701
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Poger D, Caron B, Mark AE. Effect of Methyl-Branched Fatty Acids on the Structure of Lipid Bilayers. J Phys Chem B 2014; 118:13838-48. [DOI: 10.1021/jp503910r] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Poger
- School of Chemistry and Molecular
Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bertrand Caron
- School of Chemistry and Molecular
Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alan E. Mark
- School of Chemistry and Molecular
Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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702
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Vila-Viçosa D, Teixeira VH, Santos HAF, Baptista AM, Machuqueiro M. Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid Bilayers. J Chem Theory Comput 2014; 10:5483-92. [DOI: 10.1021/ct500680q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Diogo Vila-Viçosa
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Vitor H. Teixeira
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Hugo A. F. Santos
- Faculty
of Sciences, BioFIG−Centre for Biodiversity, Functional and
Integrative Genomics, University of Lisboa, 1649-004 Lisboa, Portugal
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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703
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Itel F, Chami M, Najer A, Lörcher S, Wu D, Dinu IA, Meier W. Molecular Organization and Dynamics in Polymersome Membranes: A Lateral Diffusion Study. Macromolecules 2014. [DOI: 10.1021/ma5015403] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Fabian Itel
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Mohamed Chami
- Center
for Cellular Imaging and Nanoanalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Adrian Najer
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Samuel Lörcher
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Dalin Wu
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Ionel A. Dinu
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Wolfgang Meier
- Department
of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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704
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Yanez Arteta M, Ainalem ML, Porcar L, Martel A, Coker H, Lundberg D, Chang DP, Soltwedel O, Barker R, Nylander T. Interactions of PAMAM Dendrimers with Negatively Charged Model Biomembranes. J Phys Chem B 2014; 118:12892-906. [DOI: 10.1021/jp506510s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Marianna Yanez Arteta
- Physical
Chemistry, Center for Chemistry and Chemical Engineering, Lund University, SE-221 00 Lund, Sweden
| | | | - Lionel Porcar
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Anne Martel
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Helena Coker
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Dan Lundberg
- Physical
Chemistry, Center for Chemistry and Chemical Engineering, Lund University, SE-221 00 Lund, Sweden
- CR
Competence AB, Center for Chemistry and Chemical Engineering, SE-221
00 Lund, Sweden
| | - Debby P. Chang
- Physical
Chemistry, Center for Chemistry and Chemical Engineering, Lund University, SE-221 00 Lund, Sweden
| | - Olaf Soltwedel
- Max-Planck-Institute
for Solid State Research, Outstation at MLZ, Lichtenbergstr.
1, 85747 Garching, Germany
| | - Robert Barker
- Institut Laue-Langevin, 71 avenue
des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - Tommy Nylander
- Physical
Chemistry, Center for Chemistry and Chemical Engineering, Lund University, SE-221 00 Lund, Sweden
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705
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Aisenbrey C, Bechinger B. Molecular packing of amphipathic peptides on the surface of lipid membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:10374-10383. [PMID: 25105913 DOI: 10.1021/la500998g] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
When polypeptides bind to the membrane surface, they become confined to a restricted quasi-two-dimensional space where peptide-peptide interactions become highly relevant, and the concept of a crowded medium is appropriate. Within this crowded environment interesting effects like clustering, separation of phases, cooperative alignment, and common movements occur. Here we investigated such effects by measuring distances between fluorophore-labeled peptides in the range ≤1 nm by fluorescence self-quenching. For helical peptides with dimensions of approximately 1 × 3 nm such a small "ruler" is sensitive to the packing of the labeled peptides and thereby to their molecular arrangement. A novel approach to characterize peptide-peptide interactions within membranes is presented using the designer peptide LAH4. This sequence changes membrane topology in a controlled manner being transmembrane at neutral conditions but oriented parallel to the surface at low pH. Experimental measurements of the fluorescence self-quenching of close-by chromophores and the changes that occur upon dilution with unlabeled peptides are used to analyze the peptide distribution within the membrane surface. The data show a strong effect of electrostatic interactions and under some experimental conditions clustering of the peptides. Furthermore, the results suggest that at pH 4 the peptides arrange along the membrane surface in an ordered mesophase-like arrangement.
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Affiliation(s)
- Christopher Aisenbrey
- Institut de Chimie, UMR7177, Université de Strasbourg/CNRS , 1, rue Blaise Pascal, 67000 Strasbourg, France
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706
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Aydin F, Ludford P, Dutt M. Phase segregation in bio-inspired multi-component vesicles encompassing double tail phospholipid species. SOFT MATTER 2014; 10:6096-6108. [PMID: 25008809 DOI: 10.1039/c4sm00998c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Our aim is to investigate the phase segregation and the structure of multi-component bio-inspired phospholipid vesicles via dissipative particle dynamics. The chemical distinction in the phospholipid species arises due to different head and tail group moieties, and molecular stiffness of the hydrocarbon tails. The individual amphiphilic phospholipid molecular species are represented by a hydrophilic head group and two hydrophobic tails. The distinct chemical nature of the moieties is modeled effectively via soft repulsive interaction parameters, and the molecular rigidity is tuned via suitable three-body potential constants. We demonstrate the formation of a stable hybrid vesicle through the self-assembly of the amphiphilic phospholipid molecules in the presence of a hydrophilic solvent. We investigate and characterize the phase segregation and the structure of the binary vesicles for different phospholipid mixtures. Our results demonstrate macroscopic phase separation for phospholipid mixtures composed of species with different hydrocarbon tail groups. We also investigate the relationship between the phase segregation and thermodynamic variables such as interfacial line tension and surface tension, and obtain correspondence between existing theory and experiments, and our simulation results. We report variations in the molecular chain stiffness to have negligible contributions to the phase segregation in the mixed bilayer, and to demonstrate shape transformations of the hybrid vesicle. Our results can be used to design novel bio-inspired hybrid vehicles for potential applications in biomedicine, sensing, imaging and sustainability.
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Affiliation(s)
- Fikret Aydin
- Department of Chemical Engineering, Rutgers The State University of New Jersey, Piscataway, NJ 08854, USA.
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707
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Hertrich S, Stetter F, Rühm A, Hugel T, Nickel B. Highly hydrated deformable polyethylene glycol-tethered lipid bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:9442-7. [PMID: 25046694 DOI: 10.1021/la4045804] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The realization of a solid-supported lipid bilayer acting as a workbench for the study of membrane processes is a difficult task. For robustness, the bilayer has to be tethered to the substrate. At the same time, diffusion of the lipids and plastic deformations of the membrane should not be obstructed. Furthermore, a highly hydrated surrounding is mandatory. Here, we show that grafting of a polyethylene glycol-lipid construct (PEG2000-DSPE) to a silicon oxide surface via multiple-step silane chemistry and subsequent deposition of lipids by spin-coating result in a cushioned membrane that has the desired properties. Neutron and X-ray reflectometry measurements are combined to access thickness, density, and hydration of the bilayer and the PEG cushion. We observe a spacer of 55 Å thickness between lipid bilayer and silicon-oxide surface with a rather high hydration of up to 90 ± 3% water. While 11.5 ± 3% of the lipids are grafted to the surface, as determined from the neutron data, the diffusion constant of the lipids, as probed by diffusion of 0.5% Texas Red labeled lipids, remains rather large (D = 2.1 ± 0.1 μm(2)/s), which is a reduction of only 12% compared to a supported lipid bilayer reference without immobilized lipids. Finally, AFM indentation confirms the plastic behavior of the membrane against deformation. We show that rupture of the bilayer does not occur before the deformation exceeds 40 Å. Altogether, the presented PEG-tethered lipid bilayer mimics the deformability of natural cell membranes much better than standard solid-supported lipid bilayers.
