101
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Ghaed-Sharaf T, Yang DS, Baldelli S, Ghatee MH. From Micelles to Vesicle and Membrane Structures of Double-Strand Ionic Liquids in Water: Molecular Dynamics Simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:2780-2791. [PMID: 30681341 DOI: 10.1021/acs.langmuir.8b03773] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The structures of novel double-strand imidazolium iodide ionic liquids (ILs)-based lipid in the water phase have been studied in this research. We report the effect of alkyl chain length of 1,3-dimethyl-4,5-dialkyl-imidazolium iodide([2(Me)2(C n)im]I, n = 7, 11, 15) ILs on their structures in the aqueous solution by molecular dynamics simulation. The structure details of IL clusters lead to the various aggregation forms by increasing the alkyl chain length of ILs. The ILs with n = 7 and 11 can help develop micelle structures of different sizes, and the IL with n = 15, the benign IL, feasible to develop lipidlike vesicle. To obtain more details about bilayer properties, [2(Me)2(C15)im]I IL is investigated by different IL/water ratios in this study exclusively. The [2(Me)2(C15)im]I IL bilayer thickness and deuterium order parameters are compared with lipid membrane, and they reveal a small difference. The energies, radial distribution functions, spatial distribution function, cluster size, number density, and membrane properties all prove that the stable IL vesicle is formed in the dilute solution but the membrane is formed in the concentrated aqueous solution of [2(Me)2(C15)im]I.
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Affiliation(s)
| | - Ding-Shyue Yang
- Department of Chemistry , University of Houston , Houston , Texas 77204-5003 , United States
| | - Steven Baldelli
- Department of Chemistry , University of Houston , Houston , Texas 77204-5003 , United States
| | - Mohammad Hadi Ghatee
- Department of Chemistry , Shiraz University , Shiraz 71946 , Iran
- Department of Chemistry , University of Houston , Houston , Texas 77204-5003 , United States
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102
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Bédard F, Fliss I, Biron E. Structure-Activity Relationships of the Bacteriocin Bactofencin A and Its Interaction with the Bacterial Membrane. ACS Infect Dis 2019; 5:199-207. [PMID: 30540905 DOI: 10.1021/acsinfecdis.8b00204] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The antimicrobial peptide bactofencin A is an unmodified non-pediocin-like bacteriocin that inhibits several clinically relevant pathogens, including Listeria monocytogenes and Staphylococcus aureus. Here we report the synthesis and structure-activity relationship studies of bactofencin A and novel analogues thereof. Synthetic bactofencin A was a potent inhibitor of L. monocytogenes (MIC = 8.0 μM) and S. aureus (MIC = 4.0 μM), similar to the bacteriocin produced naturally by Lactobacillus salivarius. Of particular interest is the fact that linear analogues lacking the disulfide bond found in bactofencin A were as potent and also active against several strains of methicillin-resistant S. aureus (MRSA) and one strain of vancomycin-resistant S. aureus (VRSA). Supported by the structure-activity relationship study, investigation of the interaction of bactofencin A with bacterial membrane by molecular dynamics simulations showed the importance of the positively charged N-terminal tail for peptide-membrane interaction. These results suggest that the C-terminal macrocycle is involved in target protein binding and bacterial growth inhibition.
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Affiliation(s)
- François Bédard
- Faculty of Pharmacy and Institute of Nutrition and Functional Foods, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory of Medicinal Chemistry, CHU de Québec Research Centre, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Ismail Fliss
- STELA Dairy Research Centre, Institute of Nutrition and Functional Foods, Université Laval, Québec, Québec G1V 0A6, Canada
| | - Eric Biron
- Faculty of Pharmacy and Institute of Nutrition and Functional Foods, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory of Medicinal Chemistry, CHU de Québec Research Centre, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
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103
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Jan Akhunzada M, D'Autilia F, Chandramouli B, Bhattacharjee N, Catte A, Di Rienzo R, Cardarelli F, Brancato G. Interplay between lipid lateral diffusion, dye concentration and membrane permeability unveiled by a combined spectroscopic and computational study of a model lipid bilayer. Sci Rep 2019; 9:1508. [PMID: 30728410 PMCID: PMC6365552 DOI: 10.1038/s41598-018-37814-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023] Open
Abstract
Lipid lateral diffusion in membrane bilayers is a fundamental process exploited by cells to enable complex protein structural and dynamic reorganizations. For its importance, lipid mobility in both cellular and model bilayers has been extensively investigated in recent years, especially through the application of time-resolved, fluorescence-based, optical microscopy techniques. However, one caveat of fluorescence techniques is the need to use dye-labeled variants of the lipid of interest, thus potentially perturbing the structural and dynamic properties of the native species. Generally, the effect of the dye/tracer molecule is implicitly assumed to be negligible. Nevertheless, in view of the widespread use of optically modified lipids for studying lipid bilayer dynamics, it is highly desirable to well assess this point. Here, fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations have been combined together to uncover subtle structural and dynamic effects in DOPC planar membranes enriched with a standard Rhodamine-labeled lipid. Our findings support a non-neutral role of the dye-labeled lipids in diffusion experiments, quantitatively estimating a decrease in lipid mobility of up to 20% with respect to the unlabeled species. Moreover, results highlight the existing interplay between dye concentration, lipid lateral diffusion and membrane permeability, thus suggesting possible implications for future optical microscopy studies of biophysical processes occurring at the membrane level.
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Affiliation(s)
- Muhammad Jan Akhunzada
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126, Pisa, Italy.,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100, Pisa, Italy
| | | | - Balasubramanian Chandramouli
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126, Pisa, Italy.,Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163, Genova, Italy
| | - Nicholus Bhattacharjee
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126, Pisa, Italy.,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100, Pisa, Italy
| | - Andrea Catte
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126, Pisa, Italy.,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100, Pisa, Italy
| | - Roberto Di Rienzo
- Dipartimento di Ingegneria dell'Informazione, Università di Pisa, Via Girolamo Caruso 16, I-56122 Pisa, Italy
| | - Francesco Cardarelli
- NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, 56127, Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126, Pisa, Italy. .,Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100, Pisa, Italy.
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104
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Ruiz-Fernández AR, Tejos R, Ahumada-Gutierrez H, Muñoz-Gacitúa D, Martínez-Cifuentes M, Araya-Maturana R, Weiss-López BE. Characterisation of a new nematic lyotropic liquid crystal with natural lipids from soybean. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1504131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- A. R. Ruiz-Fernández
- Laboratorio de Fisicoquímica Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - R. Tejos
- Facultad de Recursos Naturales, Universidad Arturo Prat, Iquique, Chile
| | - H. Ahumada-Gutierrez
- Laboratorio de Química y Productos Naturales, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío Bío, Chillan, Chile
| | - D. Muñoz-Gacitúa
- Laboratorio de Fisicoquímica Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - M. Martínez-Cifuentes
- Programa Institucional de Fomento a la I+D+i, Universidad Tecnológica Metropolitana, Santiago, Chile
| | - R. Araya-Maturana
- Universidad de Talca, Instituto de Química de Recursos Naturales, Talca, Chile
| | - B. E. Weiss-López
- Laboratorio de Fisicoquímica Molecular, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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105
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Rajagopal N, Irudayanathan FJ, Nangia S. Palmitoylation of Claudin-5 Proteins Influences Their Lipid Domain Affinity and Tight Junction Assembly at the Blood–Brain Barrier Interface. J Phys Chem B 2019; 123:983-993. [DOI: 10.1021/acs.jpcb.8b09535] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Nandhini Rajagopal
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse 13244, United States
| | | | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse 13244, United States
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106
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Smith DJ, Klauda JB, Sodt AJ. Simulation Best Practices for Lipid Membranes [Article v1.0]. LIVING JOURNAL OF COMPUTATIONAL MOLECULAR SCIENCE 2019; 1:5966. [PMID: 36204133 PMCID: PMC9534443 DOI: 10.33011/livecoms.1.1.5966] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
We establish a reliable and robust standardization of settings for practical molecular dynamics (MD) simulations of pure and mixed (single- and multi-component) lipid bilayer membranes. In lipid membranes research, particle-based molecular simulations are a powerful tool alongside continuum theory, lipidomics, and model, in vitro, and in vivo experiments. Molecular simulations can provide precise and reproducible spatiotemporal (atomic- and femtosecond-level) information about membrane structure, mechanics, thermodynamics, kinetics, and dynamics. Yet the simulation of lipid membranes can be a daunting task, given the uniqueness of lipid membranes relative to conventional liquid-liquid and solid-liquid interfaces, the immense and complex thermodynamic and statistical mechanical theory, the diversity of multiscale lipid models, limitations of modern computing power, the difficulty and ambiguity of simulation controls, finite size effects, competitive continuum simulation alternatives, and the desired application, including vesicle experiments and biological membranes. These issues can complicate an essential understanding of the field of lipid membranes, and create major bottlenecks to simulation advancement. In this article, we clarify these issues and present a consistent, thorough, and user-friendly framework for the design of state-of-the-art lipid membrane MD simulations. We hope to allow early-career researchers to quickly overcome common obstacles in the field of lipid membranes and reach maximal impact in their simulations.
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Affiliation(s)
- David J. Smith
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering and Biophysics Program, University of Maryland, College Park, MD, USA
| | - Alexander J. Sodt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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107
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Moradi S, Nowroozi A, Shahlaei M. Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study. RSC Adv 2019; 9:4644-4658. [PMID: 35520151 PMCID: PMC9060685 DOI: 10.1039/c8ra08441f] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 03/12/2019] [Accepted: 01/16/2019] [Indexed: 12/20/2022] Open
Abstract
This review gives an overview about the some of the most important possible analyzes, technical challenges, and existing protocols that can be performed on the biological membrane by the molecular dynamics simulation.
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Affiliation(s)
- Sajad Moradi
- Nano Drug Delivery Research Center
- Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center
- Faculty of Pharmacy
- Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Mohsen Shahlaei
- Medical Biology Research Center
- Kermanshah University of Medical Sciences
- Kermanshah
- Iran
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108
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Tissera MJE, Disalvo EA, Martini MF, Cutró AC. Filling gaps in the knowledge of melittin on lipid membranes. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2018.10.055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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109
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Bonvicini A, Reinholdt P, Tognetti V, Joubert L, Wüstner D, Kongsted J. Rational design of novel fluorescent analogues of cholesterol: a “step-by-step” computational study. Phys Chem Chem Phys 2019; 21:15487-15503. [DOI: 10.1039/c9cp01902b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
State-of-the-art quantum chemical and molecular dynamics simulations are used as guidelines in design of novel fluorescent analogues of cholesterol.
