151
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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: 23] [Impact Index Per Article: 3.3] [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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152
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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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153
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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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154
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Hamasaka G, Muto T, Andoh Y, Fujimoto K, Kato K, Takata M, Okazaki S, Uozumi Y. Detailed Structural Analysis of a Self-Assembled Vesicular Amphiphilic NCN-Pincer Palladium Complex by Using Wide-Angle X-Ray Scattering and Molecular Dynamics Calculations. Chemistry 2017; 23:1291-1298. [PMID: 27739119 DOI: 10.1002/chem.201603494] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Indexed: 11/09/2022]
Abstract
Wide-angle X-ray scattering experiments and all-atomistic molecular dynamics calculations were performed to elucidate the detailed structure of bilayer vesicles constructed by self-assembly of an amphiphilic palladium NCN-pincer complex. We found an excellent agreement between the experimental and calculated X-ray spectra, and between the membrane thickness determined from a TEM image and that calculated from an electron-density profile, which indicated that the calculated structure was highly reliable. The analysis of the simulated bilayer structure showed that in general the membrane was softer than other phospholipid bilayer membranes. In this bilayer assemblage, the degree of alignment of complex molecules in the bilayer membrane was quite low. An analysis of the electron-density profile shows that the bilayer assemblage contains a space through which organic molecules can exit. Furthermore, the catalytically active center is near this space and is easily accessible by organic molecules, which permits the bilayer membrane to act as a nanoreactor. The free energy of permeation of water through the bilayer membrane of the amphiphilic complex was 12 kJ mol-1 , which is much lower than that for phospholipid bilayer membranes in general. Organic molecules are expected to pass though the bilayer membrane. The self-assembled vesicles were shown to be catalytically active in a Miyaura-Michael reaction in water.
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Affiliation(s)
- Go Hamasaka
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8787, Japan.,SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki, 444-8787, Japan
| | - Tsubasa Muto
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8787, Japan.,SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki, 444-8787, Japan
| | - Yoshimichi Andoh
- High-Performance Computation Section, Center for Computational Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Kazushi Fujimoto
- Department of Applied Chemistry, Faculty of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Kenichi Kato
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148, Japan
| | - Masaki Takata
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148, Japan
| | - Susumu Okazaki
- Department of Applied Chemistry, Faculty of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yasuhiro Uozumi
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8787, Japan.,SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki, 444-8787, Japan.,RIKEN Center for Sustainable Resource Science, Wako, 351-0198, Japan.,JST-CREST and JST-ACCEL, Myodaiji, Okazaki, 444-8787, Japan
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155
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Molecular Dynamics of POPC Phospholipid Bilayers through the Gel to Fluid Phase Transition: An Incoherent Quasi-Elastic Neutron Scattering Study. J CHEM-NY 2017. [DOI: 10.1155/2017/3654237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The microscopic dynamics for the gel and liquid-crystalline phase of highly aligned D2O-hydrated bilayers of 1-palmitoyl-oleoyl-sn-glycero-phosphocholine (POPC) were investigated in the temperature range from 248 to 273 K by using incoherent quasi-elastic neutrons scattering (QENS). We develop a model for describing the molecular motions of the liquid phase occurring in the 0.3 to 350 ps time range. Accordingly, the complex dynamics of hydrogen are described in terms of simple dynamical processes involving different parts of the phospholipid chain. The analysis of the data evidences the existence of three different motions: the fast motion of hydrogen vibrating around the carbon atoms, the intermediate motion of carbon atoms in the acyl chains, and the slower translational motion of the entire phospholipid molecule. The influence of the temperature on these dynamical processes is investigated. In particular, by going from gel to liquid-crystalline phase, we reveal an increase of the segmental motion mainly affecting the terminal part of the acyl chains and a change of the diffusional dynamics from a localized rattling-like motion to a confined diffusion.
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156
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Parikh N, Klimov DK. Inclusion of lipopeptides into the DMPC lipid bilayers prevents Aβ peptide insertion. Phys Chem Chem Phys 2017; 19:10087-10098. [DOI: 10.1039/c7cp01003f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lipopeptides prevent penetration of Alzheimer's Aβ peptides into lipid bilayers.
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Affiliation(s)
- Niyati Parikh
- School of Systems Biology
- George Mason University
- Manassas
- USA
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157
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Boughter CT, Monje-Galvan V, Im W, Klauda JB. Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics. J Phys Chem B 2016; 120:11761-11772. [DOI: 10.1021/acs.jpcb.6b08574] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher T. Boughter
- Department
of Chemical and Biomolecular Engineering, University of Maryland, College
Park, Maryland 20742, United States
| | - Viviana Monje-Galvan
- Department
of Chemical and Biomolecular Engineering, University of Maryland, College
Park, Maryland 20742, United States
| | - Wonpil Im
- Department
of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Jeffery B. Klauda
- Department
of Chemical and Biomolecular Engineering, University of Maryland, College
Park, Maryland 20742, United States
- Biophysics
Program, University of Maryland, College Park, Maryland 20742, United States
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158
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Pazin WM, Olivier DDS, Vilanova N, Ramos AP, Voets IK, Soares AEE, Ito AS. Interaction of Artepillin C with model membranes. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016; 46:383-393. [DOI: 10.1007/s00249-016-1183-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/11/2016] [Accepted: 10/18/2016] [Indexed: 02/05/2023]
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159
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LeBarron J, London E. Highly Hydrophilic Segments Attached to Hydrophobic Peptides Translocate Rapidly across Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10752-10760. [PMID: 27649909 DOI: 10.1021/acs.langmuir.6b02597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hydrophilic segments attached to transmembrane helices often cross membranes. In an increasing number of cases, it has become apparent that this occurs in a biologically relevant post-translational event. In this study, we investigate whether juxta-membrane (JM) hydrophilic sequences attached to hydrophobic helices are able to rapidly cross lipid bilayers via their ability or inability to block hydrophobic helix interconversion between a transmembrane (TM) and non-TM membrane-associated state. Interconversion was triggered by changing the protonation state of an Asp residue in the hydrophobic core of the peptides, and peptide configuration was monitored by the fluorescence of a Trp residue at the center of the hydrophobic sequence. In POPC vesicles, conversion of the TM to non-TM state at high pH and the non-TM to TM state at low pH was rapid (seconds or less) for KK, KKNN, and the KKNNNNNN flanking sequences on both N- and C-termini and the KLFAGHQ sequence that flanks the spontaneously TM-inserting 3A protein of polio virus. In vesicles composed of 6:4 (mol/mol) POPC/cholesterol, interconversion was still rapid, with the exception of the peptide flanked by KKNNNNNN sequences, for which the half time of interconversion slowed to minutes. This behavior suggests that, at least in membranes with low levels of cholesterol, movement of hydrophilic JM segments (and analogous hydrophobic loops in multipass TM proteins) across membranes may be more facile than previously thought. This may have important biological implications.
