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Xu C, Fracassi A, Baryiames CP, Bhattacharya A, Devaraj NK, Baiz CR. Sponge-phase Lipid Droplets as Synthetic Organelles: An Ultrafast Study of Hydrogen Bonding and Interfacial Environments. Chemphyschem 2023; 24:e202300404. [PMID: 37486881 DOI: 10.1002/cphc.202300404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023]
Abstract
Bottom-up design of biomimetic organelles has gained recent attention as a route towards understanding the transition between non-living matter and life. Despite various artificial lipid membranes being developed, the specific relations between lipid structure, composition, interfacial properties, and morphology are not currently understood. Sponge-phase droplets contain dense, nonlamellar lipid bilayer networks that capture the complexities of the endoplasmic reticulum (ER), making them ideal artificial models of such organelles. Here, we combine ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics simulations to investigate the interfacial H-bond networks in sponge-phase droplets composed of glycolipid and nonionic detergents. In the sponge phase, the interfacial environments are more hydrated and water molecules confined to the nanometer-scale aqueous channels in the sponge phase exhibit dynamics that are significantly slower compared to bulk water. Surfactant configurations and microscopic phase separation play a dominant role in determining membrane curvature and slow dynamics observed in the sponge phase. The studies suggest that H-bond networks within the nanometer-scale channels are disrupted not only by confinement but also by the interactions of surfactants, which extend 1-2 nm from the bilayer surface. The results provide a molecular-level description for controlling phase and morphology in the design of synthetic lipid organelles.
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Affiliation(s)
- Cong Xu
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St. Stop A5300, 78712-1224, Austin, TX, USA
| | - Alessandro Fracassi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, 92093, La Jolla, CA, USA
| | - Christopher P Baryiames
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St. Stop A5300, 78712-1224, Austin, TX, USA
| | - Ahanjit Bhattacharya
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, 92093, La Jolla, CA, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, 92093, La Jolla, CA, USA
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St. Stop A5300, 78712-1224, Austin, TX, USA
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2
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Li Y, Zhang J, Song P, Miao X, Liu G, Yang C, Wei X, Li N, Bian F. Small-Angle X-ray Scattering for PEGylated Liposomal Doxorubicin Drugs: An Analytical Model Comparison Study. Mol Pharm 2023; 20:4654-4663. [PMID: 37616278 DOI: 10.1021/acs.molpharmaceut.3c00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Liposomal delivery systems are recognized as efficient and safe platforms for chemotherapeutic agents, with doxorubicin-loaded liposomes being the most representative nanopharmaceuticals. Characterizing the structure of liposomal nanomedicines in high spatial and temporal resolution is critical to analyze and evaluate their stability and efficacy. Small-angle X-ray scattering (SAXS) is a powerful tool increasingly used to investigate liposomal delivery systems. In this study, we chose a Doxil-like PEGylated liposomal doxorubicin (PLD) as an example and characterized the liposomal drug structure using synchrotron SAXS. Classical analytical models, including the spherical-shell or flat-slab geometries with Gaussian or uniform electron density profiles, were used to model the internal structure of the liposomal membrane. A cylinder model was applied to fit the scattering from the drug crystal loaded in the liposomes. The high-resolution structures of the original drug, Caelyx, and a similar research drug prepared in our laboratory were characterized using these analytical models. The structural parameters of PLDs, including the thickness of the liposomal membrane and morphology of the drug crystal, were further compared. The results demonstrated that both spherical-shell and flat-slab geometries with Gaussian electron density distribution were suitable to elucidate the structural features of the liposomal membrane under a certain range of scattering vectors, while models with uniform electron density distribution exhibited poor fitting performance. This study highlights the technical features of SAXS, which provides structural information at the nanoscale for liposomal drugs. The demonstrated methods are reliable and easy-to-use for the structural analysis of liposomal drugs, which are helpful for a broader application of SAXS in the production and regulation of nanopharmaceuticals.
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Affiliation(s)
- Yiwen Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jianqiao Zhang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Panqi Song
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiaran Miao
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Guangfeng Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Chunming Yang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohui Wei
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Na Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Fenggang Bian
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Abhinav, Jurkiewicz P, Hof M, Allolio C, Sýkora J. Modulation of Anionic Lipid Bilayers by Specific Interplay of Protons and Calcium Ions. Biomolecules 2022; 12:1894. [PMID: 36551322 PMCID: PMC9775051 DOI: 10.3390/biom12121894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Biomembranes, important building blocks of living organisms, are often exposed to large local fluctuations of pH and ionic strength. To capture changes in the membrane organization under such harsh conditions, we investigated the mobility and hydration of zwitterionic and anionic lipid bilayers upon elevated H3O+ and Ca2+ content by the time-dependent fluorescence shift (TDFS) technique. While the zwitterionic bilayers remain inert to lower pH and increased calcium concentrations, anionic membranes are responsive. Specifically, both bilayers enriched in phosphatidylserine (PS) and phosphatidylglycerol (PG) become dehydrated and rigidified at pH 4.0 compared to at pH 7.0. However, their reaction to the gradual Ca2+ increase in the acidic environment differs. While the PG bilayers exhibit strong rehydration and mild loosening of the carbonyl region, restoring membrane properties to those observed at pH 7.0, the PS bilayers remain dehydrated with minor bilayer stiffening. Molecular dynamics (MD) simulations support the strong binding of H3O+ to both PS and PG. Compared to PS, PG exhibits a weaker binding of Ca2+ also at a low pH.