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Affiliation(s)
- Andrea Bonvicini
- Normandy Univ. COBRA UMR 6014 & FR 3038
- Université de Rouen
- INSA Rouen
- CNRS
- 76821 Mont Saint Aignan
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- Odense M
- Denmark
| | - Vincent Tognetti
- Normandy Univ. COBRA UMR 6014 & FR 3038
- Université de Rouen
- INSA Rouen
- CNRS
- 76821 Mont Saint Aignan
| | - Laurent Joubert
- Normandy Univ. COBRA UMR 6014 & FR 3038
- Université de Rouen
- INSA Rouen
- CNRS
- 76821 Mont Saint Aignan
| | - Daniel Wüstner
- Department of Biochemistry and Molecular Biology
- University of Southern Denmark
- DK-5230 Odense
- Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- Odense M
- Denmark
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110
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Arvayo-Zatarain JA, Favela-Rosales F, Contreras-Aburto C, Urrutia-Bañuelos E, Maldonado A. Molecular dynamics simulation study of the effect of halothane on mixed DPPC/DPPE phospholipid membranes. J Mol Model 2018; 25:4. [PMID: 30554281 DOI: 10.1007/s00894-018-3890-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 12/03/2018] [Indexed: 11/26/2022]
Abstract
We report results of a molecular dynamics simulation study of the effect of one general anesthetic, halothane, on some properties of mixed DPPC/DPPE phospholipid membranes. This is a suitable model for the study of simple, two-phospholipid membrane systems. From the simulation runs, we determined several membrane properties for five different molecular proportions of DPPC/DPPE. The effect of halothane on the studied membrane properties (area per lipid molecule, density of membrane, order parameter, etc.) was rather small. The distribution of halothane is not uniform through the bilayer thickness. Instead, there is a maximum of anesthetic concentration around 1.2 nm from the center of the membrane. The anesthetic molecule is located close to the phospholipid headgroups. The position of the halothane density maximum depends slightly on the DPPC/DPPE molar proportion. Snapshots taken over the plane of the membrane, as well as calculated two-dimensional radial distribution functions show that the anesthetic has no preference for either phospholipid (DPPC or DPPE). Our results indicate that this anesthetic molecule has only small effects on DPPC/DPPE mixed membranes. In addition, halothane displays no preferential location around DPPC or DPPE. This is probably due to the hydrophobic nature of halothane and to the fact that the chosen phospholipids have the same hydrophobic tails.
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Affiliation(s)
| | - Fernando Favela-Rosales
- Departamento de Investigación, Instituto Tecnológico Superior Zacatecas Occidente, Ave. Tecnológico 2000, 99102, Sombrerete, Zacatecas, Mexico
| | - Claudio Contreras-Aburto
- Facultad de Ciencias en Física y Matemáticas, Universidad Autónoma de Chiapas, Carretera Emiliano Zapata km 8, 29050, Tuxtla Gutiérrez, Chiapas, Mexico
| | - Efrain Urrutia-Bañuelos
- Departamento de Investigación en Física, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, Mexico
| | - Amir Maldonado
- Departamento de Física, Universidad de Sonora, Rosales y Luis Encinas s/n, 83000, Hermosillo, Sonora, Mexico.
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111
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Maity A, Sinha S, Ghosh Dastidar S. Dissecting the thermodynamic contributions of the charged residues in the membrane anchoring of Bcl-xl C-terminal domain. Chem Phys Lipids 2018; 218:112-124. [PMID: 30550879 DOI: 10.1016/j.chemphyslip.2018.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 11/20/2018] [Accepted: 12/09/2018] [Indexed: 11/28/2022]
Abstract
The C-terminal helix of the Bcl-xl is known to initiate the membrane insertion of the protein by anchoring into the mitochondrial outer membrane. The C-terminal charged residues of that helix, R232 and K233, are reported to have an important structural role in the process of that insertion. The present work provides a quantitative understanding of the thermodynamic contribution of these residues on the membrane insertion energy-profile, calculated from the Adaptive Biasing Force based MD simulations of 2.67 μs altogether. Interestingly, the effect of the single neutralizing mutations at the C-terminus, i.e. K233A or R232A, is easily tolerated by the peptide without impacting the nature of insertion energy-profile, indicating the efficiency of one positively charged residue to drive the insertion. Whereas a double mutant, i.e. R232A and K233A, makes a significant impact on the energy-profile by destabilizing the membrane-associated states, as well as the membrane-embedded states. The finding provides molecular-level mechanistic insight. The water-mediated interaction formed by the peptide polar side chains within the bilayer core is found to modulate the membrane response during peptide insertion and that subsequently regulates the insertion mechanism. Mutation of the C-terminal residues eventually alters such a cascade of interactions that results in an insertion through energetically more expensive pathway. Since any one of the positively charged residues at the terminal is critical to ensure the membrane insertion, it appears that the natural selection of 'two' instead of 'one' charged residue is redundant in the context of membrane anchoring but may be important for other biochemical events.
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Affiliation(s)
- Atanu Maity
- Division of Bioinformatics, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata, 700054, India
| | - Souvik Sinha
- Division of Bioinformatics, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata, 700054, India
| | - Shubhra Ghosh Dastidar
- Division of Bioinformatics, Bose Institute, P-1/12 C.I.T. Scheme VII M, Kolkata, 700054, India.
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112
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Jung J, Kobayashi C, Sugita Y. Optimal Temperature Evaluation in Molecular Dynamics Simulations with a Large Time Step. J Chem Theory Comput 2018; 15:84-94. [PMID: 30468577 DOI: 10.1021/acs.jctc.8b00874] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In molecular dynamics (MD) simulations, an accurate evaluation of temperature is essential for controlling temperature as well as pressure in the isothermal-isobaric conditions. According to the Tolman's equipartition theorem, all motions of all particles should share a single temperature. However, conventional temperature estimation from kinetic energy does not include Hessian terms properly, and thereby, the equipartition theorem is not satisfied with a large time step. In this paper, we show how to evaluate temperature the most accurately without increasing computational cost. We define two kinds of kinetic energies, evaluated at full- and half-time steps that underestimate or overestimate temperature, respectively. A combination of these two kinetic energies provides an optimal instantaneous temperature up to the third order of the time step. The method is tested for a one-dimensional harmonic oscillator, pure water molecules, a Bovine pancreatic trypsin inhibitor (BPTI) protein in water molecules, and a hydrated 1,2-dispalmitoyl- sn-phosphatidylcholine (DPPC) lipid bilayer in water molecules. In all tests, the optimal temperature estimator fulfills the equipartition theorem better than existing methods and reproduces well the usual physical properties for time steps up to and including 5 fs.
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Affiliation(s)
- Jaewoon Jung
- Theoretical Molecular Science Laboratory , RIKEN Cluster for Pioneering Research , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,Computational Biophysics Research Team , RIKEN Center for Computational Science , 7-1-26 Minatojima-minamimachi , Chuo-ku, Kobe , Hyogo 650-0047 , Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team , RIKEN Center for Computational Science , 7-1-26 Minatojima-minamimachi , Chuo-ku, Kobe , Hyogo 650-0047 , Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory , RIKEN Cluster for Pioneering Research , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,Computational Biophysics Research Team , RIKEN Center for Computational Science , 7-1-26 Minatojima-minamimachi , Chuo-ku, Kobe , Hyogo 650-0047 , Japan.,Laboratory for Biomolecular Function Simulation , RIKEN Center for Biosystems Dynamics Research , 6-7-1 Minatojima-minamimachi , Chuo-ku, Kobe , Hyogo 650-0047 , Japan
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113
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Leeb F, Maibaum L. Spatially Resolving the Condensing Effect of Cholesterol in Lipid Bilayers. Biophys J 2018; 115:2179-2188. [PMID: 30447996 DOI: 10.1016/j.bpj.2018.10.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 10/15/2018] [Accepted: 10/24/2018] [Indexed: 11/15/2022] Open
Abstract
We study the effect of cholesterol on the structure of dipalmitoylphosphatidylcholine phospholipid bilayers. Using extensive molecular dynamics computer simulations at atomistic resolution, we observe and quantify several structural changes upon increasing cholesterol content that are collectively known as the condensing effect: a thickening of the bilayer, an increase in lipid tail order, and a decrease in lateral area. We also observe a change in leaflet interdigitation and a lack thereof in the distributions of dipalmitoylphosphatidylcholine headgroup orientations. These results, obtained over a wide range of cholesterol mole fractions, are then used to calibrate the analysis of phospholipid properties in bilayers containing a single cholesterol molecule per leaflet, which we perform in a spatially resolved way. We find that a single cholesterol molecule affects phospholipids in its first and second solvation shells, which puts the range of this effective interaction to be on the order of 1-2 nm. We also observe a tendency of phospholipids to orient their polar headgroups toward the cholesterol, which provides additional support for the umbrella model of bilayer organization.
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Affiliation(s)
- Felix Leeb
- Department of Chemistry, University of Washington, Seattle, Washington
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington.