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Affiliation(s)
- Jamie LeBarron
- Stony Brook University Stony Brook, New York 11794-5215, United States
| | - Erwin London
- Stony Brook University Stony Brook, New York 11794-5215, United States
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160
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Kheyfets B, Galimzyanov T, Drozdova A, Mukhin S. Analytical calculation of the lipid bilayer bending modulus. Phys Rev E 2016; 94:042415. [PMID: 27841551 DOI: 10.1103/physreve.94.042415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/07/2022]
Abstract
Bending and Gaussian moduli of a homogenious single-component lipid bilayer are calculated analytically using microscopic model of the lipid hydrocarbon chains. The approach allows for thermodynamic averaging over different chains conformations. Each chain is modeled as a flexible string with finite bending rigidity and an incompressible cross-section area. The interchain steric repulsion is accounted for self-consistently determined single-chain confining parabolic potential. The model provides a simple analytical expression for the membrane bending modulus, which falls within a range of experimental values. An observed dependence of the modulus on hydrocarbon chain length is also reproduced. Correspondence between our microscopic model and the membrane theory of elasticity is established.
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Affiliation(s)
- Boris Kheyfets
- National University of Science and Technology MISIS, Leninskiy prospekt 4, Moscow 119049, Russia
| | - Timur Galimzyanov
- National University of Science and Technology MISIS, Leninskiy prospekt 4, Moscow 119049, Russia
| | - Anna Drozdova
- National University of Science and Technology MISIS, Leninskiy prospekt 4, Moscow 119049, Russia
| | - Sergei Mukhin
- National University of Science and Technology MISIS, Leninskiy prospekt 4, Moscow 119049, Russia
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161
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Kulkarni A, Pandey P, Rao P, Mahmoud A, Goldman A, Sabbisetti V, Parcha S, Natarajan SK, Chandrasekar V, Dinulescu D, Roy S, Sengupta S. Algorithm for Designing Nanoscale Supramolecular Therapeutics with Increased Anticancer Efficacy. ACS NANO 2016; 10:8154-68. [PMID: 27452234 DOI: 10.1021/acsnano.6b00241] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In the chemical world, evolution is mirrored in the origin of nanoscale supramolecular structures from molecular subunits. The complexity of function acquired in a supramolecular system over a molecular subunit can be harnessed in the treatment of cancer. However, the design of supramolecular nanostructures is hindered by a limited atomistic level understanding of interactions between building blocks. Here, we report the development of a computational algorithm, which we term Volvox after the first multicellular organism, that sequentially integrates quantum mechanical energy-state- and force-field-based models with large-scale all-atomistic explicit water molecular dynamics simulations to design stable nanoscale lipidic supramolecular structures. In one example, we demonstrate that Volvox enables the design of a nanoscale taxane supramolecular therapeutic. In another example, we demonstrate that Volvox can be extended to optimizing the ratio of excipients to form a stable nanoscale supramolecular therapeutic. The nanoscale taxane supramolecular therapeutic exerts greater antitumor efficacy than a clinically used taxane in vivo. Volvox can emerge as a powerful tool in the design of nanoscale supramolecular therapeutics for effective treatment of cancer.
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Affiliation(s)
- Ashish Kulkarni
- Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
- Harvard-MIT Division of Health Sciences and Technology , Cambridge, Massachusetts 02139, United States
| | - Prithvi Pandey
- India Innovation Research Center , Invictus Oncology, New Delhi 110092, India
| | | | | | - Aaron Goldman
- Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
- Harvard-MIT Division of Health Sciences and Technology , Cambridge, Massachusetts 02139, United States
- Harvard Digestive Diseases Center , Boston, Massachusetts 02115, United States
| | - Venkata Sabbisetti
- Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
| | | | | | | | | | - Sudip Roy
- India Innovation Research Center , Invictus Oncology, New Delhi 110092, India
| | - Shiladitya Sengupta
- Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
- Harvard-MIT Division of Health Sciences and Technology , Cambridge, Massachusetts 02139, United States
- Dana Farber Cancer Institute , Boston, Massachusetts 02115, United States
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162
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Putative membrane lytic sites of P-type and S-type cardiotoxins from snake venoms as probed by all-atom molecular dynamics simulations. J Mol Model 2016; 22:238. [DOI: 10.1007/s00894-016-3113-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/01/2016] [Indexed: 12/16/2022]
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163
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Wood I, Pickholz M. Naratriptan aggregation in lipid bilayers: perspectives from molecular dynamics simulations. J Mol Model 2016; 22:221. [PMID: 27558798 DOI: 10.1007/s00894-016-3096-8] [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: 03/30/2016] [Accepted: 08/08/2016] [Indexed: 11/27/2022]
Abstract
In order to understand the interaction between naratriptan and a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC), we carried out molecular dynamics simulations. The simulations were performed considering neutral and protonated ionization states, starting from different initial conditions. At physiological pH, the protonated state of naratriptan is predominant. It is expected that neutral compounds could have larger membrane partition than charged compounds. However, for the specific case of triptans, it is difficult to study neutral species in membranes experimentally, making computer simulations an interesting tool. When the naratriptan molecules were originally placed in water, they partitioned between the bilayer/water interface and water phase, as has been described for similar compounds. From this condition, the drugs displayed low access to the hydrophobic environment, with no significant effects on bilayer organization. The molecules anchored in the interface, due mainly to the barrier function of the polar and oriented lipid heads. On the other hand, when placed inside the bilayer, both neutral and protonated naratriptan showed self-aggregation in the lipid tail environment. In particular, the protonated species exhibited a pore-like structure, dragging water through this environment. Graphical Abstract Different behaviour of Naratriptan and Sumatriptan, when the drugs were originally placed in the lipid core.
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Affiliation(s)
- Irene Wood
- Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, CONICET, Junin 956 CP 1113, Buenos Aires, Argentina.,National Science Research Council (CONICET), Buenos Aires, Argentina
| | - Mónica Pickholz
- Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires, CONICET, Junin 956 CP 1113, Buenos Aires, Argentina. .,National Science Research Council (CONICET), Buenos Aires, Argentina.
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164
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Lim GS, Jaenicke S, Klähn M. How the spontaneous insertion of amphiphilic imidazolium-based cations changes biological membranes: a molecular simulation study. Phys Chem Chem Phys 2016; 17:29171-83. [PMID: 26466122 DOI: 10.1039/c5cp04806k] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The insertion of 1-octyl-3-methylimidazolium cations (OMIM(+)) from a diluted aqueous ionic liquid (IL) solution into a model of a bacterial cell membrane is investigated. Subsequently, the mutual interactions of cations inside the membrane and their combined effect on membrane properties are derived. The ionic liquid solution and the membrane model are simulated using molecular dynamics in combination with empirical force fields. A high propensity of OMIM(+) for membrane insertion is observed, with a cation concentration at equilibrium inside the membrane 47 times larger than in the solvent. Once inserted, cations exhibit a weak effective attraction inside the membrane at a distance of 1.3 nm. At this free energy minimum, negatively charged phosphates of the phospholipids are sandwiched between two OMIM(+) to form energetically favorable OMIM(+)-phosphate-OMIM(+) types of coordination. The cation-cation association free energy is 5.9 kJ mol(-1), whereas the activation barrier for dissociation is 10.1 kJ mol(-1). Subsequently, OMIM(+) are inserted into the leaflet of the membrane bilayer that represents the extracellular side. The cations are evenly distributed with mutual cation distances according to the found optimum distance of 1.3 nm. Because of the short length of the cation alkyl chains compared to lipid fatty acids, voids are generated in the hydrophobic core of the membrane. These voids disorder the fatty acids, because they enable fatty acids to curl into these empty spaces and also cause a thinning of the membrane by 0.6 nm. Additionally, the membrane density increases at its center. The presence of OMIM(+) in the membrane facilitates the permeation of small molecules such as ammonia through the membrane, which is chosen as a model case for small polar solutes. The permeability coefficient of the membrane with respect to ammonia increases substantially by a factor of seven. This increase is caused by a reduction of the involved free energy barriers, which is effected by the cations through the thinning of the membrane and favorable interactions of the delocalized OMIM(+) charge with ammonia inside the membrane. Overall, the results indicate the antimicrobial effect of amphiphilic imidazolium-based cations that are found in various common ILs. This effect is caused by an alteration of the permeability of the bacterial membrane and other property changes.