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Affiliation(s)
- Abhinav
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 2155/3, 182 23 Prague, Czech Republic
| | - Piotr Jurkiewicz
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 2155/3, 182 23 Prague, Czech Republic
| | - Martin Hof
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 2155/3, 182 23 Prague, Czech Republic
| | - Christoph Allolio
- Mathematical Institute of Charles University, Faculty of Mathematics and Physics, Charles University, Sokolovská 49/83, 186 75 Prague, Czech Republic
| | - Jan Sýkora
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 2155/3, 182 23 Prague, Czech Republic
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4
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Karathanou K, Bondar AN. Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183859. [PMID: 34999081 DOI: 10.1016/j.bbamem.2022.183859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Lipid membrane interfaces host reactions essential for the functioning of cells. The hydrogen-bonding environment at the membrane interface is particularly important for binding of proteins, drug molecules, and ions. We present here the implementation and applications of a depth-first search algorithm that analyzes dynamic lipid interaction networks. Lipid hydrogen-bond networks sampled transiently during simulations of lipid bilayers are clustered according to main types of topologies that characterize three-dimensional arrangements of lipids connected to each other via short water bridges. We characterize the dynamics of hydrogen-bonded lipid clusters in simulations of model POPE and POPE:POPG membranes that are often used for bacterial membrane proteins, in a model of the Escherichia coli membrane with six different lipid types, and in POPS membranes. We find that all lipids sample dynamic hydrogen-bonded networks with linear, star, or circular arrangements of the lipid headgroups, and larger networks with combinations of these three types of topologies. Overall, linear lipid-water bridges tend to be short. Water-mediated lipid clusters in all membranes with PE lipids tend to be somewhat small, with about four lipids in all membranes studied here. POPS membranes allow circular arrangements of three POPS lipids to be sampled frequently, and complex arrangements of linear, star, and circular paths may also be sampled. These findings suggest a molecular picture of the membrane interface whereby lipid molecules transiently connect in clusters with somewhat small spatial extension.
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Affiliation(s)
- Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics, Arnimallee 14, D-14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, Bucharest-Măgurele 077125, Romania; Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany.
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5
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Bohinc K, Špadina M, Reščič J, Shimokawa N, Spada S. Influence of Charge Lipid Head Group Structures on Electric Double Layer Properties. J Chem Theory Comput 2021; 18:448-460. [PMID: 34937343 PMCID: PMC8757465 DOI: 10.1021/acs.jctc.1c00800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this study we
derived a model for a multicomponent lipid monolayer
in contact with an aqueous solution by means of a generalized classical
density functional theory and Monte Carlo simulations. Some of the
important biological lipid systems were studied as monolayers composed
of head groups with different shapes and charge distributions. Starting
from the free energy of the system, which includes the electrostatic
interactions, additional internal degrees of freedom are included
as positional and orientational entropic contributions to the free
energy functional. The calculus of variation was used to derive Euler–Lagrange
equations, which were solved numerically by the finite element method.
The theory and Monte Carlo simulations predict that there are mainly
two distinct regions of the electric double layer: (1) the interfacial
region, with thickness less than or equal to the length of the fully
stretched conformation of the lipid head group, and (2) the outside
region, which follows the usual screening of the interface. In the
interfacial region, the electric double layer is strongly perturbed,
and electrostatic profiles and ion distributions have functionality
distinct to classical mean-field theories. Based purely on Coulomb
interactions, the theory suggests that the dominant effect on the
lipid head group conformation is from the charge density of the interface
and the structured lipid mole fraction in the monolayer, rather than
the salt concentration in the system.
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Affiliation(s)
- Klemen Bohinc
- Faculty of Health Sciences, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Mario Špadina
- Faculty of Health Sciences, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Jurij Reščič
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - Naofumi Shimokawa
- Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Simone Spada
- National Institute of Oceanography and Applied Geophysics - OGS, 34010 Trieste, Italy
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6
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Chen C, Chen J, Yu Q, Zhang J, Niu X, Hao L, Yang L, Zhao Y. Effects of salts on the self-assembly behavior and antibacterial activity of a surfactant-like peptide. SOFT MATTER 2020; 16:9758-9768. [PMID: 33000840 DOI: 10.1039/d0sm01519a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Self-assembling peptides have become one of the most promising antibacterial agents due to their superior properties, such as simple molecular composition, favorable assembly structures, and rich designability. For maximum application in vivo, their activities in the presence of salts are desirable, however, the potent correlation between peptide nanostructures, antibacterial activity, and salt resistance behavior remains poorly explored. Previously, we have demonstrated that the potent antibacterial activity of a designed surfactant-like peptide Ac-A9K-NH2 benefited from its high self-assembly ability and appropriate size of its self-assembled nanostructures. In this study, we investigated the effect of salts on its self-assembly behavior and antibacterial activity. The results indicated that the flexible and long nanofibrils formed by Ac-A9K-NH2 in the presence of CaCl2 were adverse to its membrane insertion, leading to the reduction of antibacterial activity. Comparatively, Ac-A9K-NH2 maintained its potent antibacterial activity in the presence of NaCl due to its suitable shape and size of nanostructures. The newly formed nanofibers and nanorods facilitated the penetration of peptides into the bacterial membrane, forming nanopores and eventually leading to the lysis of bacteria. The high antibacterial activity and NaCl tolerance of Ac-A9K-NH2 make it a promising antibacterial agent at elevated salt concentrations.
