering density profile (SDP) model for sphingomyelin lipids, we report structural parameters including the area per lipid, total bilayer thickness, and hydrocarbon thickness, in addition to lipid volumes determined by densitometry. Unconstrained all-atom simulations of PSM bilayers at 55 °C using the C36 CHARMM force field produced a lipid area of 56 Å2, a value that is 10% lower than the one determined experimentally by SDP analysis (61.9 Å2). Furthermore, scattering form factors calculated from the unconstrained simulations were in poor agreement with experimental form factors, even though segmental order parameter (SCD) profiles calculated from the simulations were in relatively good agreement with SCD profiles obtained from NMR experiments. Conversely, constrained area simulations at 61.9 Å2 resulted in good agreement between the simulation and experimental scattering form factors, but not with SCD profiles from NMR. We discuss possible reasons for the discrepancies between these two types of data that are frequently used as validation metrics for molecular dynamics force fields.
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Affiliation(s)
- Milka Doktorova
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980 Dubna, Russia.,Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University, 814 99 Bratislava, Slovakia
| | - Jacob J Kinnun
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, Florida 33620, United States
| | - Drew Marquardt
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Haden L Scott
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Stephen R Wassall
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - John Katsaras
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
| | - Frederick A Heberle
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996, United States
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2
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Okotrub KA, Zykova VA, Adichtchev SV, Surovtsev NV. Deciphering the orientation of lipid molecules by principal component analysis of Raman mapping data. Analyst 2020; 145:1466-1472. [DOI: 10.1039/c9an01499c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Raman spectroscopy reveals the orientational ordering of dry and hydrated phospholipids.
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Affiliation(s)
- Konstantin A. Okotrub
- Institute of Automation and Electrometry
- Russian Academy of Sciences
- Novosibirsk
- Russia
| | - Valeriya A. Zykova
- Institute of Automation and Electrometry
- Russian Academy of Sciences
- Novosibirsk
- Russia
| | - Sergey V. Adichtchev
- Institute of Automation and Electrometry
- Russian Academy of Sciences
- Novosibirsk
- Russia
| | - Nikolay V. Surovtsev
- Institute of Automation and Electrometry
- Russian Academy of Sciences
- Novosibirsk
- Russia
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3
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Clustering of spin-labeled cholesterol analog diluted in bilayers of saturated and unsaturated phospholipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2527-2531. [DOI: 10.1016/j.bbamem.2018.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/31/2018] [Accepted: 09/26/2018] [Indexed: 11/21/2022]
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Catte A, White GF, Wilson MR, Oganesyan VS. Direct Prediction of EPR Spectra from Lipid Bilayers: Understanding Structure and Dynamics in Biological Membranes. Chemphyschem 2018; 19:2183-2193. [PMID: 29858887 PMCID: PMC6175124 DOI: 10.1002/cphc.201800386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Indexed: 11/16/2022]
Abstract
Of the many biophysical techniques now being brought to bear on studies of membranes, electron paramagnetic resonance (EPR) of nitroxide spin probes was the first to provide information about both mobility and ordering in lipid membranes. Here, we report the first prediction of variable temperature EPR spectra of model lipid bilayers in the presence and absence of cholesterol from the results of large scale fully atomistic molecular dynamics (MD) simulations. Three types of structurally different spin probes were employed in order to study different parts of the bilayer. Our results demonstrate very good agreement with experiment and thus confirm the accuracy of the latest lipid force fields. The atomic resolution of the simulations allows the interpretation of the molecular motions and interactions in terms of their impact on the sensitive EPR line shapes. Direct versus indirect effects of cholesterol on the dynamics of spin probes are analysed. Given the complexity of structural organisation in lipid bilayers, the advantage of using a combined MD-EPR simulation approach is two-fold. Firstly, prediction of EPR line shapes directly from MD trajectories of actual phospholipid structures allows unambiguous interpretation of EPR spectra of biological membranes in terms of complex motions. Secondly, such an approach provides an ultimate test bed for the up-to-date MD simulation models employed in the studies of biological membranes, an area that currently attracts great attention.