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Affiliation(s)
- Samira Hertrich
- Fakultät für Physik & CeNS, Ludwig-Maximilians-Universität , Geschwister-Scholl-Platz 1, 80539 Munich, Germany
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708
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Aydin F, Dutt M. Bioinspired Vesicles Encompassing Two-Tail Phospholipids: Self-Assembly and Phase Segregation via Implicit Solvent Coarse-Grained Molecular Dynamics. J Phys Chem B 2014; 118:8614-23. [DOI: 10.1021/jp503376r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Fikret Aydin
- Department
of Chemical and Biochemical Engineering, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Meenakshi Dutt
- Department
of Chemical and Biochemical Engineering, Rutgers The State University of New Jersey, Piscataway, New Jersey 08854, United States
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709
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Andoh Y, Muraoka S, Okazaki S. Molecular dynamics study of changes in physico-chemical properties of DMPC lipid bilayers by addition of nonionic surfactant C12E10. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.928707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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710
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Kang H, Klauda JB. Molecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.926548] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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711
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Liu W, Zhang S, Meng F, Tang L. Molecular simulation of ibuprofen passing across POPC membrane. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500333] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Permeability assessment is an important procedure in the drug development process, and drug partitioning in membrane bilayer is related to permeability. To investigate the pH dependence on drug partitioning, the process of different ionization state of ibuprofen passing across POPC bilayer was studied using molecular dynamics simulation. The results show that both atomic charge scheme and ionization state of the drug affect the value and shape of energy profile when passing across the POPC bilayer. The neutral ibuprofen (ibuprofen under acidic condition) has a much lower energy barrier as compared with the anionic ibuprofen (ibuprofen under basic condition). Meantime, hydrogen bond analysis also certifies that it is easy for neutral ibuprofen to pass from bulk water to bilayer center. Our calculation suggests that the ionization state of ibuprofen may be changed between neutral and anionic state when passing across membrane: it may be ionized outside the membrane and neutralized inside the membrane.
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Affiliation(s)
- Wei Liu
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - Shijun Zhang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - Fancui Meng
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - Lida Tang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
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712
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Liu Y, Li M, Yang Y, Xia Y, Nieh MP. The effects of temperature, salinity, concentration and PEGylated lipid on the spontaneous nanostructures of bicellar mixtures. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1871-80. [DOI: 10.1016/j.bbamem.2014.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 12/23/2013] [Accepted: 02/11/2014] [Indexed: 10/25/2022]
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713
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Heller WT, Urban VS, Lynn GW, Weiss KL, O'Neill HM, Pingali SV, Qian S, Littrell KC, Melnichenko YB, Buchanan MV, Selby DL, Wignall GD, Butler PD, Myles DA. The Bio-SANS instrument at the High Flux Isotope Reactor of Oak Ridge National Laboratory. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714011285] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Small-angle neutron scattering (SANS) is a powerful tool for characterizing complex disordered materials, including biological materials. The Bio-SANS instrument of the High Flux Isotope Reactor of Oak Ridge National Laboratory (ORNL) is a high-flux low-background SANS instrument that is, uniquely among SANS instruments, dedicated to serving the needs of the structural biology and biomaterials communities as an open-access user facility. Here, the technical specifications and performance of the Bio-SANS are presented. Sample environments developed to address the needs of the user program of the instrument are also presented. Further, the isotopic labeling and sample preparation capabilities available in the Bio-Deuteration Laboratory for users of the Bio-SANS and other neutron scattering instruments at ORNL are described. Finally, a brief survey of research performed using the Bio-SANS is presented, which demonstrates the breadth of the research that the instrument's user community engages in.
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714
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A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2520-9. [PMID: 24953542 DOI: 10.1016/j.bbamem.2014.06.010] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/07/2014] [Accepted: 06/11/2014] [Indexed: 11/21/2022]
Abstract
Although lipid force fields (FFs) used in molecular dynamics (MD) simulations have proved to be accurate, there has not been a systematic study on their accuracy over a range of temperatures. Motivated by the X-ray and neutron scattering measurements of common phosphatidylcholine (PC) bilayers (Kučerka et al. BBA. 1808: 2761, 2011), the CHARMM36 (C36) FF accuracy is tested in this work with MD simulations of six common PC lipid bilayers over a wide range of temperatures. The calculated scattering form factors and deuterium order parameters from the C36 MD simulations agree well with the X-ray, neutron, and NMR experimental data. There is excellent agreement between MD simulations and experimental estimates for the surface area per lipid, bilayer thickness (DB), hydrophobic thickness (DC), and lipid volume (VL). The only minor discrepancy between simulation and experiment is a measure of (DB-DHH)/2 where DHH is the distance between the maxima in the electron density profile along the bilayer normal. Additional MD simulations with pure water and heptane over a range of temperatures provide explanations of possible reasons causing the minor deviation. Overall, the C36 FF is accurate for use with liquid crystalline PC bilayers of varying chain types and over biologically relevant temperatures.
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715
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Pan J, Cheng X, Monticelli L, Heberle FA, Kučerka N, Tieleman DP, Katsaras J. The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations. SOFT MATTER 2014; 10:3716-3725. [PMID: 24807693 DOI: 10.1039/c4sm00066h] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Phosphatidylserine (PS) lipids play essential roles in biological processes, including enzyme activation and apoptosis. We report on the molecular structure and atomic scale interactions of a fluid bilayer composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS). A scattering density profile model, aided by molecular dynamics (MD) simulations, was developed to jointly refine different contrast small-angle neutron and X-ray scattering data, which yielded a lipid area of 62.7 Å(2) at 25 °C. MD simulations with POPS lipid area constrained at different values were also performed using all-atom and aliphatic united-atom models. The optimal simulated bilayer was obtained using a model-free comparison approach. Examination of the simulated bilayer, which agrees best with the experimental scattering data, reveals a preferential interaction between Na(+) ions and the terminal serine and phosphate moieties. Long-range inter-lipid interactions were identified, primarily between the positively charged ammonium, and the negatively charged carboxylic and phosphate oxygens. The area compressibility modulus KA of the POPS bilayer was derived by quantifying lipid area as a function of surface tension from area-constrained MD simulations. It was found that POPS bilayers possess a much larger KA than that of neutral phosphatidylcholine lipid bilayers. We propose that the unique molecular features of POPS bilayers may play an important role in certain physiological functions.