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Affiliation(s)
- Cuixia Chen
- Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), 66 Changjiang West Road, Qingdao Economic Development Zone, Qingdao 266555, China.
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7
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Zander T, Garamus VM, Dédinaité A, Claesson PM, Bełdowski P, Górny K, Dendzik Z, Wieland DCF, Willumeit-Römer R. Influence of the Molecular Weight and the Presence of Calcium Ions on the Molecular Interaction of Hyaluronan and DPPC. Molecules 2020; 25:E3907. [PMID: 32867196 PMCID: PMC7504306 DOI: 10.3390/molecules25173907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/18/2020] [Accepted: 08/25/2020] [Indexed: 12/03/2022] Open
Abstract
Hyaluronan is an essential physiological bio macromolecule with different functions. One prominent area is the synovial fluid which exhibits remarkable lubrication properties. However, the synovial fluid is a multi-component system where different macromolecules interact in a synergetic fashion. Within this study we focus on the interaction of hyaluronan and phospholipids, which are thought to play a key role for lubrication. We investigate how the interactions and the association structures formed by hyaluronan (HA) and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) are influenced by the molecular weight of the bio polymer and the ionic composition of the solution. We combine techniques allowing us to investigate the phase behavior of lipids (differential scanning calorimetry, zeta potential and electrophoretic mobility) with structural investigation (dynamic light scattering, small angle scattering) and theoretical simulations (molecular dynamics). The interaction of hyaluronan and phospholipids depends on the molecular weight, where hyaluronan with lower molecular weight has the strongest interaction. Furthermore, the interaction is increased by the presence of calcium ions. Our simulations show that calcium ions are located close to the carboxylate groups of HA and, by this, reduce the number of formed hydrogen bonds between HA and DPPC. The observed change in the DPPC phase behavior can be attributed to a local charge inversion by calcium ions binding to the carboxylate groups as the binding distribution of hyaluronan and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine is not changed.
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Affiliation(s)
- Thomas Zander
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht: Centre for Materials and Costal Research, Max-Planck-Straße 1, 21502 Geesthacht, Germany; (T.Z.); (V.M.G.); (R.W.-R.)
| | - Vasil M. Garamus
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht: Centre for Materials and Costal Research, Max-Planck-Straße 1, 21502 Geesthacht, Germany; (T.Z.); (V.M.G.); (R.W.-R.)
| | - Andra Dédinaité
- Department of Chemistry, Surface and Corrosion Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Drottning Kristinas väg 51, SE-10044 Stockholm, Sweden; (A.D.); (P.M.C.)
- Division of Bioscience and Materials, RISE Research Institutes of Sweden, SE-114 86 Stockholm, Sweden
| | - Per M. Claesson
- Department of Chemistry, Surface and Corrosion Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Drottning Kristinas väg 51, SE-10044 Stockholm, Sweden; (A.D.); (P.M.C.)
- Division of Bioscience and Materials, RISE Research Institutes of Sweden, SE-114 86 Stockholm, Sweden
| | - Piotr Bełdowski
- Institue of Mathematics and Physics, UTP University of Science and Technology, al. Kaliskiego 7, 85-796 Bydgoszcz, Poland;
| | - Krzysztof Górny
- Faculty of Science and Technology, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500 Chorzów, Poland; (K.G.); (Z.D.)
| | - Zbigniew Dendzik
- Faculty of Science and Technology, University of Silesia in Katowice, 75 Pułku Piechoty 1A, 41-500 Chorzów, Poland; (K.G.); (Z.D.)
| | - D. C. Florian Wieland
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht: Centre for Materials and Costal Research, Max-Planck-Straße 1, 21502 Geesthacht, Germany; (T.Z.); (V.M.G.); (R.W.-R.)
| | - Regine Willumeit-Römer
- Institute of Materials Research, Helmholtz-Zentrum Geesthacht: Centre for Materials and Costal Research, Max-Planck-Straße 1, 21502 Geesthacht, Germany; (T.Z.); (V.M.G.); (R.W.-R.)