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114
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Qian Z, Zou Y, Zhang Q, Chen P, Ma B, Wei G, Nussinov R. Atomistic-level study of the interactions between hIAPP protofibrils and membranes: Influence of pH and lipid composition. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1818-1825. [PMID: 29428499 PMCID: PMC6408309 DOI: 10.1016/j.bbamem.2018.02.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/01/2018] [Accepted: 02/03/2018] [Indexed: 01/25/2023]
Abstract
The pathology of type 2 diabetes mellitus is associated with the aggregation of human islet amyloid polypeptide (hIAPP) and aggregation-mediated membrane disruption. The interactions of hIAPP aggregates with lipid membrane, as well as the effects of pH and lipid composition at the atomic level, remain elusive. Herein, using molecular dynamics simulations, we investigate the interactions of hIAPP protofibrillar oligomers with lipids, and the membrane perturbation that they induce, when they are partially inserted in an anionic dipalmitoyl-phosphatidylglycerol (DPPG) membrane or a mixed dipalmitoyl-phosphatidylcholine (DPPC)/DPPG (7:3) lipid bilayer under acidic/neutral pH conditions. We observed that the tilt angles and insertion depths of the hIAPP protofibril are strongly correlated with the pH and lipid composition. At neutral pH, the tilt angle and insertion depth of hIAPP protofibrils at a DPPG bilayer reach ~52° and ~1.62 nm with respect to the membrane surface, while they become ~77° and ~1.75 nm at a mixed DPPC/DPPG membrane. The calculated tilt angle of hIAPP at DPPG membrane is consistent with a recent chiral sum frequency generation spectroscopic study. The acidic pH induces a smaller tilt angle of ~40° and a shallower insertion depth (~1.24 nm) of hIAPP at the DPPG membrane surface, mainly due to protonation of His18 near the turn region. These differences mainly result from a combination of distinct electrostatic, van der Waals, hydrogen bonding and salt-bridge interactions between hIAPP and lipid bilayers. The hIAPP-membrane interaction energy analysis reveals that besides charged residues K1, R11 and H18, aromatic residues Phe15 and Phe23 also exhibit strong interactions with lipid bilayers, revealing the crucial role of aromatic residues in stabilizing the membrane-bound hIAPP protofibrils. hIAPP-membrane interactions disturb the lipid ordering and the local bilayer thickness around the peptides. Our results provide atomic-level information of membrane interaction of hIAPP protofibrils, revealing pH-dependent and membrane-modulated hIAPP aggregation at the early stage.
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Affiliation(s)
- Zhenyu Qian
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China; Department of Physics, State Key Laboratory of Surface physics, Key Laboratory for Computational Physical Science (Ministry of Education), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, China
| | - Yu Zou
- College of Physical Education and Training, Shanghai University of Sport, Shanghai 200438, China
| | - Qingwen Zhang
- College of Physical Education and Training, Shanghai University of Sport, Shanghai 200438, China
| | - Peijie Chen
- Key Laboratory of Exercise and Health Sciences (Ministry of Education) and School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface physics, Key Laboratory for Computational Physical Science (Ministry of Education), and Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, China.
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, MD 21702, United States; Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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115
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Navarro-Retamal C, Bremer A, Ingólfsson HI, Alzate-Morales J, Caballero J, Thalhammer A, González W, Hincha DK. Folding and Lipid Composition Determine Membrane Interaction of the Disordered Protein COR15A. Biophys J 2018; 115:968-980. [PMID: 30195939 DOI: 10.1016/j.bpj.2018.08.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/27/2018] [Accepted: 08/13/2018] [Indexed: 01/02/2023] Open
Abstract
Plants from temperate climates, such as the model plant Arabidopsis thaliana, are challenged with seasonal low temperatures that lead to increased freezing tolerance in fall in a process termed cold acclimation. Among other adaptations, this involves the accumulation of cold-regulated (COR) proteins, such as the intrinsically disordered chloroplast-localized protein COR15A. Together with its close homolog COR15B, it stabilizes chloroplast membranes during freezing. COR15A folds into amphipathic α-helices in the presence of high concentrations of low-molecular-mass crowders or upon dehydration. Under these conditions, the (partially) folded protein binds peripherally to membranes. In our study, we have used coarse-grained molecular dynamics simulations to elucidate the details of COR15A-membrane binding and its effects on membrane structure and dynamics. Simulation results indicate that at least partial folding of COR15A and the presence of highly unsaturated galactolipids in the membranes are necessary for efficient membrane binding. The bound protein is stabilized on the membrane by interactions of charged and polar amino acids with galactolipid headgroups and by interactions of hydrophobic amino acids with the upper part of the fatty acyl chains. Experimentally, the presence of liposomes made from a mixture of lipids mimicking chloroplast membranes induces additional folding in COR15A under conditions of partial dehydration, in agreement with the simulation results.
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Affiliation(s)
- Carlos Navarro-Retamal
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, Casilla, Talca, Chile
| | - Anne Bremer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, AG Groningen, The Netherlands
| | - Jans Alzate-Morales
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, Casilla, Talca, Chile
| | - Julio Caballero
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, Casilla, Talca, Chile
| | - Anja Thalhammer
- Physikalische Biochemie, Universität Potsdam, Potsdam, Germany
| | - Wendy González
- Center for Bioinformatics and Molecular Simulations, Universidad de Talca, Casilla, Talca, Chile; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Casilla, Talca, Chile
| | - Dirk K Hincha
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany.
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Sajadi F, Rowley CN. Simulations of lipid bilayers using the CHARMM36 force field with the TIP3P-FB and TIP4P-FB water models. PeerJ 2018; 6:e5472. [PMID: 30128211 PMCID: PMC6097494 DOI: 10.7717/peerj.5472] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/28/2018] [Indexed: 12/13/2022] Open
Abstract
The CHARMM36 force field for lipids is widely used in simulations of lipid bilayers. The CHARMM family of force fields were developed for use with the mTIP3P water model. This water model has an anomalously high dielectric constant and low viscosity, which limits its accuracy in the calculation of quantities like permeability coefficients. The TIP3P-FB and TIP4P-FB water models are more accurate in terms of the dielectric constant and transport properties, which could allow more accurate simulations of systems containing water and lipids. To test whether the CHARMM36 lipid force field is compatible with the TIP3P-FB and TIP4P-FB water models, we have performed simulations of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayers. The calculated headgroup area, compressibility, order parameters, and X-ray form factors are in good agreement with the experimental values, indicating that these improved water models can be used with the CHARMM36 lipid force field without modification when calculating membrane physical properties. The water permeability predicted by these models is significantly different; the mTIP3P-model diffusion in solution and at the lipid-water interface is anomalously fast due to the spuriously low viscosity of mTIP3P-model water, but the potential of mean force of permeation is higher for the TIP3P-FB and TIP4P-FB models due to their high excess chemical potentials. As a result, the rates of water permeation calculated the FB water models are slower than the experimental value by a factor of 15-17, while simulations with the mTIP3P model only underestimate the water permeability by a factor of 3.
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Affiliation(s)
- Fatima Sajadi
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, Canada
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117
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Lajunen T, Nurmi R, Wilbie D, Ruoslahti T, Johansson NG, Korhonen O, Rog T, Bunker A, Ruponen M, Urtti A. The effect of light sensitizer localization on the stability of indocyanine green liposomes. J Control Release 2018; 284:213-223. [DOI: 10.1016/j.jconrel.2018.06.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/19/2018] [Accepted: 06/25/2018] [Indexed: 10/28/2022]
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118
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Knippenberg S, Fabre G, Osella S, Di Meo F, Paloncýová M, Ameloot M, Trouillas P. Atomistic Picture of Fluorescent Probes with Hydrocarbon Tails in Lipid Bilayer Membranes: An Investigation of Selective Affinities and Fluorescent Anisotropies in Different Environmental Phases. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9072-9084. [PMID: 29983063 DOI: 10.1021/acs.langmuir.8b01164] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
By reverting to spectroscopy, changes in the biological environment of a fluorescent probe can be monitored and the presence of various phases of the surrounding lipid bilayer membranes can be detected. However, it is currently not always clear in which phase the probe resides. The well-known orange 1,1'-dioctadecyl-3,3,3',3'-tetramethylindodicarbo-cyanine perchlorate (DiI-C18(5)) fluorophore, for instance, and the new, blue BODIPY (4,4-difluoro-4-bora-3 a,4 a-diaza- s-indacene) derivative were experimentally seen to target and highlight identical parts of giant unilamellar vesicles of various compositions, comprising mixtures of dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylcholine (DOPC), sphingomyelin (SM), and cholesterol (Chol). However, it was not clear which of the coexisting membrane phases were visualized (Bacalum et al., Langmuir. 2016, 32, 3495). The present study addresses this issue by utilizing large-scale molecular dynamics simulations and the z-constraint method, which allows evaluating Gibbs free-energy profiles. The current calculations give an indication why, at room temperature, both BODIPY and DiI-C18(5) probes prefer the gel (So) phase in DOPC/DPPC (2:3 molar ratio) and the liquid-ordered (Lo) phase in DOPC/SM/Chol (1:2:1 molar ratio) mixtures. This study highlights the important differences in orientation and location and therefore in efficiency between the probes when they are used in fluorescence microscopy to screen various lipid bilayer membrane phases. Dependent on the lipid composition, the angle between the transition-state dipole moments of both probes and the normal to the membrane is found to deviate clearly from 90°. It is seen that the DiI-C18(5) probe is located in the headgroup region of the SM/Chol mixture, in close contact with water molecules. A fluorescence anisotropy study also indicates that DiI-C18(5) gives rise to a distinctive behavior in the SM/Chol membrane compared to the other considered membranes. The latter behavior has not been seen for the studied BODIPY probe, which is located deeper in the membrane.
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Affiliation(s)
- S Knippenberg
- Department of Theoretical Chemistry and Biology , KTH Royal Institute of Technology , Roslagstullsbacken 15 , S-106 91 Stockholm , Sweden
- Biomedical Research Institute , Hasselt University , Agoralaan Building C , 3590 Diepenbeek , Belgium
| | - G Fabre
- LCSN-EA1069, Faculty of Pharmacy , Limoges University , 2 rue du Dr. Marcland , 87025 Limoges Cedex , France
| | - S Osella
- Centre of New Technologies , University of Warsaw , Banacha 2C , 02-097 Warsaw , Poland
| | - F Di Meo
- Faculty of Pharmacy , INSERM UMR 1248, Limoges University , 2 rue du Docteur Marcland , 87025 Limoges Cedex , France
| | - M Paloncýová
- Department of Theoretical Chemistry and Biology , KTH Royal Institute of Technology , Roslagstullsbacken 15 , S-106 91 Stockholm , Sweden
| | - M Ameloot
- Biomedical Research Institute , Hasselt University , Agoralaan Building C , 3590 Diepenbeek , Belgium
| | - P Trouillas
- Faculty of Pharmacy , INSERM UMR 1248, Limoges University , 2 rue du Docteur Marcland , 87025 Limoges Cedex , France
- Centre of Advanced Technologies and Materials, Faculty of Science , Palacký University , tř. 17 listopadu 12 , 771 46 Olomouc , Czech Republic
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119
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Khondker A, Malenfant DJ, Dhaliwal AK, Rheinstädter MC. Carbapenems and Lipid Bilayers: Localization, Partitioning, and Energetics. ACS Infect Dis 2018; 4:926-935. [PMID: 29582993 DOI: 10.1021/acsinfecdis.7b00156] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbapenems are broad-spectrum antibiotics used today to treat otherwise antibiotic resistant bacteria. As their target transpeptidase is located within the periplasm of the Gram-negative bacteria, they can participate in nonspecific interactions between the inner leaflet of the outer membrane and the outer leaflet of the inner membrane. We, therefore, studied the interaction of the four most clinically relevant carbapenems, namely, imipenem, doripenem, ertapenem, and meropenem, with model phospholipid bilayers made of 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) using molecular dynamics (MD) simulations and X-ray diffraction at low and high concentration of the drugs corresponding to 1 and 8 mol % (with respect to the number of membrane lipids). Membrane solubility was found to decrease from imipenem to doripenem, ertapenem, and finally meropenem. At low concentrations, membrane insertion was found to be a two step process, where the drugs first adsorb to the lipid head groups before inserting through a rotation of the molecule. At higher drug concentrations, the molecules were found to form aggregates in the aqueous phase before making contact with the membranes and spontaneously inserting into the bilayers. Two populations of imipenem were found: in the headgroup at ∼17 Å from the bilayer center and an inserted population at z-values of about 7 Å. Other carbapenems were found to localize in the tail groups with meropenem at ∼10 Å, doripenem at ∼8 Å, and ertapenem at ∼8 Å. The observed membrane solubility of carbapenems can potentially impact the availability of the drug to the target penicillin-binding proteins, potentially affecting their clinical efficacy.