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Affiliation(s)
- Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
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716
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Marques I, Colaço AR, Costa PJ, Busschaert N, Gale PA, Félix V. Tris-thiourea tripodal-based molecules as chloride transmembrane transporters: insights from molecular dynamics simulations. SOFT MATTER 2014; 10:3608-3621. [PMID: 24663079 DOI: 10.1039/c3sm52140k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The interaction of six tripodal synthetic chloride transmembrane transporters with a POPC bilayer was investigated by means of molecular dynamics simulations using the general Amber force field (GAFF) for the transporters and the LIPID11 force field for phospholipids. These transporters are structurally simple molecules, based on the tris(2-aminoethyl)amine scaffold, containing three thiourea binding units coupled with three n-butyl (1), phenyl (2), fluorophenyl (3), pentafluorophenyl (4), trifluoromethylphenyl (5), or bis(trifluoromethyl)phenyl (6) substituents. The passive diffusion of 1-6⊃ Cl(-) was evaluated with the complexes initially positioned either in the water phase or inside the bilayer. In the first scenario the chloride is released in the water solution before the synthetic molecules achieve the water-lipid interface and permeate the membrane. In the latter one, only when the chloride complex reaches the interface is the anion released to the water phase, with the transporter losing the initial ggg tripodal shape. Independently of the transporter used in the membrane system, the bilayer structure is preserved and the synthetic molecules interact with the POPC molecules at the phosphate headgroup level, via N-H···O hydrogen bonds. Overall, the molecular dynamics simulations' results indicate that the small tripodal molecules in this series have a low impact on the bilayer and are able to diffuse with chloride inside the lipid environment. Indeed, these are essential conditions for these molecules to promote the transmembrane transport as anion carriers, in agreement with experimental efflux data.
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Affiliation(s)
- Igor Marques
- Departamento de Química, CICECO and Secção Autónoma de Ciências da Saúde, Universidade de Aveiro, 3810-193 Aveiro, Portugal.
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717
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Guo Y, Pogodin S, Baulin VA. General model of phospholipid bilayers in fluid phase within the single chain mean field theory. J Chem Phys 2014; 140:174903. [DOI: 10.1063/1.4873586] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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718
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Molecular dynamics simulations of homo-oligomeric bundles embedded within a lipid bilayer. Biophys J 2014; 105:1569-80. [PMID: 24094398 DOI: 10.1016/j.bpj.2013.07.053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 11/23/2022] Open
Abstract
Using molecular dynamics simulations, we studied the structure, interhelix interactions, and dynamics of transmembrane proteins. Specifically, we investigated homooligomeric helical bundle systems consisting of synthetic α-helices with either the sequence Ac-(LSLLLSL)3-NH2 (LS2) or Ac-(LSSLLSL)3-NH2 (LS3). The LS2 and LS3 helical peptides are designed to have amphipathic characteristics that form ion channels in membrane. We simulated bundles containing one to six peptides that were embedded in palmitoyl-oleoyl-phosphatidylcholine (POPC) lipid bilayer and placed between two lamellae of water. We aim to provide a fundamental understanding of how amphipathic helical peptides interact with each other and their dynamical behaviors in different homooligomeric states. To understand structural properties, we examined the helix lengths, tilt angles of individual helices and the entire bundle, interhelix distances, interhelix cross-angles, helix hydrophobic-to-hydrophilic vector projections, and the average number of interhelix hydrophilic (serine-serine) contacts lining the pore of the transmembrane channel. To analyze dynamical properties, we calculated the rotational autocorrelation function of each helix and the cross-correlation of the rotational velocity between adjacent helices. The observed structural and dynamical characteristics show that higher order bundles containing four to six peptides are composed of multiple lower order bundles of one to three peptides. For example, the LS2 channel was found to be stable in a tetrameric bundle composed of a "dimer of dimers." In addition, we observed that there is a minimum of two strong hydrophilic contacts between a pair of adjacent helices in the dimer to tetramer systems and only one strong hydrophilic interhelix contact in helix pairs of the pentamer and hexamer systems. We believe these results are general and can be applied to more complex ion channels, providing insight into ion channel stability and assembly.
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719
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Faure É, Thompson C, Blunck R. Do lipids show state-dependent affinity to the voltage-gated potassium channel KvAP? J Biol Chem 2014; 289:16452-61. [PMID: 24742679 DOI: 10.1074/jbc.m113.537134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As all integral membrane proteins, voltage-gated ion channels are embedded in a lipid matrix that regulates their channel behavior either by physicochemical properties or by direct binding. Because manipulation of the lipid composition in cells is difficult, we investigated the influence of different lipids on purified KvAP channels reconstituted in planar lipid bilayers of known composition. Lipids developed two distinct and independent effects on the KvAP channels; lipids interacting with the pore lowered the energy barriers for the final transitions, whereas voltage sensor-bound lipids shifted the midpoint of activation dependent on their electrostatic charge. Above all, the midpoint of activation was determined only by those lipids the channels came in contact with first after purification and can seemingly only be exchanged if the channel resides in the open state. The high affinity of the bound lipids to the binding site has implications not only on our understanding of the gating mechanism but also on the general experimental design of any lipid dependence study.
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Affiliation(s)
- Élise Faure
- Groupe d'étude des protéines membranaires (GÉPROM), Université de Montréal, Montréal CH3C 3J7, Canada Physiology
| | - Christine Thompson
- Groupe d'étude des protéines membranaires (GÉPROM), Université de Montréal, Montréal CH3C 3J7, CanadaFrom the Departments of Physics and
| | - Rikard Blunck
- Groupe d'étude des protéines membranaires (GÉPROM), Université de Montréal, Montréal CH3C 3J7, Canada Physiology, From the Departments of Physics and
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720
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Walsh P, Vanderlee G, Yau J, Campeau J, Sim VL, Yip CM, Sharpe S. The mechanism of membrane disruption by cytotoxic amyloid oligomers formed by prion protein(106-126) is dependent on bilayer composition. J Biol Chem 2014; 289:10419-10430. [PMID: 24554723 PMCID: PMC4036164 DOI: 10.1074/jbc.m113.515866] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 02/01/2014] [Indexed: 11/06/2022] Open
Abstract
The formation of fibrillar aggregates has long been associated with neurodegenerative disorders such as Alzheimer and Parkinson diseases. Although fibrils are still considered important to the pathology of these disorders, it is now widely understood that smaller amyloid oligomers are the toxic entities along the misfolding pathway. One characteristic shared by the majority of amyloid oligomers is the ability to disrupt membranes, a commonality proposed to be responsible for their toxicity, although the mechanisms linking this to cell death are poorly understood. Here, we describe the physical basis for the cytotoxicity of oligomers formed by the prion protein (PrP)-derived amyloid peptide PrP(106-126). We show that oligomers of this peptide kill several mammalian cells lines, as well as mouse cerebellar organotypic cultures, and we also show that they exhibit antimicrobial activity. Physical perturbation of model membranes mimicking bacterial or mammalian cells was investigated using atomic force microscopy, polarized total internal reflection fluorescence microscopy, and NMR spectroscopy. Disruption of anionic membranes proceeds through a carpet or detergent model as proposed for other antimicrobial peptides. By contrast, when added to zwitterionic membranes containing cholesterol-rich ordered domains, PrP(106-126) oligomers induce a loss of domain separation and decreased membrane disorder. Loss of raft-like domains may lead to activation of apoptotic pathways, resulting in cell death. This work sheds new light on the physical mechanisms of amyloid cytotoxicity and is the first to clearly show membrane type-specific modes of action for a cytotoxic peptide.
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Affiliation(s)
- Patrick Walsh
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8
| | - Gillian Vanderlee
- Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1
| | - Jason Yau
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8
| | - Jody Campeau
- Department of Medicine, Division of Neurology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Valerie L Sim
- Department of Medicine, Division of Neurology, University of Alberta, Edmonton, Alberta T6G 2G3, Canada
| | - Christopher M Yip
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8; Institute of Biomaterials and Biomedical Engineering, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1
| | - Simon Sharpe
- Molecular Structure and Function Program, The Hospital for Sick Children, Toronto, Ontario M5G 1X8; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8.