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Affiliation(s)
- Andrea Catte
- School of ChemistryUniversity of East AngliaNorwichNR4 7TJUK
| | - Gaye F. White
- School of ChemistryUniversity of East AngliaNorwichNR4 7TJUK
| | - Mark R. Wilson
- Department of ChemistryDurham University, Lower MountjoySouth RoadDurhamDH1 3 LEUK
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G. Reis S, del Águila-Sánchez MA, P. Guedes G, Navarro Y, A. Allão Cassaro R, B. Ferreiraa G, Calancea S, López-Ortiz F, G. F. Vaz M. Novel P,P-diphenylphosphinic amide-TEMPO radicals family: Synthesis, crystal structures, spectroscopic characterization, magnetic properties and DFT calculations. Polyhedron 2018. [DOI: 10.1016/j.poly.2018.01.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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6
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Kardash ME, Dzuba SA. Lipid-Mediated Clusters of Guest Molecules in Model Membranes and Their Dissolving in the Presence of Lipid Rafts. J Phys Chem B 2017; 121:5209-5217. [DOI: 10.1021/acs.jpcb.7b01561] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria E. Kardash
- Institute of Chemical Kinetics
and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090, Novosibirsk, Russia
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics
and Combustion, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Physics, Novosibirsk State University, 630090, Novosibirsk, Russia
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Mainali L, Raguz M, O’Brien WJ, Subczynski WK. Changes in the Properties and Organization of Human Lens Lipid Membranes Occurring with Age. Curr Eye Res 2017; 42:721-731. [PMID: 27791387 PMCID: PMC5409882 DOI: 10.1080/02713683.2016.1231325] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/01/2016] [Accepted: 08/28/2016] [Indexed: 10/20/2022]
Abstract
PURPOSE This research was undertaken to document the changes in the organization and properties of human lens lipid membranes that occur with age. METHODS Human lens lipid membranes prepared from the total lipids extracted from clear lens cortices and nuclei of donors from age groups 0-20 and 21-40 years were investigated. An electron paramagnetic resonance technique and nitroxide spin labels (analogues of phospholipids and cholesterol) were used. RESULTS Two distinct lipid domains, the phospholipid-cholesterol domain (PCD) and the pure cholesterol bilayer domain (CBD), were detected in all investigated membranes. Profiles of the acyl chain order, fluidity, hydrophobicity, and oxygen transport parameter across discriminated coexisting lipid domains were assessed. Independent of the age-related changes in phospholipid composition, the physical properties of the PCD remained the same for all age groups and were practically identical for cortical and nuclear membranes. However, the properties of pure CBDs changed significantly with the age of the donor and were related to the size of the CBD, which increased with the age of the donor and was greater in nuclear than in cortical membranes. A more detailed analysis revealed that the size of the CBD was determined mainly by the cholesterol content in the membrane. CONCLUSIONS This paper presents data from four age groups: 0-20, 21-40, 41-60, and 61-70 years. Data from age groups 41-60 and 61-70 years were published previously. Combining the previously published data with those data obtained in the present work allowed us to show the changes in the organization of cortical and nuclear lens lipid membranes as functions of age and cholesterol. It seems that the balance between age-related changes in membrane phospholipid composition and cholesterol content plays an integral role in the regulation of cholesterol-dependent processes in fiber cell membranes and in the maintenance of fiber cell membrane homeostasis.
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Affiliation(s)
- Laxman Mainali
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marija Raguz
- Department of Medical Physics and Biophysics, School of Medicine, University of Split, Split, Croatia
| | - William J. O’Brien
- Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Witold K. Subczynski
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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8
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Oliva R, Emendato A, Vitiello G, De Santis A, Grimaldi M, D'Ursi AM, Busi E, Del Vecchio P, Petraccone L, D'Errico G. On the microscopic and mesoscopic perturbations of lipid bilayers upon interaction with the MPER domain of the HIV glycoprotein gp41. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1904-13. [DOI: 10.1016/j.bbamem.2016.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/04/2016] [Accepted: 05/09/2016] [Indexed: 12/15/2022]
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9
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Song L, Liu Z, Kaur P, Esquiaqui JM, Hunter RI, Hill S, Smith GM, Fanucci GE. Toward increased concentration sensitivity for continuous wave EPR investigations of spin-labeled biological macromolecules at high fields. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2016; 265:188-196. [PMID: 26923151 DOI: 10.1016/j.jmr.2016.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 06/05/2023]
Abstract
High-field, high-frequency electron paramagnetic resonance (EPR) spectroscopy at W-(∼94 GHz) and D-band (∼140 GHz) is important for investigating the conformational dynamics of flexible biological macromolecules because this frequency range has increased spectral sensitivity to nitroxide motion over the 100 ps to 2 ns regime. However, low concentration sensitivity remains a roadblock for studying aqueous samples at high magnetic fields. Here, we examine the sensitivity of a non-resonant thin-layer cylindrical sample holder, coupled to a quasi-optical induction-mode W-band EPR spectrometer (HiPER), for continuous wave (CW) EPR analyses of: (i) the aqueous nitroxide standard, TEMPO; (ii) the unstructured to α-helical transition of a model IDP protein; and (iii) the base-stacking transition in a kink-turn motif of a large 232 nt RNA. For sample volumes of ∼50 μL, concentration sensitivities of 2-20 μM were achieved, representing a ∼10-fold enhancement compared to a cylindrical TE011 resonator on a commercial Bruker W-band spectrometer. These results therefore highlight the sensitivity of the thin-layer sample holders employed in HiPER for spin-labeling studies of biological macromolecules at high fields, where applications can extend to other systems that are facilitated by the modest sample volumes and ease of sample loading and geometry.