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8
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Szczelina R, Baczynski K, Markiewicz M, Pasenkiewicz-Gierula M. Network of lipid interconnections at the interfaces of galactolipid and phospholipid bilayers. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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9
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Teschke O, Roberto de Castro J, Soares DM. Imaging Ion Pairs Forming Structural Arrangements in Interfacial Regions. ACS OMEGA 2019; 4:15684-15693. [PMID: 31572871 PMCID: PMC6761755 DOI: 10.1021/acsomega.9b02299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Abstract
A technique to image ion pairs in solution is reported. We investigated structural and dynamic properties of ion-pair distributions deposited on highly oriented pyrolytic graphite (HOPG) surfaces in electrolyte solutions. Atomic force microscopy images of HOPG immersed in NaCl and KCl solutions display regular arrangements on top of the hexagonal carbon rings forming the HOPG atomic structure. These arrangements are the result of the low value of the aqueous interfacial dielectric constant (εr ≈ 3-11). The measured ion-pair radius is a function of the salt present in the solution; for KCl, the ion-pair radius is equal or smaller than 0.42 nm; for NaCl, the ion-pair radius is 0.36 nm. A comparison of these values with their crystalline lattice dimensions indicates that both KCl and NaCl ion pairs in solution at the HOPG/solution interfacial region exist as tight contact ion pairs in quasistationary distributions. The NaCl ion-pair distribution forms an aligned arrangement, and the KCl distribution is formed by intercalated pairs.
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Affiliation(s)
- Omar Teschke
- E-mail: . Phone: 55 (19) 3521-4148Fax: 55 (19) 3521-5637
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10
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Podewitz M, Wang Y, Gkeka P, von Grafenstein S, Liedl KR, Cournia Z. Phase Diagram of a Stratum Corneum Lipid Mixture. J Phys Chem B 2018; 122:10505-10521. [DOI: 10.1021/acs.jpcb.8b07200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maren Podewitz
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Yin Wang
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Paraskevi Gkeka
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Susanne von Grafenstein
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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11
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Rezaei Sani SM, Akhavan M, Jalili S. Salt-induced effects on natural and inverse DPPC lipid membranes: Molecular dynamics simulation. Biophys Chem 2018; 239:7-15. [DOI: 10.1016/j.bpc.2018.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/22/2018] [Accepted: 04/22/2018] [Indexed: 11/29/2022]
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12
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Frigini EN, López Cascales JJ, Porasso RD. Molecular dynamics simulations of glyphosate in a DPPC lipid bilayer. Chem Phys Lipids 2018; 213:111-117. [PMID: 29684323 DOI: 10.1016/j.chemphyslip.2018.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 11/26/2022]
Abstract
Extensive molecular dynamics simulations have been performed to study the effect of glyphosate (in their neutral and charged forms, GLYP and GLYP2-, respectively) on fully hydrated DiPalmitoylPhosphatidylCholine (DPPC) lipid bilayer. First, we calculated the free energy profile (using the Umbrella Sampling technique) for both states of charge of glyphosate. The minimum value for the free energy for GLYP is ∼-60 kJ mol-1 located at z = ±1.7 nm (from the lipid bilayer center), and there is almost no maximum at the center of the lipid bilayer. By contrast, the minimum for GLYP2- is ∼-35 kJ mol-1 located at z = ± 1.4 nm (from the lipid bilayer center), and the maximum reaches ∼35 kJ mol-1 at the center of the lipid bilayer. Then, different lipid bilayer properties were analyzed for different glyphosate:lipid (G:L) ratios. The mean area per lipid was slightly affected, increasing only 5% (in the presence of glyphosate at high concentrations), which is in agreement with the slight decrease in deuterium order parameters. As for the thickness of the bilayer, it is observed that the state of charge produces opposite effects. On one hand, the neutral state produces an increase in the thickness of the lipid bilayer; on the other, the charged form produces a decrease in the thickness, which not depend linearly on the G:L ratios, either. The orientation of the DPPC head groups is practically unaffected throughout the range of the G:L ratios studied. Finally, the mobility of the lipids of the bilayer is strongly affected by the presence of glyphosate, considerably increasing its lateral diffusion coefficient noteworthy (one order of magnitude), with increasing G:L ratio.
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Affiliation(s)
- Ezequiel N Frigini
- Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, Ejército de los Andes 950, D5700HHW San Luis, Argentina
| | - J J López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoléculas (BioMac), Área de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Rodolfo D Porasso
- Instituto de Matemática Aplicada San Luis, IMASL, Universidad Nacional de San Luis and CONICET, Ejército de los Andes 950, D5700HHW San Luis, Argentina.
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13
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Ishiyama T, Shirai S, Okumura T, Morita A. Molecular dynamics study of structure and vibrational spectra at zwitterionoic lipid/aqueous KCl, NaCl, and CaCl 2 solution interfaces. J Chem Phys 2018; 148:222801. [PMID: 29907059 DOI: 10.1063/1.5006543] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Molecular dynamics (MD) simulations of KCl, NaCl, and CaCl2 solution/dipalmytoylphosphatidylcholine lipid interfaces were performed to analyze heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectra in relation to the interfacial water structure. The present MD simulation well reproduces the experimental spectra and elucidates a specific cation effect on the interfacial structure. The K+, Na+, and Ca2+ cation species penetrate in the lipid layer more than the anions in this order, due to the electrostatic interaction with negative polar groups of lipid, and the electric double layer between the cations and anions cancels the intrinsic orientation of water at the water/lipid interface. These mechanisms explain the HD-VSFG spectrum of the water/lipid interface and its spectral perturbation by adding the ions. The lipid monolayer reverses the order of surface preference of the cations at the solution/lipid interface from that at the solution/air interface.