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721
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Van Oosten B, Marquardt D, Komljenović I, Bradshaw JP, Sternin E, Harroun TA. Small molecule interaction with lipid bilayers: A molecular dynamics study of chlorhexidine. J Mol Graph Model 2014; 48:96-104. [DOI: 10.1016/j.jmgm.2013.12.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/02/2013] [Accepted: 12/17/2013] [Indexed: 11/28/2022]
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722
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Bag N, Yap DHX, Wohland T. Temperature dependence of diffusion in model and live cell membranes characterized by imaging fluorescence correlation spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014. [DOI: 10.1016/j.bbamem.2013.10.009] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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723
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Midtgaard SR, Pedersen MC, Kirkensgaard JJK, Sørensen KK, Mortensen K, Jensen KJ, Arleth L. Self-assembling peptides form nanodiscs that stabilize membrane proteins. SOFT MATTER 2014; 10:738-752. [PMID: 24651399 DOI: 10.1039/c3sm51727f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
New methods to handle membrane bound proteins, e.g. G-protein coupled receptors (GPCRs), are highly desirable. Recently, apoliprotein A1 (ApoA1) based lipoprotein particles have emerged as a new platform for studying membrane proteins, and it has been shown that they can self-assemble in combination with phospholipids to form discoidal shaped particles that can stabilize membrane proteins. In the present study, we have investigated an ApoA1 mimetic peptide with respect to its solution structure when in complex with phospholipids. This was achieved using a powerful combination of small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) supported by coarse-grained molecular dynamics simulations. The detailed structure of the discs was determined in unprecedented detail and it was found that they adopt a discoidal structure very similar to the ApoA1 based nanodiscs. We furthermore show that, like the ApoA1 and derived nanodiscs, these peptide discs can accommodate and stabilize a membrane protein. Finally, we exploit their dynamic properties and show that the 18A discs may be used for transferring membrane proteins and associated phospholipids directly and gently into phospholipid nanodiscs.
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724
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Heftberger P, Kollmitzer B, Heberle FA, Pan J, Rappolt M, Amenitsch H, Kučerka N, Katsaras J, Pabst G. Global small-angle X-ray scattering data analysis for multilamellar vesicles: the evolution of the scattering density profile model. J Appl Crystallogr 2014; 47:173-180. [PMID: 24587787 PMCID: PMC3937811 DOI: 10.1107/s1600576713029798] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/30/2013] [Indexed: 12/04/2022] Open
Abstract
The highly successful scattering density profile (SDP) model, used to jointly analyze small-angle X-ray and neutron scattering data from unilamellar vesicles, has been adapted for use with data from fully hydrated, liquid crystalline multilamellar vesicles (MLVs). Using a genetic algorithm, this new method is capable of providing high-resolution structural information, as well as determining bilayer elastic bending fluctuations from standalone X-ray data. Structural parameters such as bilayer thickness and area per lipid were determined for a series of saturated and unsaturated lipids, as well as binary mixtures with cholesterol. The results are in good agreement with previously reported SDP data, which used both neutron and X-ray data. The inclusion of deuterated and non-deuterated MLV neutron data in the analysis improved the lipid backbone information but did not improve, within experimental error, the structural data regarding bilayer thickness and area per lipid.
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Affiliation(s)
- Peter Heftberger
- Instiute of Molecular Biosciences, Biophysics Division, University of Graz, Austria
| | - Benjamin Kollmitzer
- Instiute of Molecular Biosciences, Biophysics Division, University of Graz, Austria
| | - Frederick A. Heberle
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jianjun Pan
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Physics, University of South Florida, Tampa, FL 33620, USA
| | - Michael Rappolt
- Institute of Inorganic Chemistry, Graz University of Technology, Austria
- School of Food Science and Nutrition, University of Leeds, UK
| | - Heinz Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, Austria
| | - Norbert Kučerka
- Canadian Neutron Beam Centre, National Research Council, Chalk River, ON, Canada
| | - John Katsaras
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Joint Institute for Neutron Sciences, Oak Ridge, TN, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA
- Department of Physics, Brock University, St Catharines, ON, Canada
| | - Georg Pabst
- Instiute of Molecular Biosciences, Biophysics Division, University of Graz, Austria
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725
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Yao H, Hong M. Conformation and lipid interaction of the fusion peptide of the paramyxovirus PIV5 in anionic and negative-curvature membranes from solid-state NMR. J Am Chem Soc 2014; 136:2611-24. [PMID: 24428385 PMCID: PMC3985871 DOI: 10.1021/ja4121956] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Viral fusion proteins catalyze the merger of the virus envelope and the target cell membrane through multiple steps of protein conformational changes. The fusion peptide domain of these proteins is important for membrane fusion, but how it causes membrane curvature and dehydration is still poorly understood. We now use solid-state NMR spectroscopy to investigate the conformation, topology, and lipid and water interactions of the fusion peptide of the PIV5 virus F protein in three lipid membranes, POPC/POPG, DOPC/DOPG, and DOPE. These membranes allow us to investigate the effects of lipid chain disorder, membrane surface charge, and intrinsic negative curvature on the fusion peptide structure. Chemical shifts and spin diffusion data indicate that the PIV5 fusion peptide is inserted into all three membranes but adopts distinct conformations: it is fully α-helical in the POPC/POPG membrane, adopts a mixed strand/helix conformation in the DOPC/DOPG membrane, and is primarily a β-strand in the DOPE membrane. (31)P NMR spectra show that the peptide retains the lamellar structure and hydration of the two anionic membranes. However, it dehydrates the DOPE membrane, destabilizes its inverted hexagonal phase, and creates an isotropic phase that is most likely a cubic phase. The ability of the β-strand conformation of the fusion peptide to generate negative Gaussian curvature and to dehydrate the membrane may be important for the formation of hemifusion intermediates in the membrane fusion pathway.
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Affiliation(s)
- Hongwei Yao
- Department of Chemistry, Iowa State University , Ames, Iowa 50011 United States
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726
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Dickson CJ, Madej BD, Skjevik AA, Betz RM, Teigen K, Gould IR, Walker RC. Lipid14: The Amber Lipid Force Field. J Chem Theory Comput 2014; 10:865-879. [PMID: 24803855 PMCID: PMC3985482 DOI: 10.1021/ct4010307] [Citation(s) in RCA: 932] [Impact Index Per Article: 93.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Indexed: 11/29/2022]
Abstract
![]()
The AMBER lipid force field has been
updated to create Lipid14,
allowing tensionless simulation of a number of lipid types with the
AMBER MD package. The modular nature of this force field allows numerous
combinations of head and tail groups to create different lipid types,
enabling the easy insertion of new lipid species. The Lennard-Jones
and torsion parameters of both the head and tail groups have been
revised and updated partial charges calculated. The force field has
been validated by simulating bilayers of six different lipid types
for a total of 0.5 μs each without applying a surface tension;
with favorable comparison to experiment for properties such as area
per lipid, volume per lipid, bilayer thickness, NMR order parameters,
scattering data, and lipid lateral diffusion. As the derivation of
this force field is consistent with the AMBER development philosophy,
Lipid14 is compatible with the AMBER protein, nucleic acid, carbohydrate,
and small molecule force fields.