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Affiliation(s)
- Likai Song
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Pavanjeet Kaur
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Jackie M Esquiaqui
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA
| | - Robert I Hunter
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, United Kingdom
| | - Stephen Hill
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA; Department of Physics, Florida State University, Tallahassee, FL 32306, USA
| | - Graham M Smith
- School of Physics and Astronomy, University of St. Andrews, North Haugh, St. Andrews KY16 9SS, United Kingdom
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, FL 32611, USA.
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Kepczynski M, Róg T. Functionalized lipids and surfactants for specific applications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2362-2379. [PMID: 26946243 DOI: 10.1016/j.bbamem.2016.02.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/17/2022]
Abstract
Synthetic lipids and surfactants that do not exist in biological systems have been used for the last few decades in both basic and applied science. The most notable applications for synthetic lipids and surfactants are drug delivery, gene transfection, as reporting molecules, and as support for structural lipid biology. In this review, we describe the potential of the synergistic combination of computational and experimental methodologies to study the behavior of synthetic lipids and surfactants embedded in lipid membranes and liposomes. We focused on select cases in which molecular dynamics simulations were used to complement experimental studies aiming to understand the structure and properties of new compounds at the atomistic level. We also describe cases in which molecular dynamics simulations were used to design new synthetic lipids and surfactants, as well as emerging fields for the application of these compounds. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101, Tampere, Finland; Department of Physics, Helsinki University, P.O. Box 64, FI 00014 Helsinki, Finland.
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11
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Faller R. Molecular modeling of lipid probes and their influence on the membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2353-2361. [PMID: 26891817 DOI: 10.1016/j.bbamem.2016.02.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 01/03/2023]
Abstract
In this review a number of Molecular Dynamics simulation studies are discussed which focus on the understanding of the behavior of lipid probes in biomembranes. Experiments often use specialized probe moieties or molecules to report on the behavior of a membrane and try to gain information on the membrane as a whole from the probe lipids as these probes are the only things an experiment sees. Probes can be used to make NMR, EPR and fluorescence accessible to the membrane and use fluorescent or spin-active moieties for this purpose. Clearly membranes with and without probes are not identical which makes it worthwhile to elucidate the differences between them with detailed atomistic simulations. In almost all cases these differences are confined to the local neighborhood of the probe molecules which are sparsely used and generally present as single molecules. In general, the behavior of the bulk membrane lipids can be qualitatively understood from the probes but in most cases their properties cannot be directly quantitatively deduced from the probe behavior. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Roland Faller
- Department of Chemical Engineering & Materials Science, University of California-Davis, Davis, CA 95616, USA.