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Affiliation(s)
- Geraldine S Lim
- Institute of High Performance Computing, Agency for Science, Technology and Research, 1 Fusionopolis Way, #16-16, Connexis, Singapore 138632, Republic of Singapore
| | - Stephan Jaenicke
- National University of Singapore, Department of Chemistry, 3 Science Drive 3, Singapore 117543, Republic of Singapore
| | - Marco Klähn
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research, 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore.
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165
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Poger D, Caron B, Mark AE. Validating lipid force fields against experimental data: Progress, challenges and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1556-65. [DOI: 10.1016/j.bbamem.2016.01.029] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/07/2016] [Accepted: 01/27/2016] [Indexed: 01/16/2023]
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166
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Goldman A, Kulkarni A, Kohandel M, Pandey P, Rao P, Natarajan SK, Sabbisetti V, Sengupta S. Rationally Designed 2-in-1 Nanoparticles Can Overcome Adaptive Resistance in Cancer. ACS NANO 2016; 10:5823-5834. [PMID: 27257911 DOI: 10.1021/acsnano.6b00320] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The development of resistance is the major cause of mortality in cancer. Combination chemotherapy is used clinically to reduce the probability of evolution of resistance. A similar trend toward the use of combinations of drugs is also emerging in the application of cancer nanomedicine. However, should a combination of two drugs be delivered from a single nanoparticle or should they be delivered in two different nanoparticles for maximal efficacy? We explored these questions in the context of adaptive resistance, which emerges as a phenotypic response of cancer cells to chemotherapy. We studied the phenotypic dynamics of breast cancer cells under cytotoxic chemotherapeutic stress and analyzed the data using a phenomenological mathematical model. We demonstrate that cancer cells can develop adaptive resistance by entering into a predetermined transitional trajectory that leads to phenocopies of inherently chemoresistant cancer cells. Disrupting this deterministic program requires a unique combination of inhibitors and cytotoxic agents. Using two such combinations, we demonstrate that a 2-in-1 nanomedicine can induce greater antitumor efficacy by ensuring that the origins of adaptive resistance are terminated by deterministic spatially constrained delivery of both drugs to the target cells. In contrast, a combination of free-form drugs or two nanoparticles, each carrying a single payload, is less effective, arising from a stochastic distribution to cells. These findings suggest that 2-in-1 nanomedicines could emerge as an important strategy for targeting adaptive resistance, resulting in increased antitumor efficacy.
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Affiliation(s)
- Aaron Goldman
- Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, United States
- Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital , Boston, Massachusetts 02115, United States
- Harvard Digestive Diseases Center , Boston, Massachusetts 02115, United States
| | - Ashish Kulkarni
- Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, United States
- Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital , Boston, Massachusetts 02115, United States
| | - Mohammad Kohandel
- Department of Applied Mathematics, University of Waterloo , Waterloo, ON N2L 3G1, Canada
| | - Prithvi Pandey
- India Innovation Research Center, Invictus Oncology, New Delhi 92, India
| | - Poornima Rao
- Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital , Boston, Massachusetts 02115, United States
| | - Siva Kumar Natarajan
- Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Venkata Sabbisetti
- Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Shiladitya Sengupta
- Department of Medicine, Harvard Medical School , Boston, Massachusetts 02115, United States
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, Massachusetts 02139, United States
- Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital , Boston, Massachusetts 02115, United States
- Dana Farber Cancer Institute , Boston, Massachusetts 02115, United States
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167
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Yang J, Martí J, Calero C. Pair interactions among ternary DPPC/POPC/cholesterol mixtures in liquid-ordered and liquid-disordered phases. SOFT MATTER 2016; 12:4557-4561. [PMID: 27103534 DOI: 10.1039/c6sm00345a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Saturated phospholipids, unsaturated phospholipids, and cholesterol are essential components of cell membranes, making the understanding of their mutual interactions of great significance. We have performed microsecond molecular dynamics simulations on the ternary mixtures of DPPC/POPC/cholesterol to systematically examine lipid-lipid and cholesterol-lipid interactions in the liquid-ordered and the liquid-disordered phases. The results show that there exists a competition between the tighter packing of cholesterol-lipid and the looser packing of lipid-lipid as the membrane changes from the liquid-disordered phase to the liquid-ordered phase. Depending on the lipid saturation, the favor of lipid-lipid interactions is in the order of saturated-saturated > monounsaturated-monounsaturated > saturated-monounsaturated. Cholesterol-saturated lipid interactions are more favorable than cholesterol-monounsaturated lipid ones. The results are consistent with the push-pull forces derived from experiments and give general insights into the interactions among membrane components.
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Affiliation(s)
- Jing Yang
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
| | - Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain.
| | - Carles Calero
- Center for Polymer Studies and Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA.
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168
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LeBarron J, London E. Effect of lipid composition and amino acid sequence upon transmembrane peptide-accelerated lipid transleaflet diffusion (flip-flop). BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1812-20. [PMID: 27131444 DOI: 10.1016/j.bbamem.2016.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/21/2016] [Accepted: 04/21/2016] [Indexed: 12/15/2022]
Abstract
We examined how hydrophobic peptide-accelerated transleaflet lipid movement (flip-flop) was affected by peptide sequence and vesicle composition and properties. A peptide with a completely hydrophobic sequence had little if any effect upon flip-flop. While peptides with a somewhat less hydrophobic sequence accelerated flip-flop, the half-time remained slow (hours) with substantial (0.5mol%) peptide in the membranes. It appears that peptide-accelerated lipid flip-flop involves a rare event that may reflect a rare state of the peptide or lipid bilayer. There was no simple relationship between peptide overall hydrophobicity and flip-flop. In addition, flip-flop was not closely linked to whether the peptides were in a transmembrane or non-transmembrane (interfacial) inserted state. Flip-flop was also not associated with peptide-induced pore formation. We found that peptide-accelerated flip-flop is initially faster in small (highly curved) unilamellar vesicles relative to that in large unilamellar vesicles. Peptide-accelerated flip-flop was also affected by lipid composition, being slowed in vesicles with thick bilayers or those containing 30% cholesterol. Interestingly, these factors also slow spontaneous lipid flip-flop in the absence of peptide. Combined with previous studies, the results are most consistent with acceleration of lipid flip-flop by peptide-induced thinning of bilayer width.