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Affiliation(s)
- Adree Khondker
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Dylan J. Malenfant
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Alexander K. Dhaliwal
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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120
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Sych T, Mély Y, Römer W. Lipid self-assembly and lectin-induced reorganization of the plasma membrane. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170117. [PMID: 29632269 PMCID: PMC5904303 DOI: 10.1098/rstb.2017.0117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2018] [Indexed: 01/10/2023] Open
Abstract
The plasma membrane represents an outstanding example of self-organization in biology. It plays a vital role in protecting the integrity of the cell interior and regulates meticulously the import and export of diverse substances. Its major building blocks are proteins and lipids, which self-assemble to a fluid lipid bilayer driven mainly by hydrophobic forces. Even if the plasma membrane appears-globally speaking-homogeneous at physiological temperatures, the existence of specialized nano- to micrometre-sized domains of raft-type character within cellular and synthetic membrane systems has been reported. It is hypothesized that these domains are the origin of a plethora of cellular processes, such as signalling or vesicular trafficking. This review intends to highlight the driving forces of lipid self-assembly into a bilayer membrane and the formation of small, transient domains within the plasma membrane. The mechanisms of self-assembly depend on several factors, such as the lipid composition of the membrane and the geometry of lipids. Moreover, the dynamics and organization of glycosphingolipids into nanometre-sized clusters will be discussed, also in the context of multivalent lectins, which cluster several glycosphingolipid receptor molecules and thus create an asymmetric stress between the two membrane leaflets, leading to tubular plasma membrane invaginations.This article is part of the theme issue 'Self-organization in cell biology'.
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Affiliation(s)
- Taras Sych
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technology (FIT), Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch Cedex, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch Cedex, France
| | - Winfried Römer
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Schänzlestraße 18, 79104 Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technology (FIT), Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
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121
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Leng X, Kinnun JJ, Cavazos AT, Canner SW, Shaikh SR, Feller SE, Wassall SR. All n-3 PUFA are not the same: MD simulations reveal differences in membrane organization for EPA, DHA and DPA. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:1125-1134. [PMID: 29305832 PMCID: PMC5963985 DOI: 10.1016/j.bbamem.2018.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/19/2017] [Accepted: 01/01/2018] [Indexed: 01/01/2023]
Abstract
Eicosapentaenoic (EPA, 20:5), docosahexaenoic (DHA, 22:6) and docosapentaenoic (DPA, 22:5) acids are omega-3 polyunsaturated fatty acids (n-3 PUFA) obtained from dietary consumption of fish oils that potentially alleviate the symptoms of a range of chronic diseases. We focus here on the plasma membrane as a site of action and investigate how they affect molecular organization when taken up into a phospholipid. All atom MD simulations were performed to compare 1-stearoyl-2-eicosapentaenoylphosphatylcholine (EPA-PC, 18:0-20:5PC), 1-stearoyl-2-docosahexaenoylphosphatylcholine (DHA-PC, 18:0-22:6PC), 1-stearoyl-2-docosapentaenoylphosphatylcholine (DPA-PC, 18:0-22:5PC) and, as a monounsaturated control, 1-stearoyl-2-oleoylphosphatidylcholine (OA-PC, 18:0-18:1PC) bilayers. They were run in the absence and presence of 20mol% cholesterol. Multiple double bonds confer high disorder on all three n-3 PUFA. The different number of double bonds and chain length for each n-3 PUFA moderates the reduction in membrane order exerted (compared to OA-PC, S¯CD=0.152). EPA-PC (S¯CD=0.131) is most disordered, while DPA-PC (S¯CD=0.140) is least disordered. DHA-PC (S¯CD=0.139) is, within uncertainty, the same as DPA-PC. Following the addition of cholesterol, order in EPA-PC (S¯CD=0.169), DHA-PC (S¯CD=0.178) and DPA-PC (S¯CD=0.182) is increased less than in OA-PC (S¯CD=0.214). The high disorder of n-3 PUFA is responsible, preventing the n-3 PUFA-containing phospholipids from packing as close to the rigid sterol as the monounsaturated control. Our findings establish that EPA, DHA and DPA are not equivalent in their interactions within membranes, which possibly contributes to differences in clinical efficacy.
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Affiliation(s)
- Xiaoling Leng
- Department of Physics, IUPUI, Indianapolis, IN 46202-3273, United States
| | - Jacob J Kinnun
- Department of Physics, IUPUI, Indianapolis, IN 46202-3273, United States
| | - Andres T Cavazos
- Department of Physics, IUPUI, Indianapolis, IN 46202-3273, United States
| | - Samuel W Canner
- Department of Physics, IUPUI, Indianapolis, IN 46202-3273, United States; Department of Computer Science and Information Science, IUPUI, Indianapolis, IN 46202-5132, United States
| | - Saame Raza Shaikh
- Department of Nutrition, Gillings School of Global Public Health and School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Scott E Feller
- Department of Chemistry, Wabash College, Crawfordsville, IN 47933, United States
| | - Stephen R Wassall
- Department of Physics, IUPUI, Indianapolis, IN 46202-3273, United States.
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122
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Kumari P, Kaur S, Sharma S, Kashyap HK. Impact of amphiphilic molecules on the structure and stability of homogeneous sphingomyelin bilayer: Insights from atomistic simulations. J Chem Phys 2018; 148:165102. [DOI: 10.1063/1.5021310] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Pratibha Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Supreet Kaur
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shobha Sharma
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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123
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Penetration of antimicrobial peptides in a lung surfactant model. Colloids Surf B Biointerfaces 2018; 167:345-353. [PMID: 29689490 DOI: 10.1016/j.colsurfb.2018.04.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/30/2022]
Abstract
Molecular dynamics simulations were successfully performed to understand the absorption mechanism of antimicrobial peptides LL-37, CATH-2, and SMAP-29 in a lung surfactant model. The antimicrobial peptides quickly penetrate in the lung surfactant model in dozens or hundreds nanoseconds, but they electrostatically interact with the lipid polar heads during the simulation time of 2 μs. This electrostatic interaction should be the explanation for the inactivation of the antimicrobial peptides when co-administrated with lung surfactant. As they strongly interact with the lipid polar heads of the lung surfactant, there is no positive charge available on the antimicrobial peptide to attack the negatively charged bacteria membrane. In order to avoid the interaction of peptides with the lipid polar heads, sodium cholate was used to form nanoparticles which act as an absorption enhancer of all antimicrobial peptides used in this investigation. The nanoparticles of 150 molecules of sodium cholate with one peptide were inserted on the top of the lung surfactant model. The nanoparticles penetrated into the lung surfactant model, spreading the sodium cholate molecules around the lipid polar heads. The sodium cholate molecules seem to protect the peptides from the interaction with the lipid polar heads, leaving them free to be delivered to the water phase. The penetration of peptides alone or even the peptide nanoparticles with sodium cholate do not collapse the lung surfactant model, indicating to be a promisor drug delivery system to the lung. The implications of this finding are that antimicrobial peptides may only be co-administered with an absorption enhancer such as sodium cholate into lung surfactant in order to avoid inactivation of their antimicrobial activity.
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124
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Effect of 5-trans Isomer of Arachidonic Acid on Model Liposomal Membranes Studied by a Combined Simulation and Experimental Approach. J Membr Biol 2018; 251:475-489. [PMID: 29610947 DOI: 10.1007/s00232-018-0029-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 03/08/2018] [Indexed: 02/07/2023]
Abstract
Unsaturated fatty acids are found in humans predominantly in the cis configuration. Fatty acids in the trans configuration are primarily the result of human processing (trans fats), but can also be formed endogenously by radical stress. The cis-trans isomerization of fatty acids by free radicals could be connected to several pathologies. Trans fats have been linked to an increased risk of coronary artery disease; however, the reasons for the resulting pathogenesis remain unclear. Here, we investigate the effect of a mono-trans isomer of arachidonic acid (C20:4-5trans, 8cis, 11cis, 14cis) produced by free radicals in physiological concentration on a model erythrocyte membrane using a combined experimental and theoretical approach. Molecular Dynamics (MD) simulations of two model lipid bilayers containing arachidonic acid and its 5-trans isomer in 3 mol% were carried out for this purpose. The 5-trans isomer formation in the phospholipids was catalyzed by HOCH2CH2S· radicals, generated from the corresponding thiol by γ-irradiation, in multilamellar vesicles of SAPC. Large unilamellar vesicles were made by the extrusion method (LUVET) as a biomimetic model for cis-trans isomerization. Atomic Force Microscopy and Dynamic Light Scattering were used to measure the average size, morphology, and the z-potential of the liposomes. Both results from MD simulations and experiments are in agreement and indicate that the two model membranes display different physicochemical properties in that the bilayers containing the trans fatty acids were more ordered and more rigid than those containing solely the cis arachidonic acid. Correspondingly, the average size of the liposomes containing trans isomers was smaller than the ones without.