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12
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DeWitt BN, Dunn RC. Interaction of cholesterol in ternary lipid mixtures investigated using single-molecule fluorescence. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:995-1004. [PMID: 25531175 DOI: 10.1021/la503797w] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Fluorescence measurements of the sterol analog 23-(dipyrrometheneboron difluoride)-24-norcholesterol (BODIPY-cholesterol) are used to compare the effects of cholesterol (Chol) in monolayers of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC)/Chol and chicken egg sphingomyelin (SM)/DOPC/Chol. Monolayers are formed using the Langmuir-Blodgett technique and compared at surface pressures of 8 and 30 mN/m. In particular, these ternary lipid mixtures are compared using both ensemble and single-molecule fluorescence measurements of BODIPY-cholesterol. In mixed monolayers incorporating 0.10 mol % BODIPY-cholesterol, fluorescence microscopy measurements as a function of cholesterol added reveal similar trends in monolayer phase structure for both DPPC/DOPC/Chol and SM/DOPC/Chol films. With a probe concentration reduced to ∼10(-8) mol % BODIPY-cholesterol, single-molecule fluorescence measurements using defocused polarized total internal reflection microscopy are used to characterize the orientations of BODIPY-cholesterol in the monolayers. Population histograms of the BODIPY emission dipole tilt angle away from the membrane normal reveal distinct insertion geometries with a preferred angle observed near 78°. The measured angles and populations are relatively insensitive to added cholesterol and changes in surface pressure for monolayers of SM/DOPC/Chol. For monolayers of DPPC/DOPC/Chol, however, the single-molecule measurements reveal significant changes in the BODIPY-cholesterol insertion geometry when the surface pressure is increased to 30 mN/m. These changes are discussed in terms of a squeeze-out mechanism for BODIPY-cholesterol in these monolayers and provide insight into the partitioning and arrangement of BODIPY-cholesterol in ternary lipid mixtures.
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Affiliation(s)
- Brittany N DeWitt
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States
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Yin Q, Shi X, Ding H, Dai X, Wan G, Qiao Y. Interactions of borneol with DPPC phospholipid membranes: a molecular dynamics simulation study. Int J Mol Sci 2014; 15:20365-81. [PMID: 25383679 PMCID: PMC4264172 DOI: 10.3390/ijms151120365] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/17/2014] [Accepted: 10/22/2014] [Indexed: 01/11/2023] Open
Abstract
Borneol, known as a “guide” drug in traditional Chinese medicine, is widely used as a natural penetration enhancer in modern clinical applications. Despite a large number of experimental studies on borneol’s penetration enhancing effect, the molecular basis of its action on bio-membranes is still unclear. We carried out a series of coarse-grained molecular dynamics simulations with the borneol concentration ranging from 3.31% to 54.59% (v/v, lipid-free basis) to study the interactions of borneol with aDPPC(1,2-dipalmitoylsn-glycero-3-phosphatidylcholine) bilayer membrane, and the temperature effects were also considered. At concentrations below 21.89%, borneol’s presence only caused DPPC bilayer thinning and an increase in fluidity; A rise in temperature could promote the diffusing progress of borneol. When the concentration was 21.89% or above, inverted micelle-like structures were formed within the bilayer interior, which led to increased bilayer thickness, and an optimum temperature was found for the interaction of borneol with the DPPC bilayer membrane. These findings revealed that the choice of optimal concentration and temperature is critical for a given application in which borneol is used as a penetration enhancer. Our results not only clarify some molecular basis for borneol’s penetration enhancing effects, but also provide some guidance for the development and applications of new preparations containing borneol.
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Affiliation(s)
- Qianqian Yin
- School of Traditional Chinese Medicine, Capital Medical University, No. 10 of Xitoutiao Outside Youanmen, Fengtai District, Beijing 100069, China.
| | - Xinyuan Shi
- Key Laboratory of TCM-Information Engineer, Beijing University of Chinese Medicine, No. 6 of Zhonghuan South Road, Wangjing, Chaoyang District, Beijing 100102, China.
| | - Haiou Ding
- Civil Aviation General Hospital, No. 1 of Chaowai Takai A, Beijing 100123, China.
| | - Xingxing Dai
- Key Laboratory of TCM-Information Engineer, Beijing University of Chinese Medicine, No. 6 of Zhonghuan South Road, Wangjing, Chaoyang District, Beijing 100102, China.
| | - Guang Wan
- School of Traditional Chinese Medicine, Capital Medical University, No. 10 of Xitoutiao Outside Youanmen, Fengtai District, Beijing 100069, China.
| | - Yanjiang Qiao
- Key Laboratory of TCM-Information Engineer, Beijing University of Chinese Medicine, No. 6 of Zhonghuan South Road, Wangjing, Chaoyang District, Beijing 100102, China.