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Affiliation(s)
- Jamie LeBarron
- Dept. of Biochemistry and Cell Biology, Stony Brook, NY 11794-5215, United States
| | - Erwin London
- Dept. of Biochemistry and Cell Biology, Stony Brook, NY 11794-5215, United States
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169
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Molecular dynamics simulations of Oxprenolol and Propranolol in a DPPC lipid bilayer. J Mol Graph Model 2016; 64:153-164. [DOI: 10.1016/j.jmgm.2016.01.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 01/22/2016] [Accepted: 01/23/2016] [Indexed: 11/18/2022]
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170
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Saielli G. Fully Atomistic Simulations of the Ionic Liquid Crystal [C16mim][NO3]: Orientational Order Parameters and Voids Distribution. J Phys Chem B 2016; 120:2569-77. [DOI: 10.1021/acs.jpcb.5b12469] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giacomo Saielli
- CNR Institute
on Membrane
Technology and Department of Chemical Sciences, University of Padova, Via Marzolo, 1, 35131 Padova, Italy
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171
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Orosz KS, Jones IW, Keogh JP, Smith CM, Griffin KR, Xu J, Comi TJ, Hall HK, Saavedra SS. Photopolymerization of Dienoyl Lipids Creates Planar Supported Poly(lipid) Membranes with Retained Fluidity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1577-84. [PMID: 26794208 PMCID: PMC4755918 DOI: 10.1021/acs.langmuir.5b03437] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Polymerization of substrate-supported bilayers composed of dienoylphosphatidylcholine (PC) lipids is known to greatly enhance their chemical and mechanical stability; however, the effects of polymerization on membrane fluidity have not been investigated. Here planar supported lipid bilayers (PSLBs) composed of dienoyl PCs on glass substrates were examined to assess the degree to which UV-initiated polymerization affects lateral lipid mobility. Fluorescence recovery after photobleaching (FRAP) was used to measure the diffusion coefficients (D) and mobile fractions of rhodamine-DOPE in unpolymerized and polymerized PSLBs composed of bis-sorbyl phosphatidylcholine (bis-SorbPC), mono-sorbyl-phosphatidylcholine (mono-SorbPC), bis-dienoyl-phosphatidylcholine (bis-DenPC), and mono-dienoyl phosphatidylcholine (mono-DenPC). Polymerization was performed in both the Lα and Lβ phase for each lipid. In all cases, polymerization reduced membrane fluidity; however, measurable lateral diffusion was retained which is attributed to a low degree of polymerization. The D values for sorbyl lipids were less than those of the denoyl lipids; this may be a consequence of the distal location of polymerizable group in the sorbyl lipids which may facilitate interleaflet bonding. The D values measured after polymerization were 0.1-0.8 of those measured before polymerization, a range that corresponds to fluidity intermediate between that of a Lα phase and a Lβ phase. This D range is comparable to ratios of D values reported for liquid-disordered (Ld) and liquid-ordered (Lo) lipid phases and indicates that the effect of UV polymerization on lateral diffusion in a dienoyl PSLB is similar to the transition from a Ld phase to a Lo phase. The partial retention of fluidity in UV-polymerized PSLBs, their enhanced stability, and the activity of incorporated transmembrane proteins and peptides is discussed.
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Affiliation(s)
- Kristina S. Orosz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Ian W. Jones
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - John P. Keogh
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Christopher M. Smith
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Kaitlyn R. Griffin
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Juhua Xu
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - Troy J. Comi
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - H. K. Hall
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
| | - S. Scott Saavedra
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
- BIO5 Institute, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721
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172
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Martin L, Bilek MM, Weiss AS, Kuyucak S. Force fields for simulating the interaction of surfaces with biological molecules. Interface Focus 2016; 6:20150045. [PMID: 26855748 PMCID: PMC4686237 DOI: 10.1098/rsfs.2015.0045] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide-surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data.
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Affiliation(s)
- Lewis Martin
- Department of Applied Physics, University of Sydney, Sydney, New South Wales, Australia
| | - Marcela M. Bilek
- Department of Applied Physics, University of Sydney, Sydney, New South Wales, Australia
| | - Anthony S. Weiss
- Charles Perkins Centre, University of Sydney, Sydney, New South Wales, Australia
- Department of Molecular Bioscience, University of Sydney, Sydney, New South Wales, Australia
- Bosch Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Serdar Kuyucak
- Department of Applied Physics, University of Sydney, Sydney, New South Wales, Australia
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173
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Pavlova A, Hwang H, Lundquist K, Balusek C, Gumbart JC. Living on the edge: Simulations of bacterial outer-membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1753-9. [PMID: 26826270 DOI: 10.1016/j.bbamem.2016.01.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 01/06/2023]
Abstract
Gram-negative bacteria are distinguished in part by a second, outer membrane surrounding them. This membrane is distinct from others, possessing an outer leaflet composed not of typical phospholipids but rather large, highly charged molecules known as lipopolysaccharides. Therefore, modeling the structure and dynamics of proteins embedded in the outer membrane requires careful consideration of their native environment. In this review, we examine how simulations of such outer-membrane proteins have evolved over the last two decades, culminating most recently in detailed, highly accurate atomistic models of the outer membrane. We also draw attention to how the simulations have coupled with experiments to produce novel insights unattainable through a single approach. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Karl Lundquist
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Curtis Balusek
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, GA 30332, United States.
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174
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Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2512-2528. [PMID: 26809025 DOI: 10.1016/j.bbamem.2016.01.019] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/15/2016] [Accepted: 01/19/2016] [Indexed: 01/18/2023]
Abstract
Accurate details on the sampled atomistic resolution structures of lipid bilayers can be experimentally obtained by measuring C-H bond order parameters, spin relaxation rates and scattering form factors. These parameters can be also directly calculated from the classical atomistic resolution molecular dynamics simulations (MD) and compared to the experimentally achieved results. This comparison measures the simulation model quality with respect to 'reality'. If agreement is sufficient, the simulation model gives an atomistic structural interpretation of the acquired experimental data. Significant advance of MD models is made by jointly interpreting different experiments using the same structural model. Here we focus on phosphatidylcholine lipid bilayers, which out of all model membranes have been studied mostly by experiments and simulations, leading to the largest available dataset. From the applied comparisons we conclude that the acyl chain region structure and rotational dynamics are generally well described in simulation models. Also changes with temperature, dehydration and cholesterol concentration are qualitatively correctly reproduced. However, the quality of the underlying atomistic resolution structural changes is uncertain. Even worse, when focusing on the lipid bilayer properties at the interfacial region, e.g. glycerol backbone and choline structures, and cation binding, many simulation models produce an inaccurate description of experimental data. Thus extreme care must be applied when simulations are applied to understand phenomena where the interfacial region plays a significant role. This work is done by the NMRlipids Open Collaboration project running at https://nmrlipids.blogspot.fi and https://github.com/NMRLipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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175
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Lyubartsev AP, Rabinovich AL. Force Field Development for Lipid Membrane Simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2483-2497. [PMID: 26766518 DOI: 10.1016/j.bbamem.2015.12.033] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 02/04/2023]
Abstract
With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, SE 106 91, Stockholm, Sweden.
| | - Alexander L Rabinovich
- Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Pushkinskaya 11, Petrozavodsk, 185910, Russian Federation.