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Affiliation(s)
- Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Shinnosuke Shirai
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Tomoaki Okumura
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Akihiro Morita
- Department of Chemistry, Graduate School of Science Tohoku University, Sendai 980-8578, Japan and Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto 615-8520, Japan
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14
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The electrochemical phase behaviour of chemically asymmetric lipid bilayers supported at Au(111) electrodes. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2017.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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15
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Dynamic Water Hydrogen-Bond Networks at the Interface of a Lipid Membrane Containing Palmitoyl-Oleoyl Phosphatidylglycerol. J Membr Biol 2018. [DOI: 10.1007/s00232-018-0023-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Factor effects and mechanisms of the adsorption of Hg(II), Cd(II) and Ni(II) on charged liposomes. Colloids Surf A Physicochem Eng Asp 2018. [DOI: 10.1016/j.colsurfa.2017.11.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Sinha S, Sachar HS, Das S. Effect of Plasma Membrane Semipermeability in Making the Membrane Electric Double Layer Capacitances Significant. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:1760-1766. [PMID: 29294274 DOI: 10.1021/acs.langmuir.7b02939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Electric double layers (or EDLs) formed at the membrane-electrolyte interface (MEI) and membrane-cytosol interface (MCI) of a charged lipid bilayer plasma membrane develop finitely large capacitances. However, these EDL capacitances are often much larger than the intrinsic capacitance of the membrane, and all of these capacitances are in series. Consequently, the effect of these EDL capacitances in dictating the overall membrane-EDL effective capacitance Ceff becomes negligible. In this paper, we challenge this conventional notion pertaining to the membrane-EDL capacitances. We demonstrate that, on the basis of the system parameters, the EDL capacitance for both the permeable and semipermeable membranes can be small enough to influence Ceff. For the semipermeable membranes, however, this lowering of the EDL capacitance can be much larger, ensuring a reduction of Ceff by more than 20-25%. Furthermore, for the semipermeable membranes, the reduction in Ceff is witnessed over a much larger range of system parameters. We attribute such an occurrence to the highly nonintuitive electrostatic potential distribution associated with the recently discovered phenomena of charge-inversion-like electrostatics and the attainment of a positive zeta potential at the MCI for charged semipermeable membranes. We anticipate that our findings will impact the quantification and the identification of a large number of biophysical phenomena that are probed by measuring the plasma membrane capacitance.
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Affiliation(s)
- Shayandev Sinha
- Department of Mechanical Engineering, University of Maryland , College Park, Maryland 20742, United States
| | - Harnoor Singh Sachar
- Department of Mechanical Engineering, University of Maryland , College Park, Maryland 20742, United States
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland , College Park, Maryland 20742, United States
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18
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A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids. Molecules 2017; 23:molecules23010077. [PMID: 29301229 PMCID: PMC6017617 DOI: 10.3390/molecules23010077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022] Open
Abstract
In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.
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19
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Jing H, Das S. Electric double layer electrostatics of lipid-bilayer-encapsulated nanoparticles: Toward a better understanding of protocell electrostatics. Electrophoresis 2017; 39:752-759. [PMID: 29235657 DOI: 10.1002/elps.201700286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/08/2017] [Accepted: 11/08/2017] [Indexed: 11/09/2022]
Abstract
Lipid-bilayer-encapsulated nanoparticles (LBLENPs) or NP-supported LBL systems, such as protocells (which are lipid bilayer encapsulated mesoporous silica nanoparticles or MSNPs) have received extensive attention for applications like targeted drug and gene deliveries, multimodal diagnostics, characterization of membrane-geometry sensitive molecules, etc. Very often electrostatic-mediated interactions have been hypothesized to play key roles in the functioning of these LBLENPs. Despite that, very little has been done to theoretically quantify the fundamental electric double layer (EDL) electrostatics of such LBLENPs. In this study, we develop an EDL theory to describe the electrostatics of such LBLENPs. We show that the electrostatics is a manifestation of the charged/dielectric nature of the NP, LBL structure and charging, and the ionic environment in which the LBLENPs are present. We also establish that for certain conditions of charging of the NP one witnesses a most remarkable charge inversion like electrostatics within the LBL membrane or the NP itself. We anticipate that our findings will provide an extremely useful platform for better understanding the fabrication and functioning of such LBLENPs and discuss examples where our theory can be useful.