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Affiliation(s)
- Callum J Dickson
- Department of Chemistry and Institute of Chemical Biology, Imperial College London , South Kensington SW7 2AZ, United Kingdom
| | - Benjamin D Madej
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, United States ; Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, United States
| | - Age A Skjevik
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, United States ; Department of Biomedicine, University of Bergen , N-5009 Bergen, Norway
| | - Robin M Betz
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, United States
| | - Knut Teigen
- Department of Biomedicine, University of Bergen , N-5009 Bergen, Norway
| | - Ian R Gould
- Department of Chemistry and Institute of Chemical Biology, Imperial College London , South Kensington SW7 2AZ, United Kingdom
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, United States ; Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive MC0505, La Jolla, California 92093-0505, United States
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727
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Huynh L, Perrot N, Beswick V, Rosilio V, Curmi PA, Sanson A, Jamin N. Structural properties of POPC monolayers under lateral compression: computer simulations analysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:564-573. [PMID: 24397263 DOI: 10.1021/la4043809] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a lipid comprising a saturated and an unsaturated acyl chain, belongs to the class of glycerophosphatidylcholines, major lipids in eukaryotic cell membranes. To get insight into the structural properties of this lipid within monolayers as membrane models, we performed molecular dynamics (MD) simulations of POPC monolayers under compression at the air/water interface. MD simulations were carried out at 300 K and at different surface pressures using the all-atom general Amber force field (GAFF). A good agreement was found between the simulated data and experimental isotherms. At surface pressures greater than 15 mN/m, two orientations of the head groups clearly appear: one nearly parallel to the monolayer interface and another one pointing toward the water. On the basis of the analysis of headgroup dihedral angles, we propose that the conformational variations around the bonds connecting the phosphorus atom to the adjacent oxygens are involved in these two orientations of the headgroup. The glycerol group orientation is characterized by a large distribution centered around 50° with respect to the monolayer normal. The acyl chains are predominantly in trans configuration from 7.5 to 43 mN/m surface pressures. Moreover, the calculated order parameter profiles of both chains suggest an independent behavior of the saturated and unsaturated chains that could be correlated with the formation of chain-type clusters observed along the simulated trajectories.
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Affiliation(s)
- Lucie Huynh
- INSERM, U829, Laboratoire Structure - Activité des Biomolécules Normales et Pathologiques, Université d'Evry-Val-d'Essonne , F-91025 Evry, France
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728
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Size-dependent ultrafast structural dynamics inside phospholipid vesicle bilayers measured with 2D IR vibrational echoes. Proc Natl Acad Sci U S A 2014; 111:918-23. [PMID: 24395796 DOI: 10.1073/pnas.1323110111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ultrafast structural dynamics inside the bilayers of dilauroylphosphatidylcholine (DLPC) and dipalmitoylphosphatidylcholine vesicles with 70, 90, and 125 nm diameters were directly measured with 2D IR vibrational echo spectroscopy. The antisymmetric CO stretch of tungsten hexacarbonyl was used as a vibrational probe and provided information on spectral diffusion (structural dynamics) in the alkyl region of the bilayers. Although the CO stretch absorption spectra remain the same, the interior structural dynamics become faster as the size of the vesicles decrease, with the size dependence greater for dipalmitoylphosphatidylcholine than for DLPC. As DLPC vesicles become larger, the interior dynamics approach those of the planar bilayer.
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729
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Wang J, Liu KW, Segatori L, Biswal SL. Lipid Bilayer Phase Transformations Detected Using Microcantilevers. J Phys Chem B 2013; 118:171-8. [DOI: 10.1021/jp4095112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jinghui Wang
- Department of Chemical and
Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Kai-Wei Liu
- Department of Chemical and
Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Laura Segatori
- Department of Chemical and
Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
| | - Sibani Lisa Biswal
- Department of Chemical and
Biomolecular Engineering, Rice University, Houston, Texas 77005, United States
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730
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Marquardt D, Williams JA, Kinnun JJ, Kučerka N, Atkinson J, Wassall SR, Katsaras J, Harroun TA. Dimyristoyl phosphatidylcholine: a remarkable exception to α-tocopherol's membrane presence. J Am Chem Soc 2013; 136:203-10. [PMID: 24308426 DOI: 10.1021/ja408288f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using data obtained from different physical techniques (i.e., neutron diffraction, NMR and UV spectroscopy), we present evidence which explains some of the conflicting and inexplicable data found in the literature regarding α-tocopherol's (aToc's) behavior in dimyristoyl phosphatidylcholine (di-14:0PC) bilayers. Without exception, the data point to aToc's active chromanol moiety residing deep in the hydrophobic core of di-14:0PC bilayers, a location that is in stark contrast to aToc's location in other PC bilayers. Our result is a clear example of the importance of lipid species diversity in biological membranes and importantly, it suggests that measurements of aToc's oxidation kinetics, and its associated byproducts observed in di-14:0PC bilayers, should be reexamined, this time taking into account its noncanonical location in this bilayer.
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Affiliation(s)
- Drew Marquardt
- Department of Physics, Brock University , St. Catharines, Ontario L2S 3A1, Canada
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731
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A microscopic multiphase diffusion model of viable epidermis permeability. Biophys J 2013; 104:2307-20. [PMID: 23708370 DOI: 10.1016/j.bpj.2013.03.056] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 11/21/2022] Open
Abstract
A microscopic model of passive transverse mass transport of small solutes in the viable epidermal layer of human skin is formulated on the basis of a hexagonal array of cells (i.e., keratinocytes) bounded by 4-nm-thick, anisotropic lipid bilayers and separated by 1-μm layers of extracellular fluid. Gap junctions and tight junctions with adjustable permeabilities are included to modulate the transport of solutes with low membrane permeabilities. Two keratinocyte aspect ratios are considered to represent basal and spinous cells (longer) and granular cells (more flattened). The diffusion problem is solved in a unit cell using a coordinate system conforming to the hexagonal cross section, and an efficient two-dimensional treatment is applied to describe transport in both the cell membranes and intercellular spaces, given their thinness. Results are presented in terms of an effective diffusion coefficient, D¯(epi), and partition coefficient, K¯(epi/w), for a homogenized representation of the microtransport problem. Representative calculations are carried out for three small solutes-water, L-glucose, and hydrocortisone-covering a wide range of membrane permeability. The effective transport parameters and their microscopic interpretation can be employed within the context of existing three-layer models of skin transport to provide more realistic estimates of the epidermal concentrations of topically applied solutes.