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176
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Li Y, Guan L, Lu T, Li H, Li Z, Li F. Interactions of the N-terminal domain of human islet amyloid polypeptide with lipid membranes: the effect of cholesterol. RSC Adv 2016. [DOI: 10.1039/c6ra19714k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cholesterol facilitates the insertion and aggregation of hIAPP1–19 in membrane and the CARC motif mediates the peptide–cholesterol interaction.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Supramolecular Structure and Materials
- Jilin University
- Changchun 130012
- P. R. China
| | - Liping Guan
- State Key Laboratory of Supramolecular Structure and Materials
- Jilin University
- Changchun 130012
- P. R. China
| | - Tong Lu
- State Key Laboratory of Supramolecular Structure and Materials
- Jilin University
- Changchun 130012
- P. R. China
| | - Haichao Li
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- Jilin University
- Changchun 130012
- P. R. China
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology & Engineering
- The Ministry of Education
- Jilin University
- Changchun 130012
- P. R. China
| | - Fei Li
- State Key Laboratory of Supramolecular Structure and Materials
- Jilin University
- Changchun 130012
- P. R. China
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177
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Ruiz-Fernández AR, López-Cascales JJ, Giner-Casares JJ, Araya-Maturana R, Díaz-Baños FG, Muñoz-Gacitúa D, Weiss-López BE. Effect of shape and bending modulus on the properties of nematic lyotropic liquid crystals. RSC Adv 2016. [DOI: 10.1039/c5ra24019k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Variation in the structure of the molecular aggregate associated with the increase of the TTAC concentration in the liquid crystal.
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Affiliation(s)
| | - J. J. López-Cascales
- Uni. Politécnica de Cartagena
- Grupo de Bioinformática y Macromoléculas (BioMac)
- 30203 Cartagena
- Spain
| | - J. J. Giner-Casares
- CIC biomaGUNE
- Biofunctional Nanomaterials – Laboratory 6 Parque tecnológico de San Sebastián
- 20009 Donostia – San Sebastián
- Spain
| | | | - F. G. Díaz-Baños
- Uni. de Murcia
- Fac. de Química
- Dep. de Química Física
- 30100 Espinardo
- Spain
| | - D. Muñoz-Gacitúa
- Uni. de Chile
- Fac. de Ciencias
- Departamento de Química
- Santiago
- Chile
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178
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Qian Z, Jia Y, Wei G. Binding Orientations and Lipid Interactions of Human Amylin at Zwitterionic and Anionic Lipid Bilayers. J Diabetes Res 2016; 2016:1749196. [PMID: 26649316 PMCID: PMC4663351 DOI: 10.1155/2016/1749196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 03/22/2015] [Accepted: 04/15/2015] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence suggests that the interaction of human islet amyloid polypeptide (hIAPP) with lipids may facilitate hIAPP aggregation and cause the death of pancreatic islet β-cells. However, the detailed hIAPP-membrane interactions and the influences of lipid compositions are unclear. In this study, as a first step to understand the mechanism of membrane-mediated hIAPP aggregation, we investigate the binding behaviors of hIAPP monomer at zwitterionic palmitoyloleoyl-phosphatidylcholine (POPC) bilayer by performing atomistic molecular dynamics simulations. The results are compared with those of hIAPP at anionic palmitoyloleoyl-phosphatidylglycerol (POPG) bilayers. We find that the adsorption of hIAPP to POPC bilayer is mainly initiated from the C-terminal region and the peptide adopts a helical structure with multiple binding orientations, while the adsorption to POPG bilayer is mostly initiated from the N-terminal region and hIAPP displays one preferential binding orientation, with its hydrophobic residues exposed to water. hIAPP monomer inserts into POPC lipid bilayers more readily than into POPG bilayers. Peptide-lipid interaction analyses show that the different binding features of hIAPP at POPC and POPG bilayers are attributed to different magnitudes of electrostatic and hydrogen-bonding interactions with lipids. This study provides mechanistic insights into the different interaction behaviors of hIAPP with zwitterionic and anionic lipid bilayers.
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Affiliation(s)
- Zhenyu Qian
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai 200433, China
| | - Yan Jia
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai 200433, China
| | - Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai 200433, China
- *Guanghong Wei:
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179
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Alwarawrah M, Hussain F, Huang J. Alteration of lipid membrane structure and dynamics by diacylglycerols with unsaturated chains. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:253-63. [PMID: 26607007 DOI: 10.1016/j.bbamem.2015.11.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/05/2015] [Accepted: 11/18/2015] [Indexed: 01/15/2023]
Abstract
Diacylglycerols (DAGs) with unsaturated acyl chains play many important roles in biomembranes, such as a second messenger and activator for protein kinase C. In this study, three DAGs of distinctly different chain unsaturations (i.e. di16:0DAG (DPG), 16:0-18:1DAG (POG), and di18:1DAG (DOG)) are studied using atomistic MD simulation to compare their roles in the structure and dynamics of 16:0-18:1phosphatidylcholine (POPC) membranes. All three DAGs are able to produce the so-called 'condensing effect' in POPC membranes: decreasing area-per-lipid, and increasing acyl chain order and bilayer thickness. Our visual and quantitative analyses clearly show that DAG with unsaturated chains induce larger spacing between POPC headgroups, compared with DAG with saturated chains; this particular effect has long been hypothesized to be crucial for activating enzymes and receptors in cell membranes. DAGs with unsaturated chains are also located closer to the bilayer/aqueous interface than DPG and are more effective in slowing down lateral diffusion of molecules. We show that DAG molecules seek the "umbrella coverage" from neighboring phospholipid headgroups - similar to cholesterol. Unlike cholesterol, DAGs also hide their chains from water by laterally inserting their chains into the surrounding. Thus, acyl chains of DAG are more spread and disordered than those of PC due to the insertion. By calculating the potential of mean force (PMF) for POPC in POPC/DAG bilayers, we found that all three DAGs can significantly increase the free energy barrier for POPC to flip-flop, but only DAGs with unsaturated chains can additionally increase the free energy of POPC desorption.
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Affiliation(s)
- Mohammad Alwarawrah
- Department of Physics, Texas Tech University, Lubbock, TX 79409, United States
| | - Fazle Hussain
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX 79409, United States
| | - Juyang Huang
- Department of Physics, Texas Tech University, Lubbock, TX 79409, United States.
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180
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Mao L, Yang L, Zhang Q, Jiang H, Yang H. Effects of ion interactions with a cholesterol-rich bilayer. Biochem Biophys Res Commun 2015; 468:125-9. [PMID: 26529547 DOI: 10.1016/j.bbrc.2015.10.149] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 10/27/2015] [Indexed: 11/24/2022]
Abstract
Previous molecular dynamics (MD) simulations of ion-lipid interactions have focused on pure phospholipid bilayers. Many functional microdomains in membranes have a complex composition of cholesterol and phospholipids. Here, we reveal the distinctiveness of the interactions and the effects of the ions on a cholesterol-rich bilayer by performing MD simulations of a cholesterol-rich bilayer with a Na(+)/K(+) mixture or a Na(+)/K(+)/Ca(2+)/Mg(2+) mixture. The simulations reveal that Ca(2+) maintains its dominant role in the interaction with the cholesterol-rich bilayer, but the binding affinity of Mg(2+) to the cholesterol-rich bilayer is even weaker than the affinities of Na(+) and K(+), whereas its interaction with pure phospholipid bilayers is strong and is only slightly weaker than that of Ca(2+). Additionally, it was found that the presence of additional divalent cations induces the headgroups of phospholipids to be more perpendicular to the membrane surface, reducing the lateral movement of lipids and slightly altering the ordering and packing of the cholesterol-rich bilayer, different from divalent cations, which strongly influence that ordering and packing of pure phospholipid bilayers. Therefore, this study indicates that cholesterol in the membrane could affect the interactions between membrane and cations. The findings could be helpful in understanding the biological processes relevant to regulation of cations in cholesterol-rich regions.