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Affiliation(s)
- Haoyuan Jing
- Department of Mechanical Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland, College Park, MD, 20742, USA
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20
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Vosahlikova M, Ujcikova H, Chernyavskiy O, Brejchova J, Roubalova L, Alda M, Svoboda P. Effect of therapeutic concentration of lithium on live HEK293 cells; increase of Na + /K + -ATPase, change of overall protein composition and alteration of surface layer of plasma membrane. Biochim Biophys Acta Gen Subj 2017; 1861:1099-1112. [DOI: 10.1016/j.bbagen.2017.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 01/20/2017] [Accepted: 02/10/2017] [Indexed: 12/19/2022]
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21
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Chakraborty H, Lentz BR, Kombrabail M, Krishnamoorthy G, Chattopadhyay A. Depth-Dependent Membrane Ordering by Hemagglutinin Fusion Peptide Promotes Fusion. J Phys Chem B 2017; 121:1640-1648. [DOI: 10.1021/acs.jpcb.7b00684] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hirak Chakraborty
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
- School
of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Barry R. Lentz
- Department
of Biochemistry and Biophysics and Program in Molecular and Cellular
Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | - Mamata Kombrabail
- Department
of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhaba Road, Mumbai, India
| | - G. Krishnamoorthy
- Department
of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhaba Road, Mumbai, India
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22
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Tarafdar PK, Chakraborty H, Bruno MJ, Lentz BR. Phosphatidylserine-Dependent Catalysis of Stalk and Pore Formation by Synaptobrevin JMR-TMD Peptide. Biophys J 2016; 109:1863-72. [PMID: 26536263 DOI: 10.1016/j.bpj.2015.08.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 08/16/2015] [Accepted: 08/26/2015] [Indexed: 12/18/2022] Open
Abstract
Although the importance of a SNARE complex in neurotransmitter release is widely accepted, there exist different views on how the complex promotes fusion. One hypothesis is that the SNARE complex's ability to bring membranes into contact is sufficient for fusion, another points to possible roles of juxtamembrane regions (JMRs) and transmembrane domains (TMDs) in catalyzing lipid rearrangement, and another notes the complex's presumed ability to bend membranes near the point of contact. Here, we performed experiments with highly curved vesicles brought into contact using low concentrations of polyethylene glycol (PEG) to investigate the influence of the synaptobrevin (SB) TMD with an attached JMR (SB-JMR-TMD) on the rates of stalk and pore formation during vesicle fusion. SB-JMR-TMD enhanced the rates of stalk and fusion pore (FP) formation in a sharply sigmoidal fashion. We observed an optimal influence at an average of three peptides per vesicle, but only with phosphatidylserine (PS)-containing vesicles. Approximately three SB-JMR-TMDs per vesicle optimally ordered the bilayer interior and excluded water in a similar sigmoidal fashion. The catalytic influences of hexadecane and SB-JMR-TMD on fusion kinetics showed little in common, suggesting different mechanisms. Both kinetic and membrane structure measurements support the hypotheses that SB-JMR-TMD 1) catalyzes initial intermediate formation as a result of its basic JMR disrupting ordered interbilayer water and permitting closer interbilayer approach, and 2) catalyzes pore formation by forming a membrane-spanning complex that increases curvature stress at the circumference of the hemifused diaphragm of the prepore intermediate state.
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Affiliation(s)
- Pradip K Tarafdar
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Hirak Chakraborty
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Michael J Bruno
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Barry R Lentz
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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23
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Casciola M, Tarek M. A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2278-2289. [PMID: 27018309 DOI: 10.1016/j.bbamem.2016.03.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/26/2022]
Abstract
The transport of chemical compounds across the plasma membrane into the cell is relevant for several biological and medical applications. One of the most efficient techniques to enhance this uptake is reversible electroporation. Nevertheless, the detailed molecular mechanism of transport of chemical species (dyes, drugs, genetic materials, …) following the application of electric pulses is not yet fully elucidated. In the past decade, molecular dynamics (MD) simulations have been conducted to model the effect of pulsed electric fields on membranes, describing several aspects of this phenomenon. Here, we first present a comprehensive review of the results obtained so far modeling the electroporation of lipid membranes, then we extend these findings to study the electrotransfer across lipid bilayers subject to microsecond pulsed electric fields of Tat11, a small hydrophilic charged peptide, and of siRNA. We use in particular a MD simulation protocol that allows to characterize the transport of charged species through stable pores. Unexpectedly, our results show that for an electroporated bilayer subject to transmembrane voltages in the order of 500mV, i.e. consistent with experimental conditions, both Tat11 and siRNA can translocate through nanoelectropores within tens of ns. We discuss these results in comparison to experiments in order to rationalize the mechanism of drug uptake by cells. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Maura Casciola
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; Department of Information Engineering, Electronics and Telecommunications (D.I.E.T), Sapienza University of Rome, 00184 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy
| | - Mounir Tarek
- Université de Lorraine, UMR 7565, F-54506 Vandoeuvre les Nancy, France; CNRS, UMR 7565, F-54506 Vandoeuvre les Nancy, France.