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732
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Kollmitzer B, Heftberger P, Rappolt M, Pabst G. Monolayer spontaneous curvature of raft-forming membrane lipids. SOFT MATTER 2013; 9:10877-10884. [PMID: 24672578 PMCID: PMC3963256 DOI: 10.1039/c3sm51829a] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Monolayer spontaneous curvatures for cholesterol, DOPE, POPE, DOPC, DPPC, DSPC, POPC, SOPC, and egg sphingomyelin were obtained using small-angle X-ray scattering (SAXS) on inverted hexagonal phases (HII). Spontaneous curvatures of bilayer forming lipids were estimated by adding controlled amounts to a HII forming template following previously established protocols. Spontaneous curvatures of both phosphatidylethanolamines and cholesterol were found to be at least a factor of two more negative than those of phosphatidylcholines, whose J0 values are closer to zero. Interestingly, a significant positive J0 value was retrieved for DPPC. We further determined the temperature dependence of the spontaneous curvatures J0(T) in the range from 15 to 55 °C, resulting in a quite narrow distribution of -1 to -3 × 10-3 (nm °C)-1 for most investigated lipids. The data allowed us to estimate the monolayer spontaneous curvatures of ternary lipid mixtures showing liquid ordered/liquid disordered phase coexistence. We report spontaneous curvature phase diagrams for DSPC/DOPC/Chol, DPPC/DOPC/Chol and SM/POPC/Chol and discuss effects on protein insertion and line tension.
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Affiliation(s)
- Benjamin Kollmitzer
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Austria. ; ; Tel: +43 316 4120-342
| | - Peter Heftberger
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Austria. ; ; Tel: +43 316 4120-342
| | - Michael Rappolt
- Institute of Inorganic Chemistry, Graz University of Technology, Austria ; School of Food Science and Nutrition, University of Leeds, UK
| | - Georg Pabst
- Institute of Molecular Biosciences, Biophysics Division, University of Graz, Austria. ; ; Tel: +43 316 4120-342
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733
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Weinrich M, Worcester DL. Xenon and other volatile anesthetics change domain structure in model lipid raft membranes. J Phys Chem B 2013; 117:16141-7. [PMID: 24299622 DOI: 10.1021/jp411261g] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Inhalation anesthetics have been in clinical use for over 160 years, but the molecular mechanisms of action continue to be investigated. Direct interactions with ion channels received much attention after it was found that anesthetics do not change the structure of homogeneous model membranes. However, it was recently found that halothane, a prototypical anesthetic, changes domain structure of a binary lipid membrane. The noble gas xenon is an excellent anesthetic and provides a pivotal test of the generality of this finding, extended to ternary lipid raft mixtures. We report that xenon and conventional anesthetics change the domain equilibrium in two canonical ternary lipid raft mixtures. These findings demonstrate a membrane-mediated mechanism whereby inhalation anesthetics can affect the lipid environment of transmembrane proteins.
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Affiliation(s)
- Michael Weinrich
- Eunice Kennedy Shriver National Institute of Child Health and Human Development , Bethesda, Maryland 20892, United States
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734
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Braunger JA, Kramer C, Morick D, Steinem C. Solid supported membranes doped with PIP2: influence of ionic strength and pH on bilayer formation and membrane organization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14204-13. [PMID: 24199623 DOI: 10.1021/la402646k] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Phosphoinositides and in particular L-α-phosphatidylinositol-4,5-bisphosphate (PIP2) are key lipids controlling many cellular events and serve as receptors for a large number of intracellular proteins. To quantitatively analyze protein-PIP2 interactions in vitro in a time-resolved manner, planar membranes on solid substrates are highly desirable. Here, we describe an optimized protocol to form PIP2 containing planar solid supported membranes on silicon surfaces by vesicle spreading. Supported lipid bilayers (SLBs) were obtained by spreading POPC/PIP2 (92:8) small unilamellar vesicles onto hydrophilic silicon substrates at a low pH of 4.8. These membranes were capable of binding ezrin, resulting in large protein coverage as concluded from reflectometric interference spectroscopy and fluorescence microscopy. As deduced from fluorescence microscopy, only under low pH conditions, a homogeneously appearing distribution of fluorescently labeled PIP2 molecules in the membrane was achieved. Fluorescence recovery after photobleaching experiments revealed that PIP2 is not mobile in the bottom layer of the SLBs, while PIP2 is fully mobile in the top layer with diffusion coefficients of about 3 μm(2)/s. This diffusion coefficient was considerably reduced by a factor of about 3 if ezrin has been bound to PIP2 in the membrane.
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Affiliation(s)
- Julia A Braunger
- Institut für Organische und Biomolekulare Chemie, Georg-August Universität , Tammannstr. 2, 37077 Göttingen, Germany
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735
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Bortolus M, De Zotti M, Formaggio F, Maniero AL. Alamethicin in bicelles: Orientation, aggregation, and bilayer modification as a function of peptide concentration. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2620-7. [DOI: 10.1016/j.bbamem.2013.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/24/2013] [Accepted: 07/08/2013] [Indexed: 10/26/2022]
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736
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Minner DE, Herring VL, Siegel AP, Kimble-Hill A, Johnson MA, Naumann CA. Iterative layer-by-layer assembly of polymer-tethered multi-bilayers using maleimide–thiol coupling chemistry. SOFT MATTER 2013; 9:9643-9650. [PMID: 26029773 DOI: 10.1039/c3sm51446c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The current study reports on the layer-by-layer assembly of a polymer-tethered lipid multi-bilayer stack using the iterative addition and roll out of giant unilamellar vesicles (GUVs) containing constituents with thiol and maleimide functional groups, respectively. Confocal microscopy and photobleaching experiments confirm stack integrity and stability over time, as well as the lateral fluidity of individual bilayers within the stacks. Complementary wide-field single molecule fluorescence microscopy and atomic force microscopy experiments show that increasing bilayer-substrate distances are associated with changes in lipid lateral mobility and bilayer morphology. Importantly, the described iterative approach can be employed to assemble multi-bilayer stacks with more than two bilayers, thus further reducing the influence of the underlying solid substrate on membrane behavior. Furthermore, the presence of lipopolymers within the multi-bilayer stacks results in fascinating membrane dynamics and organization properties, with interesting parallels to those found in plasma membranes. In that sense, the described multi-bilayer architecture represents an attractive model membrane platform for a variety of different biophysical studies.
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Affiliation(s)
- Daniel E Minner
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202-3274, USA
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737
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Lee V, Hawa T. Investigation of the effect of bilayer membrane structures and fluctuation amplitudes on SANS/SAXS profile for short membrane wavelength. J Chem Phys 2013; 139:124905. [DOI: 10.1063/1.4821816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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738
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Tikhonova IG, Selvam B, Ivetac A, Wereszczynski J, McCammon JA. Simulations of biased agonists in the β(2) adrenergic receptor with accelerated molecular dynamics. Biochemistry 2013; 52:5593-603. [PMID: 23879802 PMCID: PMC3763781 DOI: 10.1021/bi400499n] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signaling pathway a GPCR promotes intracellular signals though β-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signaling through the G protein and β-arrestin. Here we report on the dynamics of the β2 adrenergic receptor bound to the β-arrestin and G protein-biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring of the transition within the nanosecond time scale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the β-arrestin-biased agonist N-cyclopentylbutanepherine, we observe a different pattern of motions in helix 7 when compared to simulations with the G protein-biased agonist salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs.
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Affiliation(s)
- Irina G Tikhonova
- Molecular Therapeutics, School of Pharmacy, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland, UK.