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Kemmerer S, Voss JC, Faller R. Molecular dynamics simulation of dipalmitoylphosphatidylcholine modified with a MTSL nitroxide spin label in a lipid membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2770-7. [DOI: 10.1016/j.bbamem.2013.07.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/22/2013] [Accepted: 07/31/2013] [Indexed: 11/16/2022]
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15
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Möbius K, Lubitz W, Savitsky A. High-field EPR on membrane proteins - crossing the gap to NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 75:1-49. [PMID: 24160760 DOI: 10.1016/j.pnmrs.2013.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/15/2013] [Accepted: 07/15/2013] [Indexed: 06/02/2023]
Abstract
In this review on advanced EPR spectroscopy, which addresses both the EPR and NMR communities, considerable emphasis is put on delineating the complementarity of NMR and EPR concerning the measurement of molecular interactions in large biomolecules. From these interactions, detailed information can be revealed on structure and dynamics of macromolecules embedded in solution- or solid-state environments. New developments in pulsed microwave and sweepable cryomagnet technology as well as ultrafast electronics for signal data handling and processing have pushed to new horizons the limits of EPR spectroscopy and its multifrequency extensions concerning the sensitivity of detection, the selectivity with respect to interactions, and the resolution in frequency and time domains. One of the most important advances has been the extension of EPR to high magnetic fields and microwave frequencies, very much in analogy to what happens in NMR. This is exemplified by referring to ongoing efforts for signal enhancement in both NMR and EPR double-resonance techniques by exploiting dynamic nuclear or electron spin polarization via unpaired electron spins and their electron-nuclear or electron-electron interactions. Signal and resolution enhancements are particularly spectacular for double-resonance techniques such as ENDOR and PELDOR at high magnetic fields. They provide greatly improved orientational selection for disordered samples that approaches single-crystal resolution at canonical g-tensor orientations - even for molecules with small g-anisotropies. Exchange of experience between the EPR and NMR communities allows for handling polarization and resolution improvement strategies in an optimal manner. Consequently, a dramatic improvement of EPR detection sensitivity could be achieved, even for short-lived paramagnetic reaction intermediates. Unique structural and dynamic information is thus revealed that can hardly be obtained by any other analytical techniques. Micromolar quantities of sample molecules have become sufficient to characterize stable and transient reaction intermediates of complex molecular systems - offering highly interesting applications for chemists, biochemists and molecular biologists. In three case studies, representative examples of advanced EPR spectroscopy are reviewed: (I) High-field PELDOR and ENDOR structure determination of cation-anion radical pairs in reaction centers from photosynthetic purple bacteria and cyanobacteria (Photosystem I); (II) High-field ENDOR and ELDOR-detected NMR spectroscopy on the oxygen-evolving complex of Photosystem II; and (III) High-field electron dipolar spectroscopy on nitroxide spin-labelled bacteriorhodopsin for structure-function studies. An extended conclusion with an outlook to further developments and applications is also presented.
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Affiliation(s)
- Klaus Möbius
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany; Department of Physics, Free University Berlin, Arnimallee 14, D-14195 Berlin, Germany.
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16
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On the mechanism of ion transport through lipid membranes mediated by PEGylated cyclic oligosaccharides (CyPLOS): An ESR study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2074-82. [DOI: 10.1016/j.bbamem.2013.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 04/19/2013] [Accepted: 05/15/2013] [Indexed: 12/25/2022]
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17
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Jeschke G. Conformational dynamics and distribution of nitroxide spin labels. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 72:42-60. [PMID: 23731861 DOI: 10.1016/j.pnmrs.2013.03.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 06/02/2023]
Abstract
Long-range distance measurements based on paramagnetic relaxation enhancement (PRE) in NMR, quantification of surface water dynamics near biomacromolecules by Overhauser dynamic nuclear polarization (DNP) and sensitivity enhancement by solid-state DNP all depend on introducing paramagnetic species into an otherwise diamagnetic NMR sample. The species can be introduced by site-directed spin labeling, which offers precise control for positioning the label in the sequence of a biopolymer. However, internal flexibility of the spin label gives rise to dynamic processes that potentially influence PRE and DNP behavior and leads to a spatial distribution of the electron spin even in solid samples. Internal dynamics of spin labels and their static conformational distributions have been studied mainly by electron paramagnetic resonance spectroscopy and molecular dynamics simulations, with a large body of results for the most widely applied methanethiosulfonate spin label MTSL. These results are critically discussed in a unifying picture based on rotameric states of the group that carries the spin label. Deficiencies in our current understanding of dynamics and conformations of spin labeled groups and of their influence on NMR observables are highlighted and directions for further research suggested.
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Affiliation(s)
- Gunnar Jeschke
- ETH Zürich, Laboratory Physical Chemistry, Zürich, Switzerland.