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125
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Location of fluorescent probes (2′-hydroxy derivatives of 2,5-diaryl-1,3-oxazole) in lipid membrane studied by fluorescence spectroscopy and molecular dynamics simulation. Biophys Chem 2018; 235:9-18. [DOI: 10.1016/j.bpc.2018.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 11/20/2022]
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126
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Della Ripa LA, Petros ZA, Cioffi AG, Piehl DW, Courtney JM, Burke MD, Rienstra CM. Solid-State NMR of highly 13C-enriched cholesterol in lipid bilayers. Methods 2018; 138-139:47-53. [PMID: 29366688 DOI: 10.1016/j.ymeth.2018.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 12/25/2022] Open
Abstract
Cholesterol (Chol) is vital for cell function as it is essential to a myriad of biochemical and biophysical processes. The atomistic details of Chol's interactions with phospholipids and proteins is therefore of fundamental interest, and NMR offers unique opportunities to interrogate these properties at high resolution. Towards this end, here we describe approaches for examining the structure and dynamics of Chol in lipid bilayers using high levels of 13C enrichment in combination with magic-angle spinning (MAS) methods. We quantify the incorporation levels and demonstrate high sensitivity and resolution in 2D 13C-13C and 1H-13C spectra, enabling de novo assignments and site-resolved order parameter measurements obtained in a fraction of the time required for experiments with natural abundance sterols. We envision many potential future applications of these methods to study sterol interactions with drugs, lipids and proteins.
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Affiliation(s)
- Lisa A Della Ripa
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zoe A Petros
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Alexander G Cioffi
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Dennis W Piehl
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Joseph M Courtney
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Martin D Burke
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA.
| | - Chad M Rienstra
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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127
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Mukherjee S, Kar RK, Nanga RPR, Mroue KH, Ramamoorthy A, Bhunia A. Accelerated molecular dynamics simulation analysis of MSI-594 in a lipid bilayer. Phys Chem Chem Phys 2018; 19:19289-19299. [PMID: 28702543 DOI: 10.1039/c7cp01941f] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multidrug resistance against the existing antibiotics is one of the most challenging threats across the globe. Antimicrobial peptides (AMPs), in this regard, are considered to be one of the effective alternatives that can overcome bacterial resistance. MSI-594, a 24-residue linear alpha-helical cationic AMP, has been shown to function via the carpet mechanism to disrupt bacterial membrane systems. To better understand the role of lipid composition in the function of MSI-594, in the present study, eight different model membrane systems have been studied using accelerated molecular dynamics (aMD) simulations. The simulated results are helpful in discriminating the particular effects of cationic MSI-594 against zwitterionic POPC, anionic POPG and POPS, and neutral POPE lipid moieties. Additionally, the effects of various heterogeneous POPC/POPG (7 : 3), POPC/POPS (7 : 3), and POPG/POPE (1 : 3 and 3 : 1) bilayer systems on the dynamic interaction of MSI-594 have also been investigated. The effect on the lipid bilayer due to the interaction with the peptide is characterized by lipid acyl-chain order, membrane thickness, and acyl-chain dynamics. Our simulation results show that the lipid composition affects the membrane interaction of MSI-594, suggesting that membrane selectivity is crucial to its mechanism of action. The results reported in this study are helpful to obtain accurate atomistic-level information governing MSI-594 and its membrane disruptive antimicrobial mechanism of action, and to design next generation potent antimicrobial peptides.
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Affiliation(s)
- Shruti Mukherjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.
| | - Rajiv K Kar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.
| | - Ravi Prakash Reddy Nanga
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA. and Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kamal H Mroue
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Ayyalusamy Ramamoorthy
- Biophysics Program and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700 054, India.
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128
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Stereospecific Interactions of Cholesterol in a Model Cell Membrane: Implications for the Membrane Dipole Potential. J Membr Biol 2018; 251:507-519. [DOI: 10.1007/s00232-018-0016-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/25/2018] [Indexed: 12/11/2022]
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129
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Patra MC, Choi S. Insight into Phosphatidylinositol-Dependent Membrane Localization of the Innate Immune Adaptor Protein Toll/Interleukin 1 Receptor Domain-Containing Adaptor Protein. Front Immunol 2018; 9:75. [PMID: 29434596 PMCID: PMC5796906 DOI: 10.3389/fimmu.2018.00075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 01/11/2018] [Indexed: 01/23/2023] Open
Abstract
The toll/interleukin 1 receptor (TIR) domain-containing adaptor protein (TIRAP) plays an important role in the toll-like receptor (TLR) 2, TLR4, TLR7, and TLR9 signaling pathways. TIRAP anchors to phosphatidylinositol (PI) 4,5-bisphosphate (PIP2) on the plasma membrane and PI (3,4,5)-trisphosphate (PIP3) on the endosomal membrane and assists in recruitment of the myeloid differentiation primary response 88 protein to activated TLRs. To date, the structure and mechanism of TIRAP’s membrane association are only partially understood. Here, we modeled an all-residue TIRAP dimer using homology modeling, threading, and protein–protein docking strategies. Molecular dynamics simulations revealed that PIP2 creates a stable microdomain in a dipalmitoylphosphatidylcholine bilayer, providing TIRAP with its physiologically relevant orientation. Computed binding free energy values suggest that the affinity of PI-binding domain (PBD) for PIP2 is stronger than that of TIRAP as a whole for PIP2 and that the short PI-binding motif (PBM) contributes to the affinity between PBD and PIP2. Four PIP2 molecules can be accommodated by distinct lysine-rich surfaces on the dimeric PBM. Along with the known PI-binding residues (K15, K16, K31, and K32), additional positively charged residues (K34, K35, and R36) showed strong affinity toward PIP2. Lysine-to-alanine mutations at the PI-binding residues abolished TIRAP’s affinity for PIP2; however, K34, K35, and R36 consistently interacted with PIP2 headgroups through hydrogen bond (H-bond) and electrostatic interactions. TIRAP exhibited a PIP2-analogous intermolecular contact and binding affinity toward PIP3, aided by an H-bond network involving K34, K35, and R36. The present study extends our understanding of TIRAP’s membrane association, which could be helpful in designing peptide decoys to block TLR2-, TLR4-, TLR7-, and TLR9-mediated autoimmune diseases.
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Affiliation(s)
- Mahesh Chandra Patra
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, South Korea
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130
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Salas-Estrada LA, Leioatts N, Romo TD, Grossfield A. Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions. Biophys J 2018; 114:355-367. [PMID: 29401433 PMCID: PMC5984976 DOI: 10.1016/j.bpj.2017.11.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/20/2017] [Accepted: 11/09/2017] [Indexed: 10/18/2022] Open
Abstract
Rhodopsin, a prototypical G protein-coupled receptor, is a membrane protein that can sense dim light. This highly effective photoreceptor is known to be sensitive to the composition of its lipidic environment, but the molecular mechanisms underlying this fine-tuned modulation of the receptor's function and structural stability are not fully understood. There are two competing hypotheses to explain how this occurs: 1) lipid modulation occurs via solvent-like interactions, where lipid composition controls membrane properties like hydrophobic thickness, which in turn modulate the protein's conformational equilibrium; or 2) protein-lipid interactions are ligand-like, with specific hot spots and long-lived binding events. By analyzing an ensemble of all-atom molecular dynamics simulations of five different states of rhodopsin, we show that a local ordering effect takes place in the membrane upon receptor activation. Likewise, docosahexaenoic acid acyl tails and phosphatidylethanolamine headgroups behave like weak ligands, preferentially binding to the receptor in inactive-like conformations and inducing subtle but significant structural changes.
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Affiliation(s)
- Leslie A Salas-Estrada
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Nicholas Leioatts
- Department of Theoretical and Computational Biophysics, Max Plank Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tod D Romo
- Center for Integrated Research Computing, University of Rochester, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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131
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Zhang T, Qiu Y, Luo Q, Zhao L, Yan X, Ding Q, Jiang H, Yang H. The Mechanism by Which Luteolin Disrupts the Cytoplasmic Membrane of Methicillin-Resistant Staphylococcus aureus. J Phys Chem B 2018; 122:1427-1438. [PMID: 29309144 DOI: 10.1021/acs.jpcb.7b05766] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most versatile human pathogens. Luteolin (LUT) has anti-MRSA activity by disrupting the MRSA cytoplasmic membrane. However, the mechanism by which luteolin disrupts the membrane remains unclear. Here, we performed differential scanning calorimetry (DSC) and all-atomic molecular dynamics (AA-MD) simulations to investigate the interactions and effects of LUT on model membranes composed of phosphatidylcholine (PC) and phosphatidylglycerol (PG). We detected the transition thermodynamic parameters of dipalmitoylphosphatidylcholine (DPPC) liposomes, dipalmitoylphosphatidylglycerol (DPPG) liposomes, and liposomes composed of both DPPC and DPPG at different LUT concentrations and showed that LUT molecules were located between polar heads and the hydrophobic region of DPPC/DPPG. In the MD trajectories, LUT molecules ranging from 5 to 50 had different effects on the membranes thickness, fluidity and ordered property of lipids, and lateral pressure of lipid bilayers composed of dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylglycerol (DOPG). Also, most LUT molecules were distributed in the region between the phosphorus atoms and C9 atoms of DOPC and DOPG. On the basis of the combination of these results, we conclude that the distinct effects of LUT on lipid bilayers composed of PCs and PGs may elucidate the mechanism by which LUT disrupts the cytoplasmic membrane of MRSA.
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Affiliation(s)
- Tao Zhang
- School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237, China
| | - Yunguang Qiu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Qichao Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Lifen Zhao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xin Yan
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University , 393 Huaxiazhong Road, Shanghai 201210, China
| | - Qiaoce Ding
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237, China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Huaiyu Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
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132
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Zaki AM, Carbone P. How the Incorporation of Pluronic Block Copolymers Modulates the Response of Lipid Membranes to Mechanical Stress. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13284-13294. [PMID: 29084428 DOI: 10.1021/acs.langmuir.7b02244] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We employ atomistic molecular dynamics simulations to investigate the effect that the incorporation of the nonionic amphiphilic copolymer known as Pluronic L64 has on the mechanical stability of a DPPC membrane. The simulations reveal that the incorporation of the polymer chains leads to membranes that can sustain increasing mechanical stresses. Analysis of mechanical, structural, and dynamic properties of the membrane shows that the polymer chains interact strongly with the lipids in the vicinity, restraining their mobility and imparting better mechanical stability to the membrane. The hybrid membranes under tension remain thicker, more ordered, and stiffer in comparison to their lipid analogues. Trans-bilayer lipid movements (flip-flop) are observed and appear to be triggered by the presence of the polymer chains. A careful analysis of the pore formation under high tensions reveals two distinctive mechanisms that depend on the distribution of the hydrophilic polymer blocks in the bilayer. Finally, the rate of growth of the formed membrane defects is slowed down in the presence of polymers. These findings show that Pluronic block copolymers could be exploited for the formation of optimized hybrid nanodevices with controlled elastic and dynamic properties.