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Affiliation(s)
- Lingxue Mao
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Linlin Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Qiansen Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 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 Science, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Huaiyu Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai 201203, China.
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181
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Leng X, Kinnun JJ, Marquardt D, Ghefli M, Kučerka N, Katsaras J, Atkinson J, Harroun TA, Feller SE, Wassall SR. α-Tocopherol Is Well Designed to Protect Polyunsaturated Phospholipids: MD Simulations. Biophys J 2015; 109:1608-18. [PMID: 26488652 PMCID: PMC4624157 DOI: 10.1016/j.bpj.2015.08.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 08/20/2015] [Accepted: 08/24/2015] [Indexed: 01/08/2023] Open
Abstract
The presumptive function for alpha-tocopherol (αtoc) in membranes is to protect polyunsaturated lipids against oxidation. Although the chemistry of the process is well established, the role played by molecular structure that we address here with atomistic molecular-dynamics simulations remains controversial. The simulations were run in the constant particle NPT ensemble on hydrated lipid bilayers composed of SDPC (1-stearoyl-2-docosahexaenoylphosphatidylcholine, 18:0-22:6PC) and SOPC (1-stearoyl-2-oleoylphosphatidylcholine, 18:0-18:1PC) in the presence of 20 mol % αtoc at 37°C. SDPC with SA (stearic acid) for the sn-1 chain and DHA (docosahexaenoic acid) for the sn-2 chain is representative of polyunsaturated phospholipids, while SOPC with OA (oleic acid) substituted for the sn-2 chain serves as a monounsaturated control. Solid-state (2)H nuclear magnetic resonance and neutron diffraction experiments provide validation. The simulations demonstrate that high disorder enhances the probability that DHA chains at the sn-2 position in SDPC rise up to the bilayer surface, whereby they encounter the chromanol group on αtoc molecules. This behavior is reflected in the van der Waals energy of interaction between αtoc and acyl chains, and illustrated by density maps of distribution for acyl chains around αtoc molecules that were constructed. An ability to more easily penetrate deep into the bilayer is another attribute conferred upon the chromanol group in αtoc by the high disorder possessed by DHA. By examining the trajectory of single molecules, we found that αtoc flip-flops across the SDPC bilayer on a submicrosecond timescale that is an order-of-magnitude greater than in SOPC. Our results reveal mechanisms by which the sacrificial hydroxyl group on the chromanol group can trap lipid peroxyl radicals within the interior and near the surface of a polyunsaturated membrane. At the same time, water-soluble reducing agents that regenerate αtoc can access the chromanol group when it locates at the surface.
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Affiliation(s)
- Xiaoling Leng
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana
| | - Jacob J Kinnun
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana
| | - Drew Marquardt
- Department of Physics, Brock University, St. Catharines, Ontario, Canada; Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Mikel Ghefli
- Department of Chemistry, Brock University, St. Catharines, Ontario, Canada
| | - Norbert Kučerka
- Canadian Neutron Beam Centre, National Research Council, Chalk River, Ontario, Canada; Faculty of Pharmacy, Comenius University, Bratislava, Slovakia
| | - John Katsaras
- Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Joint Institute for Neutron Sciences, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee
| | - Jeffrey Atkinson
- Department of Chemistry, Brock University, St. Catharines, Ontario, Canada
| | - Thad A Harroun
- Department of Physics, Brock University, St. Catharines, Ontario, Canada
| | - Scott E Feller
- Department of Chemistry, Wabash College, Crawfordsville, Indiana
| | - Stephen R Wassall
- Department of Physics, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana.
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182
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Soussi J, Chalopin Y. Electric polarizability of lipid bilayers: The influence of the structure. J Chem Phys 2015; 143:144904. [DOI: 10.1063/1.4932340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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183
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Pham QD, Topgaard D, Sparr E. Cyclic and Linear Monoterpenes in Phospholipid Membranes: Phase Behavior, Bilayer Structure, and Molecular Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:11067-11077. [PMID: 26375869 DOI: 10.1021/acs.langmuir.5b00856] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Monoterpenes are abundant in essential oils extracted from plants. These relatively small and hydrophobic molecules have shown important biological functions, including antimicrobial activity and membrane penetration enhancement. The interaction between the monoterpenes and lipid bilayers is considered important to the understanding of the biological functions of monoterpenes. In this study, we investigated the effect of cyclic and linear monoterpenes on the structure and dynamics of lipids in model membranes. We have studied the ternary system 1,2-dimyristoyl-sn-glycero-3-phosphocholine-monoterpene-water as a model with a focus on dehydrated conditions. By combining complementary techniques, including differential scanning calorimetry, solid-state nuclear magnetic resonance, and small- and wide-angle X-ray scattering, bilayer structure, phase transitions, and lipid molecular dynamics were investigated at different water contents. Monoterpenes cause pronounced melting point depression and phase segregation in lipid bilayers, and the extent of these effects depends on the hydration conditions. The addition of a small amount of thymol to the fluid bilayer (volume fraction of 0.03 in the bilayer) leads to an increased order in the acyl chain close to the bilayer interface. The findings are discussed in relation to biological systems and lipid formulations.
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Affiliation(s)
- Quoc Dat Pham
- Division of Physical Chemistry, Chemistry Department, Lund University , P.O. Box 124, 22100 Lund, Sweden
| | - Daniel Topgaard
- Division of Physical Chemistry, Chemistry Department, Lund University , P.O. Box 124, 22100 Lund, Sweden
| | - Emma Sparr
- Division of Physical Chemistry, Chemistry Department, Lund University , P.O. Box 124, 22100 Lund, Sweden
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184
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Nåbo LJ, List NH, Witzke S, Wüstner D, Khandelia H, Kongsted J. Design of new fluorescent cholesterol and ergosterol analogs: Insights from theory. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2188-99. [DOI: 10.1016/j.bbamem.2015.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 04/24/2015] [Accepted: 04/29/2015] [Indexed: 12/23/2022]
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185
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Ma H, Irudayanathan FJ, Jiang W, Nangia S. Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model. J Phys Chem B 2015; 119:14668-82. [DOI: 10.1021/acs.jpcb.5b07122] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Huilin Ma
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | | | - Wenjuan Jiang
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
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186
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Madej BD, Gould IR, Walker RC. A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field. J Phys Chem B 2015; 119:12424-35. [PMID: 26359797 DOI: 10.1021/acs.jpcb.5b04924] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Amber Lipid14 force field is expanded to include cholesterol parameters for all-atom cholesterol and lipid bilayer molecular dynamics simulations. The General Amber and Lipid14 force fields are used as a basis for assigning atom types and basic parameters. A new RESP charge derivation for cholesterol is presented, and tail parameters are adapted from Lipid14 alkane tails. 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers are simulated at a range of cholesterol contents. Experimental bilayer structural properties are compared with bilayer simulations and are found to be in good agreement. With this parameterization, another component of complex membranes is available for molecular dynamics with the Amber Lipid14 force field.