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739
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Ojwang' LM, Cook RL. Environmental conditions that influence the ability of humic acids to induce permeability in model biomembranes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:8280-8287. [PMID: 23805776 DOI: 10.1021/es4004922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The interaction of humic acids (HAs) with 1-palmitoyl-2-oleoyl-Sn-glycero-3-phosphocholine (POPC) large unilamellar vesicle (LUV) model biomembrane system was studied by fluorescence spectroscopy. HAs from aquatic and terrestrial (including coal) sources were studied. The effects of HA concentration and temperature over environmentally relevant ranges of 0 to 20 mg C/L and 10 to 30 °C, respectively, were investigated. The dosage studies revealed that the aquatic Suwannee River humic acid (SRHA) causes an increased biomembrane perturbation (percent leakage of the fluorescent dye, Sulforhodamine B) over the entire studied concentration range. The two terrestrial HAs, namely Leonardite humic acid (LAHA) and Florida peat humic acid (FPHA), at concentrations above 5 mg C/L, show a decrease or a plateau effect attributable to the competition within the HA mixture and/or the formation of "partial aggregates". The temperature studies revealed that biomembrane perturbation increases with decreasing temperature for all three HAs. Kinetic studies showed that the membrane perturbation process is complex with both fast and slow absorption (sorption into the bilayer) components and that the slow component could be fitted by first order kinetics. A mechanism based on "lattice errors" within the POPC LUVs is put forward to explain the fast and slow components. A rationale behind the concentration and temperature findings is provided, and the environmental implications are discussed.
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Affiliation(s)
- Loice M Ojwang'
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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740
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The Observation of Highly Ordered Domains in Membranes with Cholesterol. PLoS One 2013; 8:e66162. [PMID: 23823623 PMCID: PMC3688844 DOI: 10.1371/journal.pone.0066162] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/02/2013] [Indexed: 12/22/2022] Open
Abstract
Rafts, or functional domains, are transient nano- or mesoscopic structures in the exoplasmic leaflet of the plasma membrane, and are thought to be essential for many cellular processes. Using neutron diffraction and computer modelling, we present evidence for the existence of highly ordered lipid domains in the cholesterol-rich (32.5 mol%) liquid-ordered ([Formula: see text]) phase of dipalmitoylphosphatidylcholine membranes. The liquid ordered phase in one-component lipid membranes has previously been thought to be a homogeneous phase. The presence of highly ordered lipid domains embedded in a disordered lipid matrix implies non-uniform distribution of cholesterol between the two phases. The experimental results are in excellent agreement with recent computer simulations of DPPC/cholesterol complexes [Meinhardt, Vink and Schmid (2013). Proc Natl Acad Sci USA 110(12): 4476-4481], which reported the existence of nanometer size [Formula: see text] domains in a liquid disordered lipid environment.
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741
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Coimbra JT, Sousa SF, Fernandes PA, Rangel M, Ramos MJ. Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble. J Biomol Struct Dyn 2013; 32:88-103. [DOI: 10.1080/07391102.2012.750250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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742
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Marquardt D, Williams JA, Kučerka N, Atkinson J, Wassall SR, Katsaras J, Harroun TA. Tocopherol activity correlates with its location in a membrane: a new perspective on the antioxidant vitamin E. J Am Chem Soc 2013; 135:7523-33. [PMID: 23581571 DOI: 10.1021/ja312665r] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We show evidence of an antioxidant mechanism for vitamin E which correlates strongly with its physical location in a model lipid bilayer. These data address the overlooked problem of the physical distance between the vitamin's reducing hydrogen and lipid acyl chain radicals. Our combined data from neutron diffraction, NMR, and UV spectroscopy experiments all suggest that reduction of reactive oxygen species and lipid radicals occurs specifically at the membrane's hydrophobic-hydrophilic interface. The latter is possible when the acyl chain "snorkels" to the interface from the hydrocarbon matrix. Moreover, not all model lipids are equal in this regard, as indicated by the small differences in vitamin's location. The present result is a clear example of the importance of lipid diversity in controlling the dynamic structural properties of biological membranes. Importantly, our results suggest that measurements of aToc oxidation kinetics, and its products, should be revisited by taking into consideration the physical properties of the membrane in which the vitamin resides.
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Affiliation(s)
- Drew Marquardt
- Department of Physics, Brock University, St. Catharines, Ontario L2S 3A1, Canada
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743
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Nitsche JM, Kasting GB. Permeability of fluid-phase phospholipid bilayers: assessment and useful correlations for permeability screening and other applications. J Pharm Sci 2013; 102:2005-2032. [PMID: 23605505 DOI: 10.1002/jps.23471] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 12/20/2012] [Accepted: 01/18/2013] [Indexed: 12/14/2022]
Abstract
Permeability data (P(lip/w) ) for liquid crystalline phospholipid bilayers composed of egg lecithin and dimyristoylphosphatidylcholine (DMPC) are analyzed in terms of a mathematical model that accounts for free surface area and chain-ordering effects in the bilayer as well as size and lipophilicity of the permeating species. Free surface area and chain ordering are largely determined by temperature and cholesterol content of the membrane, molecular size is represented by molecular weight, and lipophilicity of the barrier region is represented by the 1,9-decadiene/water partition coefficient, following earlier work by Xiang, Anderson, and coworkers. A correlating variable χ = MW(n) σ/(1 -σ) is used to link the results from different membrane systems, where different values of n are tried, and σ denotes a reduced phospholipid density. The group (1 -σ)/σ is a measure of free surface area, but can also be interpreted in terms of free volume. A single exponential function of χ is developed that is able to correlate 39 observations of P(lip/w) for different compounds in egg lecithin at low density, and 22 observations for acetic acid in DMPC at higher densities, spanning nine orders of magnitude to within an rms error for log 10 P(lip/w) of 0.20. The best fit found for n = 0.87 ultimately makes χ much closer to the ratio of molecular to free volumes than surface areas. The results serve as a starting point for estimating passive permeability of cell membranes to nonionized solutes as a function of temperature and cholesterol content of the membrane.
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Affiliation(s)
- Johannes M Nitsche
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York, 14260-4200.
| | - Gerald B Kasting
- James L. Winkle College of Pharmacy, University of Cincinnati Academic Health Center, Cincinnati, Ohio, 45267-0004
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744
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Needham D, Dewhirst MW. Materials Science and Engineering of the Low Temperature Sensitive Liposome (LTSL): Composition-Structure-Property Relationships That Underlie its Design and Performance. SMART MATERIALS FOR DRUG DELIVERY 2013. [DOI: 10.1039/9781849736800-00033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This chapter presents the material science and materials engineering concepts that went into the design and testing of the Low Temperature-Sensitive Liposome (LTSL), including: the roles of each of the components that make up the composite membrane; how the molecular and nanostructures that they form might influence the already anomalous permeability at the phase transition of the bilayer; and how this thermally sensitive “Smart Drug Delivery System” leads to ultrafast release of a loaded doxorubicin drug, triggered and controlled in the micro-vasculature of tumors by applied mild hyperthermia. This formulation approach, as ThermoDox®, has been used in a completed 700-patient Phase III human clinical trial in liver cancer (HEAT study), is in a Phase II trial in chest wall recurrence of cancer (DIGNITY study) and has been used in a Phase I trial of patients with colorectal liver metastases (ABLATE study). With additional research and preclinical studies underway, and a range of other drugs, imaging agents and biological modifiers poised for encapsulation, the LTSL could provide a new paradigm for drug and agent delivery for the treatment of localized tumors: rapid triggered drug release in the tumor bloodstream and deep penetration of drug into the tumor tissue.