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Affiliation(s)
- Afroditi Maria Zaki
- School of Chemical Engineering and Analytical Science, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Paola Carbone
- School of Chemical Engineering and Analytical Science, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
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133
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Baul U, Vemparala S. Influence of lipid composition of model membranes on methacrylate antimicrobial polymer-membrane interactions. SOFT MATTER 2017; 13:7665-7676. [PMID: 28991313 DOI: 10.1039/c7sm01211j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Using atomistic molecular dynamics simulations, the role of lipid composition in the interactions of multiple methacrylate antimicrobial polymer agents with model membranes, and the consequent response of the membranes is studied. In our earlier study, methacrylate polymers were observed to induce phase demixing and associated thickness mismatch in a POPE-POPG model microbial membrane. In this work, we probe (1) the role of varying the degree of saturation in lipid acyl chains in the membrane interactions of methacrylate polymers, and (2) whether electrostatics (addition of anionic lipids) can influence the interactions of the polymers with model mammalian membranes. Lipid composition is observed to significantly modify membrane-polymer interactions, leading to differences in both the mode of partitioning and the conformations adopted by the polymers, in addition to impacting membrane properties differently. The results strongly suggest that the oft-cited electrostatic interactions between the antimicrobial agents and the microbial membranes do not fully account for the recognition and subsequent partitioning of the antimicrobial agents. The ability of the methacrylate polymers to sense interfacial lipid packing defects, determined by the PE/PC head groups of lipids, is also found to be influential in their membrane partitioning. Deliberate inclusion of charged anionic lipids into a model mammalian membrane, leading to additional favorable electrostatics, does not reproduce a similar polymer partitioning mechanism to that in its microbial counterpart. The differences observed in the interactions of methacrylate polymers with the various model membranes can be instrumental in extending our understanding of underlying modes of membrane disruption by general antimicrobial agents as well.
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Affiliation(s)
- Upayan Baul
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St., A5300, Austin, TX 78712-1224, USA.
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134
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Dong X, Sun Y, Wei G, Nussinov R, Ma B. Binding of protofibrillar Aβ trimers to lipid bilayer surface enhances Aβ structural stability and causes membrane thinning. Phys Chem Chem Phys 2017; 19:27556-27569. [PMID: 28979963 PMCID: PMC5647258 DOI: 10.1039/c7cp05959k] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease, a common neurodegenerative disease, is characterized by the aggregation of amyloid-β (Aβ) peptides. The interactions of Aβ with membranes cause changes in membrane morphology and ion permeation, which are responsible for its neurotoxicity and can accelerate fibril growth. However, the Aβ-lipid interactions and how these induce membrane perturbation and disruption at the atomic level and the consequences for the Aβ organization are not entirely understood. Here, we perform multiple atomistic molecular dynamics simulations on three protofibrillar Aβ9-40 trimers. Our simulations show that, regardless of the morphologies and the initial orientations of the three different protofibrillar Aβ9-40 trimers, the N-terminal β-sheet of all trimers preferentially binds to the membrane surface. The POPG lipid bilayers enhance the structural stability of protofibrillar Aβ trimers by stabilizing inter-peptide β-sheets and D23-K28 salt-bridges. The interaction causes local membrane thinning. We found that the trimer structure related to Alzheimer's disease brain tissue () is the most stable both in water solution and at membrane surface, and displays slightly stronger membrane perturbation capability. These results provide mechanistic insights into the membrane-enhanced structural stability of protofibrillar Aβ oligomers and the first step of Aβ-induced membrane disruption at the atomic level.
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Affiliation(s)
- Xuewei Dong
- Department of Physics, State Key Laboratory of Surface physics, Key Laboratory for Computational Physical Science (Ministry of Education), Collaborative Innovation Center of Advanced Microstructures (Nanjing), Fudan University, Shanghai 200433, People's Republic of China
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135
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Abellón-Ruiz J, Kaptan SS, Baslé A, Claudi B, Bumann D, Kleinekathöfer U, van den Berg B. Structural basis for maintenance of bacterial outer membrane lipid asymmetry. Nat Microbiol 2017; 2:1616-1623. [PMID: 29038444 DOI: 10.1038/s41564-017-0046-x] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/21/2017] [Indexed: 11/09/2022]
Abstract
The Gram-negative bacterial outer membrane (OM) is a unique bilayer that forms an efficient permeation barrier to protect the cell from noxious compounds 1,2 . The defining characteristic of the OM is lipid asymmetry, with phospholipids comprising the inner leaflet and lipopolysaccharides comprising the outer leaflet 1-3 . This asymmetry is maintained by the Mla pathway, a six-component system that is widespread in Gram-negative bacteria and is thought to mediate retrograde transport of misplaced phospholipids from the outer leaflet of the OM to the cytoplasmic membrane 4 . The OM lipoprotein MlaA performs the first step in this process via an unknown mechanism that does not require external energy input. Here we show, using X-ray crystallography, molecular dynamics simulations and in vitro and in vivo functional assays, that MlaA is a monomeric α-helical OM protein that functions as a phospholipid translocation channel, forming a ~20-Å-thick doughnut embedded in the inner leaflet of the OM with a central, amphipathic pore. This architecture prevents access of inner leaflet phospholipids to the pore, but allows outer leaflet phospholipids to bind to a pronounced ridge surrounding the channel, followed by diffusion towards the periplasmic space. Enterobacterial MlaA proteins form stable complexes with OmpF/C 5,6 , but the porins do not appear to play an active role in phospholipid transport. MlaA represents a lipid transport protein that selectively removes outer leaflet phospholipids to help maintain the essential barrier function of the bacterial OM.
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Affiliation(s)
- Javier Abellón-Ruiz
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Shreyas S Kaptan
- Department of Physics & Earth Sciences, Jacobs University Bremen, 28759, Bremen, Germany
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Beatrice Claudi
- Focal Area Infection Biology, University of Basel, CH-4056, Basel, Switzerland
| | - Dirk Bumann
- Focal Area Infection Biology, University of Basel, CH-4056, Basel, Switzerland
| | - Ulrich Kleinekathöfer
- Department of Physics & Earth Sciences, Jacobs University Bremen, 28759, Bremen, Germany
| | - Bert van den Berg
- Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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136
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Piggot TJ, Allison JR, Sessions RB, Essex JW. On the Calculation of Acyl Chain Order Parameters from Lipid Simulations. J Chem Theory Comput 2017; 13:5683-5696. [PMID: 28876925 DOI: 10.1021/acs.jctc.7b00643] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For molecular dynamics simulations of biological membrane systems to live up to the potential of providing accurate atomic level detail into membrane properties and functions, it is essential that the force fields used to model such systems are as accurate as possible. One membrane property that is often used to assess force field accuracy is the carbon-hydrogen (or carbon-deuterium) order parameters of the lipid tails, which can be accurately measured using experimental NMR techniques. There are a variety of analysis tools available to calculate these order parameters from simulations and it is essential that these computational tools work correctly to ensure the accurate assessment of the simulation force fields. In this work we compare many of these computational tools for calculating the order parameters of POPC membranes. While tools that work on all-atom systems and tools that work on saturated lipid tails in general work extremely well, we demonstrate that the majority of the tested tools that calculate the order parameters for unsaturated united-atom lipid tails do so incorrectly. We identify tools that do perform accurate calculations and include one such program with this work, enabling rapid and accurate calculation of united-atom lipid order parameters. Furthermore, we discuss cases in which it is nontrivial to appropriately predict the unsaturated carbon order parameters in united-atom systems. Finally, we examine order parameter splitting for carbon 2 in sn-2 lipid chains, demonstrating substantial deviations from experimental values in several all-atom and united-atom lipid force fields.
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Affiliation(s)
- Thomas J Piggot
- Chemical, Biological and Radiological Sciences, Defence Science and Technology Laboratory , Porton Down, Salisbury, Wiltshire SP4 0JQ, U.K.,Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | - Jane R Allison
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University , Auckland 0632, New Zealand
| | - Richard B Sessions
- School of Biochemistry, University of Bristol , University Walk, Bristol BS8 1TD, U.K
| | - Jonathan W Essex
- Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
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137
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Lockhart C, Klimov DK. Cholesterol Changes the Mechanisms of Aβ Peptide Binding to the DMPC Bilayer. J Chem Inf Model 2017; 57:2554-2565. [PMID: 28910085 DOI: 10.1021/acs.jcim.7b00431] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using isobaric-isothermal all-atom replica-exchange molecular dynamics (REMD) simulations, we investigated the equilibrium binding of Aβ10-40 monomers to the zwitterionic dimyristoylphosphatidylcholine (DMPC) bilayer containing cholesterol. Our previous REMD simulations, which studied binding of the same peptide to the cholesterol-free DMPC bilayer, served as a control, against which we measured the impact of cholesterol. Our findings are as follows. First, addition of cholesterol to the DMPC bilayer partially expels the Aβ peptide from the hydrophobic core and promotes its binding to bilayer polar headgroups. Using thermodynamic and energetics analyses, we argued that Aβ partial expulsion is not related to cholesterol-induced changes in lateral pressure within the bilayer but is caused by binding energetics, which favors Aβ binding to the surface of the densely packed cholesterol-rich bilayer. Second, cholesterol has a protective effect on the DMPC bilayer structure against perturbations caused by Aβ binding. More specifically, cholesterol reduces bilayer thinning and overall depletion of bilayer density beneath the Aβ binding footprint. Third, we found that the Aβ peptide contains a single cholesterol binding site, which involves hydrophobic C-terminal amino acids (Ile31-Val36), Phe19, and Phe20 from the central hydrophobic cluster, and cationic Lys28 from the turn region. This binding site accounts for about 76% of all Aβ-cholesterol interactions. Because cholesterol binding site in the Aβ10-40 peptide does not contain the GXXXG motif featured in cholesterol interactions with the transmembrane domain C99 of the β-amyloid precursor protein, we argued that the binding mechanisms for Aβ and C99 are distinct reflecting their different conformations and positions in the lipid bilayer. Fourth, cholesterol sharply reduces the helical propensity in the bound Aβ peptide. As a result, cholesterol largely eliminates the emergence of helical structure observed upon Aβ transition from a water environment to the cholesterol-free DMPC bilayer. We explain this effect by the formation of hydrogen bonds between cholesterol and the Aβ backbone, which prevent helix formation. Taken together, we expect that our simulations will advance understanding of a molecular-level mechanism behind the role of cholesterol in Alzheimer's disease.