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Affiliation(s)
- Benjamin D Madej
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States.,San Diego Supercomputer Center , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States
| | - Ian R Gould
- Department of Chemistry and Institute of Chemical Biology, Imperial College London , South Kensington SW7 2AZ, United Kingdom
| | - Ross C Walker
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States.,San Diego Supercomputer Center , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States
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187
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Qu G, Xue C, Han Y, Liang S, Cheng J, Ding W. Molecular Dynamics Study ofN-Dodecyl-N,N-Dimethyl-3-Ammonio-1-Propanesulfonate Mono-Layer Adsorbed at the Air/Water Interface. J DISPER SCI TECHNOL 2015. [DOI: 10.1080/01932691.2015.1080612] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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188
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Debnath A, Schäfer LV. Structure and Dynamics of Phospholipid Nanodiscs from All-Atom and Coarse-Grained Simulations. J Phys Chem B 2015; 119:6991-7002. [PMID: 25978497 DOI: 10.1021/acs.jpcb.5b02101] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated structural and dynamical properties of nanodiscs comprising dimyristoylphosphatidylcholine (DMPC) lipids and major scaffold protein MSP1Δ(1-22) from human apolipoprotein A-1 using combined all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. The computational efficiency of the Martini-CG force field enables the spontaneous self-assembly of lipids and scaffold proteins into stable nanodisc structures on time scales up to tens of microseconds. Subsequent all-atom and CG-MD simulations reveal that the lipids in the nanodisc have lower configurational entropy and higher acyl tail order than in a lamellar bilayer phase. These altered average properties arise from rather differential behavior of lipids, depending on their location in the nanodisc. Since the scaffold proteins exert constrictive forces from the outer rim of the disc toward its center, lipids at the center of the nanodisc are highly ordered, whereas annular lipids that are in contact with the MSP proteins are remarkably disordered due to perturbed packing. Although specific differences between all-atom and CG simulations are also evident, the results obtained at both levels of resolution are in overall good agreement with each other and provide atomic level interpretations of recent experiments. Thus, the present study highlights the applicability of multiscale simulation approaches for nanodisc systems and opens the way for future applications, including the study of nanodisc-embedded membrane proteins.
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Affiliation(s)
- Ananya Debnath
- †Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342 011, India
| | - Lars V Schäfer
- ‡Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, D-44780 Bochum, Germany
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189
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Davoudi S, Amjad‐Iranagh S, Zaeifi Yamchi M. Molecular dynamic simulation of Ca
2+
‐ATPase interacting with lipid bilayer membrane. IET Nanobiotechnol 2015; 9:85-94. [DOI: 10.1049/iet-nbt.2013.0073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Samaneh Davoudi
- Chemical Engineering DepartmentAmirkabir University of TechnologyTehranIran
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190
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Benedetto A, Bingham RJ, Ballone P. Structure and dynamics of POPC bilayers in water solutions of room temperature ionic liquids. J Chem Phys 2015; 142:124706. [DOI: 10.1063/1.4915918] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Antonio Benedetto
- School of Physics, University College Dublin, Dublin 4, Ireland
- Laboratory for Neutron Scattering and Imaging, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Richard J. Bingham
- York Centre for Complex Systems Analysis, University of York, York YO10 5GE, United Kingdom
| | - Pietro Ballone
- Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia (IIT), 00185 Roma, Italy
- Department of Physics, Università di Roma “La Sapienza,” 00185 Roma, Italy
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191
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Marbella LE, Yin B, Spence MM. Investigating the Order Parameters of Saturated Lipid Molecules under Various Curvature Conditions on Spherical Supported Lipid Bilayers. J Phys Chem B 2015; 119:4194-202. [DOI: 10.1021/jp510322t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lauren E. Marbella
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Bocheng Yin
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Megan M. Spence
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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192
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Carr M, MacPhee CE. Membrainy: a 'smart', unified membrane analysis tool. SOURCE CODE FOR BIOLOGY AND MEDICINE 2015; 10:3. [PMID: 26060507 PMCID: PMC4460882 DOI: 10.1186/s13029-015-0033-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/19/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND The study of biological membranes using Molecular Dynamics has become an increasingly popular means by which to investigate the interactions of proteins, peptides and potentials with lipid bilayers. These interactions often result in changes to the properties of the lipids which can modify the behaviour of the membrane. Membrainy is a unified membrane analysis tool that contains a broad spectrum of analytical techniques to enable: measurement of acyl chain order parameters; presentation of 2D surface and thickness maps; determination of lateral and axial headgroup orientations; measurement of bilayer and leaflet thickness; analysis of the annular shell surrounding membrane-embedded objects; quantification of gel percentage; time evolution of the transmembrane voltage; area per lipid calculations; and quantification of lipid mixing/demixing entropy. RESULTS Each analytical component within Membrainy has been tested on a variety of lipid bilayer systems and was found to be either comparable to or an improvement upon existing software. For the analytical techniques that have no direct comparable software, our results were confirmed with experimental data. CONCLUSIONS Membrainy is a user-friendly, intelligent membrane analysis tool that automatically interprets a variety of input formats and force fields, is compatible with both single and double bilayers, and capable of handling asymmetric bilayers and lipid flip-flopping. Membrainy has been designed for ease of use, requiring no installation or configuration and minimal user-input to operate.
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Affiliation(s)
- Matthew Carr
- Institute for Condensed Matter and Complex Systems, School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh, UK
| | - Cait E MacPhee
- Institute for Condensed Matter and Complex Systems, School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh, UK
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193
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Guo C, Côté S, Mousseau N, Wei G. Distinct helix propensities and membrane interactions of human and rat IAPP(1-19) monomers in anionic lipid bilayers. J Phys Chem B 2015; 119:3366-76. [PMID: 25646717 DOI: 10.1021/jp5111357] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Islet amyloid polypeptide, IAPP or amylin, is a 37-residue peptide hormone coexpressed with insulin by pancreatic β-cells. The aggregation of human IAPP (hIAPP) into amyloid deposits is associated with type II diabetes. Substantial evidence suggests that the interaction of anionic membranes with hIAPP may facilitate peptide aggregation and the N-terminal 1-19 fragment (IAPP(1-19)) plays an important role in peptide-membrane interaction. As a first step to understand how structural differences between human and rat IAPP peptides in membranes may influence the later oligomerization process, we have investigated the structures and orientations of hIAPP(1-19) and the less toxic rIAPP(1-19) (i.e., the H18R mutant of hIAPP(1-19)) monomers in anionic POPG bilayers by performing replica exchange molecular dynamics (REMD) simulations. On the basis of ∼20 μs REMD simulations started from a random coil conformation of the peptide placed in water, we find that unfolded h(r)IAPP(1-19) can insert into the bilayers and the membrane-bound peptide stays mainly at the lipid head-tail interface. hIAPP(1-19) displays higher helix propensity than rIAPP(1-19), especially in the L12-L16 region. The helix is oriented parallel to the bilayer surface and buried in the membrane 0.3-0.8 nm below the phosphorus atoms, consistent with previous electron paramagnetic resonance data. The helical conformation is an amphiphilic helix with its hydrophilic and hydrophobic faces pointing, respectively, to the lipid head and tail regions. The H18R substitution enhances the electrostatic interactions of IAPP(1-19) with the membrane, while it weakens the intrapeptide interactions crucial for helix formation, thus leading to lower helix propensity of rIAPP(1-19). Implications of our simulation results on the membrane-mediated IAPP(1-19) oligomerization are discussed.