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24
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Smolentsev N, Lütgebaucks C, Okur HI, de Beer AGF, Roke S. Intermolecular Headgroup Interaction and Hydration as Driving Forces for Lipid Transmembrane Asymmetry. J Am Chem Soc 2016; 138:4053-60. [DOI: 10.1021/jacs.5b11776] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Nikolay Smolentsev
- Laboratory for Fundamental
BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute
of Materials Science (IMX), School of Engineering (STI), and Lausanne
Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Cornelis Lütgebaucks
- Laboratory for Fundamental
BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute
of Materials Science (IMX), School of Engineering (STI), and Lausanne
Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Halil I. Okur
- Laboratory for Fundamental
BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute
of Materials Science (IMX), School of Engineering (STI), and Lausanne
Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Alex G. F. de Beer
- Laboratory for Fundamental
BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute
of Materials Science (IMX), School of Engineering (STI), and Lausanne
Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sylvie Roke
- Laboratory for Fundamental
BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute
of Materials Science (IMX), School of Engineering (STI), and Lausanne
Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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25
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26
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Pasenkiewicz-Gierula M, Baczynski K, Markiewicz M, Murzyn K. Computer modelling studies of the bilayer/water interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2305-2321. [PMID: 26825705 DOI: 10.1016/j.bbamem.2016.01.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/18/2016] [Accepted: 01/21/2016] [Indexed: 01/24/2023]
Abstract
This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Krzysztof Baczynski
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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27
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Basu I, Manna M, Mukhopadhyay C. Insights into the behavioral difference of water in the presence of GM1. FEBS Lett 2015; 589:3887-92. [DOI: 10.1016/j.febslet.2015.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/16/2015] [Accepted: 11/16/2015] [Indexed: 11/26/2022]
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28
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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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29
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Murzyn K, Pasenkiewicz-Gierula M. Structural Properties of the Water/Membrane Interface of a Bilayer Built of the E. coli Lipid A. J Phys Chem B 2015; 119:5846-56. [DOI: 10.1021/jp5119629] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Krzysztof Murzyn
- Department
of Computational
Biophysics and Bioinformatics, Faculty of Biochemistry,
Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Marta Pasenkiewicz-Gierula
- Department
of Computational
Biophysics and Bioinformatics, Faculty of Biochemistry,
Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
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30
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Curtis E, Xiao X, Sofou S, Hall CK. Phase separation behavior of mixed lipid systems at neutral and low pH: coarse-grained simulations with DMD/LIME. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:1086-1094. [PMID: 25549801 PMCID: PMC4310635 DOI: 10.1021/la504082x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/22/2014] [Indexed: 05/29/2023]
Abstract
We extend LIME, an intermediate resolution, implicit solvent model for phospholipids previously used in discontinuous molecular dynamics simulations of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer formation at 325 K, to the description of the geometry and energetics of 1,2-distearoyl-sn-glycero-3-phospho-L-serine (DSPS) and 1,2-dihenarachidoyl-sn-glycero-3-phosphocholine (21PC) and mixtures thereof at both neutral and low pH at 310 K. A multiscale modeling approach is used to calculate the LIME parameters from atomistic simulation data on a mixed DPPC/DSPS system at different pH values. In the model, 17 coarse-grained sites represent DSPS and 18 coarse-grained sites represent 21PC. Each of these coarse-grained sites is classified as 1 of 9 types. LIME/DMD simulations of equimolar bilayers show the following: (1) 21PC/DSPS bilayers with and without surface area restrictions separate faster at low pH than at neutral pH, (2) 21PC/DSPS systems separate at approximately the same rate regardless of whether they are subjected to surface area restrictions, and (3) bilayers with a molar ratio of 9:1 (21PC:DSPS) phase separate to form heterogeneous domains faster at low pH than at neutral pH. Our results are consistent with experimental findings of Sofou and co-workers (Bandekar et al. Mol. Pharmaceutics, 2013, 10, 152-160; Karve et al. Biomaterials, 2010, 31, 4409-4416) that more doxorubicin is released from 21PC/DSPS liposomes at low pH than at neutral pH, presumably because greater phase separation is achieved at low pH than at neutral pH. These are the first molecular-level simulations of the phase separation in mixed lipid bilayers induced by a change in pH.
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Affiliation(s)
- Emily
M. Curtis
- Department
of Chemical and Biomolecular Engineering, North Carolina State University, Engineering
Building I, 911 Partners Way, Raleigh, North Carolina 27695-7905, United States
| | - Xingqing Xiao
- Department
of Chemical and Biomolecular Engineering, North Carolina State University, Engineering
Building I, 911 Partners Way, Raleigh, North Carolina 27695-7905, United States
| | - Stavroula Sofou
- Department
of Biomedical Engineering, Rutgers School
of Engineering, 599 Taylor
Road, Piscataway, New Jersey 08854, United States
| | - Carol K. Hall
- Department
of Chemical and Biomolecular Engineering, North Carolina State University, Engineering
Building I, 911 Partners Way, Raleigh, North Carolina 27695-7905, United States
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31
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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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32
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Re S, Nishima W, Tahara T, Sugita Y. Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations. J Phys Chem Lett 2014; 5:4343-4348. [PMID: 26273985 DOI: 10.1021/jz502299m] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ordering of water structures near the surface of biological membranes has been recently extensively studied using interface-selective techniques like vibrational sum frequency generation (VSFG) spectroscopy. The detailed structures of interface water have emerged for charged lipids, but those for neutral zwitterionic lipids remain obscure. We analyze an all-atom molecular dynamics (MD) trajectory of a hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer to characterize the orientation of interface waters in different chemical environments. The structure and dynamics of interfacial waters strongly depend on both their vertical position along the bilayer normal as well as vicinal lipid charged groups. Water orientation in the vicinity of phosphate groups is opposite to that around choline groups. The results are consistent with observed VSFG spectra and demonstrate that a mosaic of water orientation structures exists on the surface of a neutral zwitterionic phospholipid bilayer, reflecting rapid water exchange and the influence of local chemical environments.