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Affiliation(s)
- Christopher Lockhart
- School of Systems Biology, George Mason University , Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University , Manassas, Virginia 20110, United States
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138
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da Cunha AR, Duarte EL, Stassen H, Lamy MT, Coutinho K. Experimental and theoretical studies of emodin interacting with a lipid bilayer of DMPC. Biophys Rev 2017; 9:729-745. [PMID: 28940105 DOI: 10.1007/s12551-017-0323-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/29/2017] [Indexed: 12/23/2022] Open
Abstract
Emodin is one of the most abundant anthraquinone derivatives found in nature. It is the active principle of some traditional herbal medicines with known biological activities. In this work, we combined experimental and theoretical studies to reveal information about location, orientation, interaction and perturbing effects of Emodin on lipid bilayers, where we have taken into account the neutral form of the Emodin (EMH) and its anionic/deprotonated form (EM-). Using both UV/Visible spectrophotometric techniques and molecular dynamics (MD) simulations, we showed that both EMH and EM- are located in a lipid membrane. Additionally, using MD simulations, we revealed that both forms of Emodin are very close to glycerol groups of the lipid molecules, with the EMH inserted more deeply into the bilayer and more disoriented relative to the normal of the membrane when compared with the EM-, which is more exposed to interfacial water. Analysis of several structural properties of acyl chains of the lipids in a hydrated pure DMPC bilayer and in the presence of Emodin revealed that both EMH and EM- affect the lipid bilayer, resulting in a remarkable disorder of the bilayer in the vicinity of the Emodin. However, the disorder caused by EMH is weaker than that caused by EM-. Our results suggest that these disorders caused by Emodin might lead to distinct effects on lipid bilayers including its disruption which are reported in the literature.
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Affiliation(s)
- Antonio R da Cunha
- Universidade Federal do Maranhão, UFMA, Campus Balsas, Maranhão, 06500-000, Brazil.,Instituto de Física da Universidade de São Paulo, 05508-090, Cidade Universitária, São Paulo, Brazil
| | - Evandro L Duarte
- Instituto de Física da Universidade de São Paulo, 05508-090, Cidade Universitária, São Paulo, Brazil
| | - Hubert Stassen
- Grupo de Química Teórica, Instituto de Química, UFRGS, Av. Bento Gonçalves 9500, Porto Alegre, 91540-000, Brazil
| | - M Teresa Lamy
- Instituto de Física da Universidade de São Paulo, 05508-090, Cidade Universitária, São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física da Universidade de São Paulo, 05508-090, Cidade Universitária, São Paulo, Brazil.
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139
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Huang FY, Chiu CC. Interplay between alkyl chain asymmetry and cholesterol addition in the rigid ion pair amphiphile bilayer systems. J Chem Phys 2017; 146:035102. [PMID: 28109215 DOI: 10.1063/1.4974089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ion pair amphiphile (IPA), a molecular complex composed of a pair of cationic and anionic surfactants, has been proposed as a novel phospholipid substitute. Controlling the physical stability of IPA vesicles is important for its application developments such as cosmetic and drug deliveries. To investigate the effects of IPA alkyl chain combinations and the cholesterol additive on the structural and mechanical properties of IPA vesicular bilayers, we conducted a series of molecular dynamics studies on the hexadecyltrimethylammonium-dodecylsulfate (HTMA-DS) and dodecyltrimethylammonium-hexadecylsulfate (DTMA-HS) IPA bilayers with cholesterol. We found that both IPA bilayers are in the gel phase at 298 K, consistent with experimental observations. Compared with the HTMA-DS system, the DTMA-HS bilayer has more disordered alkyl chains in the hydrophobic region. When adding cholesterol, it induces alkyl chain ordering around its rigid sterol ring. Yet, cholesterol increases the molecular areas for all species and disturbs the molecular packing near the hydrophilic region and the bilayer core. Cholesterol also promotes the alkyl chain mismatch between the IPA moieties, especially for the DTMA-HS bilayer. The combined effects lead to non-monotonically enhancement of the membrane mechanical moduli for both IPA-cholesterol systems. Furthermore, cholesterol can form H-bonds with the alkylsulfate and thus enhance the contribution of alkylsulfate to the overall mechanical moduli. Combined results provide valuable molecular insights into the roles of each IPA component and the cholesterol on modulating the IPA bilayer properties.
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Affiliation(s)
- Fong-Yin Huang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chi-Cheng Chiu
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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140
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Brehm M, Saddiq G, Watermann T, Sebastiani D. Influence of Small Fluorophilic and Lipophilic Organic Molecules on Dipalmitoylphosphatidylcholine Bilayers. J Phys Chem B 2017; 121:8311-8321. [DOI: 10.1021/acs.jpcb.7b06520] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Martin Brehm
- Institut für Chemie—Theoretische
Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Ghulam Saddiq
- Institut für Chemie—Theoretische
Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Tobias Watermann
- Institut für Chemie—Theoretische
Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Daniel Sebastiani
- Institut für Chemie—Theoretische
Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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141
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Barrera EE, Frigini EN, Porasso RD, Pantano S. Modeling DMPC lipid membranes with SIRAH force-field. J Mol Model 2017; 23:259. [PMID: 28799119 DOI: 10.1007/s00894-017-3426-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/19/2017] [Indexed: 10/19/2022]
Abstract
Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations ( http://www.sirahff.com ). We show that the present model not only achieves a correct reproduction of structural parameters as area per lipid and thickness, but also dynamic descriptors such as diffusion coefficient, order parameters, and proper temperature driven variations. Adding phospholipid membranes to the existing aqueous solution, protein and DNA representations of the SIRAH force field permit considering the most common problems tackled by the biomolecular simulation community.
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Affiliation(s)
- Exequiel E Barrera
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay.
| | - Ezequiel N Frigini
- Instituto de Matemática Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, 5700, San Luis, Argentina
| | - Rodolfo D Porasso
- Instituto de Matemática Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, 5700, San Luis, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay
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142
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Takechi-Haraya Y, Sakai-Kato K, Goda Y. Membrane Rigidity Determined by Atomic Force Microscopy Is a Parameter of the Permeability of Liposomal Membranes to the Hydrophilic Compound Calcein. AAPS PharmSciTech 2017; 18:1887-1893. [PMID: 27645470 DOI: 10.1208/s12249-016-0624-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/29/2016] [Indexed: 01/01/2023] Open
Abstract
We determined the permeability coefficient of a model hydrophilic drug, calcein, encapsulated within saturated lipid-based nano-sized liposomes of various lipid profiles. We demonstrated that the addition of cholesterol to liposomes containing saturated lipids increased the permeability of the liposomal membrane to calcein via a decrease in the membrane bending modulus, as determined by means of atomic force microscopy. We found an inverse correlation between the membrane bending modulus of saturated lipid-based nano-sized liposomes and the permeability coefficient of encapsulated calcein, demonstrating that bending modulus, as determined by means of atomic force microscopy, is a quantitative parameter describing the permeability of liposomal membranes to calcein.
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143
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Ayee MAA, LeMaster E, Shentu TP, Singh DK, Barbera N, Soni D, Tiruppathi C, Subbaiah PV, Berdyshev E, Bronova I, Cho M, Akpa BS, Levitan I. Molecular-Scale Biophysical Modulation of an Endothelial Membrane by Oxidized Phospholipids. Biophys J 2017; 112:325-338. [PMID: 28122218 DOI: 10.1016/j.bpj.2016.12.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 12/31/2022] Open
Abstract
The influence of two bioactive oxidized phospholipids on model bilayer properties, membrane packing, and endothelial cell biomechanics was investigated computationally and experimentally. The truncated tail phospholipids, 1-palmitoyl-2-(5-oxovaleroyl)-sn-glycero-3-phosphocholine (POVPC) and 1-palmitoyl-2-glutaroyl-sn-glycero-3-phosphocholine (PGPC), are two major oxidation products of the unsaturated phospholipid 1-palmitoyl-2-arachidonoyl-sn-glycero-phosphocholine. A combination of coarse-grained molecular dynamics simulations, Laurdan multiphoton imaging, and atomic force microscopy microindentation experiments was used to determine the impact of POVPC and PGPC on the structure of a multicomponent phospholipid bilayer and to assess the consequences of their incorporation on membrane packing and endothelial cell stiffness. Molecular simulations predicted differential bilayer perturbation effects of the two oxidized phospholipids based on the chemical identities of their truncated tails, including decreased bilayer packing, decreased bilayer bending modulus, and increased water penetration. Disruption of lipid order was consistent with Laurdan imaging results indicating that POVPC and PGPC decrease the lipid packing of both ordered and disordered membrane domains. Computational predictions of a larger membrane perturbation effect by PGPC correspond to greater stiffness of PGPC-treated endothelial cells observed by measuring cellular elastic moduli using atomic force microscopy. Our results suggest that disruptions in membrane structure by oxidized phospholipids play a role in the regulation of overall endothelial cell stiffness.
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Affiliation(s)
- Manuela A A Ayee
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Elizabeth LeMaster
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Tzu Pin Shentu
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Dev K Singh
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Nicolas Barbera
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Dheeraj Soni
- Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois
| | | | - Papasani V Subbaiah
- Division of Endocrinology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | | | | | - Michael Cho
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Belinda S Akpa
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina
| | - Irena Levitan
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois.