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Mainali L, Raguz M, O'Brien WJ, Subczynski WK. Properties of membranes derived from the total lipids extracted from the human lens cortex and nucleus. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1828:1432-40. [PMID: 23438364 PMCID: PMC3633468 DOI: 10.1016/j.bbamem.2013.02.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 02/08/2013] [Accepted: 02/14/2013] [Indexed: 11/21/2022]
Abstract
Human lens lipid membranes prepared using a rapid solvent exchange method from the total lipids extracted from the clear lens cortex and nucleus of 41- to 60-year-old donors were investigated using electron paramagnetic resonance spin-labeling. Profiles of the phospholipid alkyl-chain order, fluidity, oxygen transport parameter, and hydrophobicity were assessed across coexisting membrane domains. Membranes prepared from the lens cortex and nucleus were found to contain two distinct lipid environments, the bulk phospholipid-cholesterol domain and the cholesterol bilayer domain (CBD). The alkyl chains of phospholipids were strongly ordered at all depths, indicating that the amplitude of the wobbling motion of alkyl chains was small. However, profiles of the membrane fluidity, which explicitly contain time (expressed as the spin-lattice relaxation rate) and depend on the rotational motion of spin labels, show relatively high fluidity of alkyl chains close to the membrane center. Profiles of the oxygen transport parameter and hydrophobicity have a rectangular shape and also indicate a high fluidity and hydrophobicity of the membrane center. The amount of CBD was greater in nuclear membranes than in cortical membranes. The presence of the CBD in lens lipid membranes, which at 37°C showed a permeability coefficient for oxygen about 60% smaller than across a water layer of the same thickness, would be expected to raise the barrier for oxygen transport across the fiber cell membrane. Properties of human membranes are compared with those obtained for membranes made of lipids extracted from cortex and nucleus of porcine and bovine eye lenses.
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Affiliation(s)
- Laxman Mainali
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Mainali L, Hyde JS, Subczynski WK. Using spin-label W-band EPR to study membrane fluidity profiles in samples of small volume. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 226:35-44. [PMID: 23207176 PMCID: PMC3529815 DOI: 10.1016/j.jmr.2012.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 10/15/2012] [Accepted: 11/03/2012] [Indexed: 05/18/2023]
Abstract
Conventional and saturation-recovery (SR) EPR at W-band (94GHz) using phosphatidylcholine spin labels (labeled at the alkyl chain [n-PC] and headgroup [T-PC]) to obtain profiles of membrane fluidity has been demonstrated. Dimyristoylphosphatidylcholine (DMPC) membranes with and without 50 mol% cholesterol have been studied, and the results have been compared with similar studies at X-band (9.4 GHz) (L. Mainali, J.B. Feix, J.S. Hyde, W.K. Subczynski, J. Magn. Reson. 212 (2011) 418-425). Profiles of the spin-lattice relaxation rate (T(1)(-1)) obtained from SR EPR measurements for n-PCs and T-PC were used as a convenient quantitative measure of membrane fluidity. Additionally, spectral analysis using Freed's MOMD (microscopic-order macroscopic-disorder) model (E. Meirovitch, J.H. Freed J. Phys. Chem. 88 (1984) 4995-5004) provided rotational diffusion coefficients (R(perpendicular) and R(||)) and order parameters (S(0)). Spectral analysis at X-band provided one rotational diffusion coefficient, R(perpendicular). T(1)(-1), R(perpendicular), and R(||) profiles reflect local membrane dynamics of the lipid alkyl chain, while the order parameter shows only the amplitude of the wobbling motion of the lipid alkyl chain. Using these dynamic parameters, namely T(1)(-1), R(perpendicular), and R(||), one can discriminate the different effects of cholesterol at different depths, showing that cholesterol has a rigidifying effect on alkyl chains to the depth occupied by the rigid steroid ring structure and a fluidizing effect at deeper locations. The nondynamic parameter, S(0), shows that cholesterol has an ordering effect on alkyl chains at all depths. Conventional and SR EPR measurements with T-PC indicate that cholesterol has a fluidizing effect on phospholipid headgroups. EPR at W-band provides more detailed information about the depth-dependent dynamic organization of the membrane compared with information obtained at X-band. EPR at W-band has the potential to be a powerful tool for studying membrane fluidity in samples of small volume, ~30 nL, compared with a representative sample volume of ~3 μL at X-band.
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Affiliation(s)
| | | | - Witold K. Subczynski
- Author to whom correspondence should be addressed: Witold Karol Subczynski, Ph.D., D.Sc., Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509, Phone: (414) 456-4038, Fax: (414) 456-6512,
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