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Affiliation(s)
- Cong Guo
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University , 220 Handan Road, Shanghai 200433, China
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194
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Abstract
In this chapter we describe the use of solid state nuclear magnetic spectroscopy to study the structure of lyotropic phases and lipid model membranes and show its ability to probe, site specifically, at a sub-Ångstrom resolution. Here, we demonstrate the immense versatility of the technique and its ability to provide information on the different liquid crystalline phases present. A multinuclear for example (31)P, (1)H, and (13)C approach is able to elucidate both the structure and dynamics over a wide variety of timescales. This coupled with a non-perturbing label (2)H is able to provide information such as the order parameters for a wide variety of different liquid phases.
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Affiliation(s)
- Arwen I I Tyler
- Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK,
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195
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Filipe HAL, Santos LS, Prates Ramalho JP, Moreno MJ, Loura LMS. Behaviour of NBD-head group labelled phosphatidylethanolamines in POPC bilayers: a molecular dynamics study. Phys Chem Chem Phys 2015; 17:20066-79. [DOI: 10.1039/c5cp01596k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An NBD-diC16PE/POPC bilayer with typical fluorophore inverted-snorkelling configurations, and mass density profiles across the membrane. The wide distribution of the NBD fluorophore lies at the origin of its complex emission kinetics.
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Affiliation(s)
- Hugo A. L. Filipe
- Departamento de Química
- Faculty of Science and Technnology
- University of Coimbra
- Rua Larga
- Portugal
| | - Lennon S. Santos
- Departamento de Química
- Faculty of Science and Technnology
- University of Coimbra
- Rua Larga
- Portugal
| | - J. P. Prates Ramalho
- Departamento de Química
- Escola de Ciências e Tecnologia
- Universidade de Évora
- Rua Romão Ramalho
- Portugal
| | - Maria João Moreno
- Departamento de Química
- Faculty of Science and Technnology
- University of Coimbra
- Rua Larga
- Portugal
| | - Luís M. S. Loura
- Centro de Química de Coimbra
- Rua Larga
- Portugal
- Centro de Neurociências e Biologia Celular
- Universidade de Coimbra
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196
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Padilla-Chavarría HI, Guizado TRC, Pimentel AS. Molecular dynamics of dibenz[a,h]anthracene and its metabolite interacting with lung surfactant phospholipid bilayers. Phys Chem Chem Phys 2015. [DOI: 10.1039/c5cp01443c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Dibenz[a,h]anthracene and its metabolite may form aggregates, which have implications in the clearance process of the lung surfactant phospholipid bilayers.
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Affiliation(s)
- Helmut I. Padilla-Chavarría
- Departamento de Química
- Pontifícia Universidade Católica do Rio de Janeiro
- Rua Marques de São Vicente
- Rio de Janeiro
- Brazil
| | - Teobaldo R. C. Guizado
- Departamento de Química
- Pontifícia Universidade Católica do Rio de Janeiro
- Rua Marques de São Vicente
- Rio de Janeiro
- Brazil
| | - Andre S. Pimentel
- Departamento de Química
- Pontifícia Universidade Católica do Rio de Janeiro
- Rua Marques de São Vicente
- Rio de Janeiro
- Brazil
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197
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Slingsby JG, Vyas S, Maupin CM. A charge-modified general amber force field for phospholipids: improved structural properties in the tensionless ensemble. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.985675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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198
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Free energy simulations of amylin I26P mutation in a lipid bilayer. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 44:37-47. [DOI: 10.1007/s00249-014-0999-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
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199
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Baker MK, Abrams CF. Dynamics of lipids, cholesterol, and transmembrane α-helices from microsecond molecular dynamics simulations. J Phys Chem B 2014; 118:13590-600. [PMID: 25380392 PMCID: PMC4254001 DOI: 10.1021/jp507027t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Extensive all-atom molecular dynamics (∼24 μs total) allowed exploration of configurational space and calculation of lateral diffusion coefficients of the components of a protein-embedded, cholesterol-containing model bilayer. The three model membranes are composed of an ∼50/50 (by mole) dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayer and contained an α-helical transmembrane protein (HIV-1 gp41 TM). Despite the high concentration of cholesterol, normal Brownian motion was observed and the calculated diffusion coefficients (on the order of 10(-9) cm(2)/s) are consistent with experiments. Diffusion is sensitive to a variety of parameters, and a temperature difference of ∼4 K from thermostat artifacts resulted in 2-10-fold differences in diffusion coefficients and significant differences in lipid order, membrane thickness, and unit cell area. Also, the specific peptide sequence likely underlies the consistently observed faster diffusion in one leaflet. Although the simulations here present molecular dynamics (MD) an order of magnitude longer than those from previous studies, the three systems did not approach ergodicity. The distributions of cholesterol and DPPC around the peptides changed on the microsecond time scale, but not significantly enough to thoroughly explore configurational space. These simulations support conclusions of other recent microsecond MD in that even longer time scales are needed for equilibration of model membranes and simulations of more realistic cellular or viral bilayers.
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Affiliation(s)
- Michelle K Baker
- Department of Chemical and Biological Engineering, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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200
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Laner M, Horta BAC, Hünenberger PH. Long-timescale motions in glycerol-monopalmitate lipid bilayers investigated using molecular dynamics simulation. J Mol Graph Model 2014; 55:48-64. [PMID: 25437095 DOI: 10.1016/j.jmgm.2014.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 10/24/2022]
Abstract
The occurrence of long-timescale motions in glycerol-1-monopalmitate (GMP) lipid bilayers is investigated based on previously reported 600 ns molecular dynamics simulations of a 2×8×8 GMP bilayer patch in the temperature range 302-338 K, performed at three different hydration levels, or in the presence of the cosolutes methanol or trehalose at three different concentrations. The types of long-timescale motions considered are: (i) the possible phase transitions; (ii) the precession of the relative collective tilt-angle of the two leaflets in the gel phase; (iii) the trans-gauche isomerization of the dihedral angles within the lipid aliphatic tails; and (iv) the flipping of single lipids across the two leaflets. The results provide a picture of GMP bilayers involving a rich spectrum of events occurring on a wide range of timescales, from the 100-ps range isomerization of single dihedral angles, via the 100-ns range of tilt precession motions, to the multi-μs range of phase transitions and lipid-flipping events.
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Affiliation(s)
- Monika Laner
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.
| | - Bruno A C Horta
- Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland; Dpto. de Engenharia Elétrica, PUC-Rio, Rio de Janeiro, Brazil; Dpto. de Ciências Biológicas, UEZO, Rio de Janeiro, Brazil.
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