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144
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Sciacca MFM, Lolicato F, Di Mauro G, Milardi D, D'Urso L, Satriano C, Ramamoorthy A, La Rosa C. The Role of Cholesterol in Driving IAPP-Membrane Interactions. Biophys J 2017; 111:140-51. [PMID: 27410742 DOI: 10.1016/j.bpj.2016.05.050] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 05/15/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023] Open
Abstract
Our knowledge of the molecular events underlying type 2 diabetes mellitus-a protein conformational disease characterized by the aggregation of islet amyloid polypeptide (IAPP) in pancreatic β cells-is limited. However, amyloid-mediated membrane damage is known to play a key role in IAPP cytotoxicity, and therefore the effects of lipid composition on modulating IAPP-membrane interactions have been the focus of intense research. In particular, membrane cholesterol content varies with aging and consequently with adverse environmental factors such as diet and lifestyle, but its role in the development of the disease is controversial. In this study, we employ a combination of experimental techniques and in silico molecular simulations to shed light on the role of cholesterol in IAPP aggregation and the related membrane disruption. We show that if anionic POPC/POPS vesicles are used as model membranes, cholesterol has a negligible effect on the kinetics of IAPP fibril growth on the surface of the bilayer. In addition, cholesterol inhibits membrane damage by amyloid-induced poration on membranes, but enhances leakage through fiber growth on the membrane surface. Conversely, if 1:2 DOPC/DPPC raft-like model membranes are used, cholesterol accelerates fiber growth. Next, it enhances pore formation and suppresses fiber growth on the membrane surface, leading to leakage. Our results highlight a twofold effect of cholesterol on the amyloidogenicity of IAPP and help explain its debated role in type 2 diabetes mellitus.
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Affiliation(s)
- Michele F M Sciacca
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Fabio Lolicato
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy; Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Giacomo Di Mauro
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Danilo Milardi
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Catania, Italy
| | - Luisa D'Urso
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Cristina Satriano
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy
| | - Ayyalusamy Ramamoorthy
- Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Chemistry, University of Michigan, Ann Arbor, Michigan; Institute for Advanced Study, Technische Universität München, Lichtenbergstrasse, Garching, Germany.
| | - Carmelo La Rosa
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Catania, Italy.
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145
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Liebau J, Ye W, Mäler L. Characterization of fast-tumbling isotropic bicelles by PFG diffusion NMR. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:395-404. [PMID: 26662467 DOI: 10.1002/mrc.4399] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
Small isotropic bicelles are versatile membrane mimetics, which, in contrast to micelles, provide a lipid bilayer and are at the same time suitable for solution-state NMR studies. The lipid composition of the bilayer is flexible allowing for incorporation of various head groups and acyl chain types. In bicelles, lipids are solubilized by detergents, which are localized in the rim of the disk-shaped lipid bilayer. Bicelles have been characterized by a broad array of biophysical methods, pulsed-field gradient NMR (PFG NMR) being one of them. PFG NMR can readily be used to measure diffusion coefficients of macromolecules. It is thus employed to characterize bicelle size and morphology. Even more importantly, PFG NMR can be used to study the degree of protein association to membranes. Here, we present the advances that have been made in producing small, fast-tumbling isotropic bicelles from a variety of lipids and detergents, together with insights on the morphology of such mixtures gained from PFG NMR. Furthermore, we review approaches to study protein-membrane interaction by PFG NMR. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jobst Liebau
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Weihua Ye
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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146
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Javanainen M, Martinez-Seara H, Vattulainen I. Nanoscale Membrane Domain Formation Driven by Cholesterol. Sci Rep 2017; 7:1143. [PMID: 28442766 PMCID: PMC5430823 DOI: 10.1038/s41598-017-01247-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/27/2017] [Indexed: 11/09/2022] Open
Abstract
Biological membranes generate specific functions through compartmentalized regions such as cholesterol-enriched membrane nanodomains that host selected proteins. Despite the biological significance of nanodomains, details on their structure remain elusive. They cannot be observed via microscopic experimental techniques due to their small size, yet there is also a lack of atomistic simulation models able to describe spontaneous nanodomain formation in sufficiently simple but biologically relevant complex membranes. Here we use atomistic simulations to consider a binary mixture of saturated dipalmitoylphosphatidylcholine and cholesterol - the "minimal standard" for nanodomain formation. The simulations reveal how cholesterol drives the formation of fluid cholesterol-rich nanodomains hosting hexagonally packed cholesterol-poor lipid nanoclusters, both of which show registration between the membrane leaflets. The complex nanodomain substructure forms when cholesterol positions itself in the domain boundary region. Here cholesterol can also readily flip-flop across the membrane. Most importantly, replacing cholesterol with a sterol characterized by a less asymmetric ring region impairs the emergence of nanodomains. The model considered explains a plethora of controversial experimental results and provides an excellent basis for further computational studies on nanodomains. Furthermore, the results highlight the role of cholesterol as a key player in the modulation of nanodomains for membrane protein function.
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Affiliation(s)
- Matti Javanainen
- Laboratory of Physics, Tampere University of Technology, Tampere, Finland.,Department of Physics, University of Helsinki, Helsinki, Finland
| | - Hector Martinez-Seara
- Laboratory of Physics, Tampere University of Technology, Tampere, Finland. .,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology, Tampere, Finland. .,Department of Physics, University of Helsinki, Helsinki, Finland. .,MEMPHYS - Centre for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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147
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Jafari M, Mehrnejad F, Aghdami R, Chaparzadeh N, Razaghi Moghadam Kashani Z, Doustdar F. Identification of the Crucial Residues in the Early Insertion of Pardaxin into Different Phospholipid Bilayers. J Chem Inf Model 2017; 57:929-941. [DOI: 10.1021/acs.jcim.6b00693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Majid Jafari
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Faramarz Mehrnejad
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 14395-1561, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5746, Iran
| | - Raheleh Aghdami
- Department of Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz 53714-161, Iran
| | - Nader Chaparzadeh
- Department of Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz 53714-161, Iran
| | - Zahra Razaghi Moghadam Kashani
- Department of Life Sciences Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran 14395-1561, Iran
| | - Farahnoosh Doustdar
- Department of Microbiology, Faculty of
Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
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148
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Briones R, Aponte-Santamaría C, de Groot BL. Localization and Ordering of Lipids Around Aquaporin-0: Protein and Lipid Mobility Effects. Front Physiol 2017; 8:124. [PMID: 28303107 PMCID: PMC5332469 DOI: 10.3389/fphys.2017.00124] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Hydrophobic matching, lipid sorting, and protein oligomerization are key principles by which lipids and proteins organize in biological membranes. The Aquaporin-0 channel (AQP0), solved by electron crystallography (EC) at cryogenic temperatures, is one of the few protein-lipid complexes of which the structure is available in atomic detail. EC and room-temperature molecular dynamics (MD) of dimyristoylglycerophosphocholine (DMPC) annular lipids around AQP0 show similarities, however, crystal-packing and temperature might affect the protein surface or the lipids distribution. To understand the role of temperature, lipid phase, and protein mobility in the localization and ordering of AQP0-lipids, we used MD simulations of an AQP0-DMPC bilayer system. Simulations were performed at physiological and at DMPC gel-phase temperatures. To decouple the protein and lipid mobility effects, we induced gel-phase in the lipids or restrained the protein. We monitored the lipid ordering effects around the protein. Reducing the system temperature or inducing lipid gel-phase had a marginal effect on the annular lipid localization. However, restraining the protein mobility increased the annular lipid localization around the whole AQP0 surface, resembling EC. The distribution of the inter-phosphate and hydrophobic thicknesses showed that stretching of the DMPC annular layer around AQP0 surface is the mechanism that compensates the hydrophobic mismatch in this system. The distribution of the local area-per-lipid and the acyl-chain order parameters showed particular fluid- and gel-like areas that involved several lipid layers. These areas were in contact with the surfaces of higher and lower protein mobility, respectively. We conclude that the AQP0 surfaces induce specific fluid- and gel-phase prone areas. The presence of these areas might guide the AQP0 lipid sorting interactions with other membrane components, and is compatible with the squared array oligomerization of AQP0 tetramers separated by a layer of annular lipids.
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Affiliation(s)
- Rodolfo Briones
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry Göttingen, Germany
| | - Camilo Aponte-Santamaría
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies and Interdisciplinary Center for Scientific Computing Heidelberg, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry Göttingen, Germany
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149
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Willems N, Urtizberea A, Verre AF, Iliut M, Lelimousin M, Hirtz M, Vijayaraghavan A, Sansom MSP. Biomimetic Phospholipid Membrane Organization on Graphene and Graphene Oxide Surfaces: A Molecular Dynamics Simulation Study. ACS NANO 2017; 11:1613-1625. [PMID: 28165704 DOI: 10.1021/acsnano.6b07352] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Supported phospholipid membrane patches stabilized on graphene surfaces have shown potential in sensor device functionalization, including biosensors and biocatalysis. Lipid dip-pen nanolithography (L-DPN) is a method useful in generating supported membrane structures that maintain lipid functionality, such as exhibiting specific interactions with protein molecules. Here, we have integrated L-DPN, atomic force microscopy, and coarse-grained molecular dynamics simulation methods to characterize the molecular properties of supported lipid membranes (SLMs) on graphene and graphene oxide supports. We observed substantial differences in the topologies of the stabilized lipid structures depending on the nature of the surface (polar graphene oxide vs nonpolar graphene). Furthermore, the addition of water to SLM systems resulted in large-scale reorganization of the lipid structures, with measurable effects on lipid lateral mobility within the supported membranes. We also observed reduced lipid ordering within the supported structures relative to free-standing lipid bilayers, attributed to the strong hydrophobic interactions between the lipids and support. Together, our results provide insight into the molecular effects of graphene and graphene oxide surfaces on lipid bilayer membranes. This will be important in the design of these surfaces for applications such as biosensor devices.
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Affiliation(s)
- Nathalie Willems
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Ainhoa Urtizberea
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrea F Verre
- School of Materials and National Graphene Institute, University of Manchester , Manchester M13 9PL, United Kingdom
| | - Maria Iliut
- School of Materials and National Graphene Institute, University of Manchester , Manchester M13 9PL, United Kingdom
| | - Mickael Lelimousin
- CERMAV, CNRS and Université Grenoble Alpes , BP 53, Grenoble 38041 Cedex 9, France
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen, Germany
| | - Aravind Vijayaraghavan
- School of Materials and National Graphene Institute, University of Manchester , Manchester M13 9PL, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford , South Parks Road, Oxford OX1 3QU, United Kingdom
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150
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Gorai B, Sivaraman T. Delineating residues for haemolytic activities of snake venom cardiotoxin 1 from Naja naja as probed by molecular dynamics simulations and in vitro validations. Int J Biol Macromol 2017; 95:1022-1036. [DOI: 10.1016/j.ijbiomac.2016.10.091] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/26/2016] [Indexed: 02/05/2023]
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