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Affiliation(s)
- David Needham
- Department of Mechanical Engineering and Material Science Duke University, Durham NC 27705, USA, and DNRF Niels Bohr Professor, and HCA Academy Visiting Professor, University Southern Denmark DK-5230 Odense M, Denmark
| | - Mark W. Dewhirst
- Gustavo S. Montana Professor Director of Tumor Microcirculation Laboratory, Department of Radiation Oncology, Duke University Medical Center, Duke University, Durham, NC 27708 USA
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745
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Pan J, Heberle FA, Petruzielo RS, Katsaras J. Using small-angle neutron scattering to detect nanoscopic lipid domains. Chem Phys Lipids 2013; 170-171:19-32. [PMID: 23518250 DOI: 10.1016/j.chemphyslip.2013.02.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 02/27/2013] [Accepted: 02/28/2013] [Indexed: 11/25/2022]
Abstract
The cell plasma membrane is a complex system, which is thought to be capable of exhibiting non-random lateral organization. Studies of live cells and model membranes have yielded mechanisms responsible for the formation, growth, and maintenance of nanoscopic heterogeneities, although the existence and mechanisms that give rise to these heterogeneities remain controversial. Small-angle neutron scattering (SANS) is a tool ideally suited to interrogate lateral heterogeneity in model membranes, primarily due to its unique spatial resolution (i.e., ~5-100nm) and its ability to resolve structure with minimal perturbation to the membrane. In this review we examine several methods used to analyze the SANS signal arising from freely suspended unilamellar vesicles containing lateral heterogeneity. Specifically, we discuss an analytical model for a single, round domain on a spherical vesicle. We then discuss a numerical method that uses Monte Carlo simulation to describe systems with multiple domains and/or more complicated morphologies. Also discussed are several model-independent approaches that are sensitive to membrane heterogeneity. The review concludes with several recent applications of SANS to the study of membrane raft mixtures.
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Affiliation(s)
- Jianjun Pan
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
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746
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Pester O, Barrett PJ, Hornburg D, Hornburg P, Pröbstle R, Widmaier S, Kutzner C, Dürrbaum M, Kapurniotu A, Sanders CR, Scharnagl C, Langosch D. The backbone dynamics of the amyloid precursor protein transmembrane helix provides a rationale for the sequential cleavage mechanism of γ-secretase. J Am Chem Soc 2013; 135:1317-29. [PMID: 23265086 PMCID: PMC3560327 DOI: 10.1021/ja3112093] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The etiology of Alzheimer's disease depends on the relative abundance of different amyloid-β (Aβ) peptide species. These peptides are produced by sequential proteolytic cleavage within the transmembrane helix of the 99 residue C-terminal fragment of the amyloid precursor protein (C99) by the intramembrane protease γ-secretase. Intramembrane proteolysis is thought to require local unfolding of the substrate helix, which has been proposed to be cleaved as a homodimer. Here, we investigated the backbone dynamics of the substrate helix. Amide exchange experiments of monomeric recombinant C99 and of synthetic transmembrane domain peptides reveal that the N-terminal Gly-rich homodimerization domain exchanges much faster than the C-terminal cleavage region. MD simulations corroborate the differential backbone dynamics, indicate a bending motion at a diglycine motif connecting dimerization and cleavage regions, and detect significantly different H-bond stabilities at the initial cleavage sites. Our results are consistent with the following hypotheses about cleavage of the substrate: First, the GlyGly hinge may precisely position the substrate within γ-secretase such that its catalytic center must start proteolysis at the known initial cleavage sites. Second, the ratio of cleavage products formed by subsequent sequential proteolysis could be influenced by differential extents of solvation and by the stabilities of H-bonds at alternate initial sites. Third, the flexibility of the Gly-rich domain may facilitate substrate movement within the enzyme during sequential proteolysis. Fourth, dimerization may affect substrate processing by decreasing the dynamics of the dimerization region and by increasing that of the C-terminal part of the cleavage region.
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Affiliation(s)
- Oxana Pester
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Paul J. Barrett
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Daniel Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Philipp Hornburg
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Rasmus Pröbstle
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Simon Widmaier
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Christoph Kutzner
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Milena Dürrbaum
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
| | - Aphrodite Kapurniotu
- Fachgebiet Peptidbiochemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Charles R. Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee USA 37232-8725
| | - Christina Scharnagl
- Fakultät für Physik E14, Technische Universität München, Maximus-von-Imhof-Forum 4, 85354 Freising, Germany
| | - Dieter Langosch
- Lehrstuhl Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, and Munich Center For Integrated Protein Science (CIPS), Germany
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747
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A Coarse-Grained Molecular Dynamics Study of DLPC, DMPC, DPPC, and DSPC Mixtures in Aqueous Solution. J CHEM-NY 2013. [DOI: 10.1155/2013/931051] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural and dynamics properties of the bilayer comprising 128 molecules of dipalmitoylphosphatidylcholine (DPPC), dilauroylphosphatidylcholine (DLPC), dimyristoylphosphatidylcholine (DMPC), and distearoylphosphatidylcholine (DSPC) in water were investigated using a coarse-grained molecular dynamics (CG-MD) simulation technique. The model mixture system was simulated at 298 K under semi-isotropic pressure conditions. The aggregation was initiated from the random configurations followed by the formation of a bilayer over a period of 500 ns. The calculated values of the area per lipid, thickness, and lateral diffusion for the mixed model were different from when a single lipid was used. Our results confirmed that the chain length of the lipid molecules strongly affects the phospholipid bilayer’s physical properties.
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748
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Abstract
One of the many aspects of membrane biophysics dealt with in this Faraday Discussion regards the material moduli that describe energies at a supramolecular level. This introductory lecture first critically reviews differences in reported numerical values of the bending modulus K(C), which is a central property for the biologically important flexibility of membranes. It is speculated that there may be a reason that the shape analysis method tends to give larger values of K(C) than the micromechanical manipulation method or the more recent X-ray method that agree very well with each other. Another theme of membrane biophysics is the use of simulations to provide exquisite detail of structures and processes. This lecture critically reviews the application of atomic level simulations to the quantitative structure of simple single component lipid bilayers and diagnostics are introduced to evaluate simulations. Another theme of this Faraday Discussion was lateral heterogeneity in biomembranes with many different lipids. Coarse grained simulations and analytical theories promise to synergistically enhance experimental studies when their interaction parameters are tuned to agree with experimental data, such as the slopes of experimental tie lines in ternary phase diagrams. Finally, attention is called to contributions that add relevant biological molecules to bilayers and to contributions that study the exciting shape changes and different non-bilayer structures with different lipids.
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Affiliation(s)
- John F Nagle
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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749
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Moore SJ, Haynes CJE, González J, Sutton JL, Brooks SJ, Light ME, Herniman J, Langley GJ, Soto-Cerrato V, Pérez-Tomás R, Marques I, Costa PJ, Félix V, Gale PA. Chloride, carboxylate and carbonate transport by ortho-phenylenediamine-based bisureas. Chem Sci 2013. [DOI: 10.1039/c2sc21112b] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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750
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Pan J, Cheng X, Heberle FA, Mostofian B, Kučerka N, Drazba P, Katsaras J. Interactions between ether phospholipids and cholesterol as determined by scattering and molecular dynamics simulations. J Phys Chem B 2012. [PMID: 23199292 DOI: 10.1021/jp310345j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol's molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup's phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.
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Affiliation(s)
- Jianjun Pan
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.
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