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Affiliation(s)
- Suyong Re
- †RIKEN Theoretical Molecular Science Laboratory, ‡Molecular Spectroscopy Laboratory, §Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), and ¶RIKEN iTHES, RIKEN , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- #RIKEN Advanced Institute for Computational Science and ⊥RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, RIKEN, 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Wataru Nishima
- †RIKEN Theoretical Molecular Science Laboratory, ‡Molecular Spectroscopy Laboratory, §Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), and ¶RIKEN iTHES, RIKEN , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- #RIKEN Advanced Institute for Computational Science and ⊥RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, RIKEN, 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tahei Tahara
- †RIKEN Theoretical Molecular Science Laboratory, ‡Molecular Spectroscopy Laboratory, §Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), and ¶RIKEN iTHES, RIKEN , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- #RIKEN Advanced Institute for Computational Science and ⊥RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, RIKEN, 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- †RIKEN Theoretical Molecular Science Laboratory, ‡Molecular Spectroscopy Laboratory, §Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), and ¶RIKEN iTHES, RIKEN , 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
- #RIKEN Advanced Institute for Computational Science and ⊥RIKEN Quantitative Biology Center, International Medical Device Alliance (IMDA) 6F, RIKEN, 1-6-5 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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33
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Kubo G, Sakamoto S, Fujii S, Sanada Y, Yasunaga T, Takahara A, Sakurai K. Transformation from Multi- to Single-lamellar Vesicle by Addition of a Cationic Lipid to 1,2-Dilauroyl- sn-glycero-3-phosphocholine Explored with SAXS and TEM. CHEM LETT 2014. [DOI: 10.1246/cl.140668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Genki Kubo
- Department of Chemistry and Biochemistry, The University of Kitakyushu
| | - Shunsuke Sakamoto
- Department of Chemistry and Biochemistry, The University of Kitakyushu
- Structural Materials Science Laboratory, RIKEN SPring-8 Center
| | - Shota Fujii
- Structural Materials Science Laboratory, RIKEN SPring-8 Center
- Graduate School of Engineering and Institute of Materials Chemistry and Engineering, Kyushu University
| | - Yusuke Sanada
- Department of Chemistry and Biochemistry, The University of Kitakyushu
- Structural Materials Science Laboratory, RIKEN SPring-8 Center
| | - Takuo Yasunaga
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology
- SENTAN, JST
| | - Atsushi Takahara
- Structural Materials Science Laboratory, RIKEN SPring-8 Center
- Graduate School of Engineering and Institute of Materials Chemistry and Engineering, Kyushu University
| | - Kazuo Sakurai
- Department of Chemistry and Biochemistry, The University of Kitakyushu
- Structural Materials Science Laboratory, RIKEN SPring-8 Center
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34
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Hong C, Tieleman DP, Wang Y. Microsecond molecular dynamics simulations of lipid mixing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:11993-2001. [PMID: 25237736 PMCID: PMC4196744 DOI: 10.1021/la502363b] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/11/2014] [Indexed: 05/19/2023]
Abstract
Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (3:1) and POPC:cholesterol (2:1), as well as a pure POPC bilayer, were each simulated for up to 2 μs. These simulations show that POPE:POPG and POPC:cholesterol are each fully miscible at the simulated conditions, with the final states of the mixed bilayers similar to a random mixture. By simulating three POPE:POPG bilayers at different NaCl concentrations (0, 0.15, and 1 M), we also examined the effect of salt concentration on lipid mixing. While an increase in NaCl concentration is shown to affect the area per lipid, tail order, and lipid lateral diffusion, the final states of mixing remain unaltered, which is explained by the largely uniform increase in Na(+) ions around POPE and POPG. Direct measurement of water permeation reveals that the POPE:POPG bilayer with 1 M NaCl has reduced water permeability compared with those at zero or low salt concentration. Our calculations provide a benchmark to estimate the convergence time scale of all-atom MD simulations of lipid mixing. Additionally, equilibrated structures of POPE:POPG and POPC:cholesterol, which are frequently used to mimic bacterial and mammalian membranes, respectively, can be used as starting points of simulations involving these membranes.
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Affiliation(s)
- Chunkit Hong
- Department of Physics, Chinese University
of Hong Kong, Shatin, N.T., Hong Kong
| | - D. Peter Tieleman
- Department of Biological
Sciences and Center for Molecular Simulation, University of Calgary, Calgary, Alberta Canada
| | - Yi Wang
- Department of Physics, Chinese University
of Hong Kong, Shatin, N.T., Hong Kong
- E-mail: (Y.W.)
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35
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Vošahlíková M, Jurkiewicz P, Roubalová L, Hof M, Svoboda P. High- and low-affinity sites for sodium in δ-OR-Gi1α (Cys (351)-Ile (351)) fusion protein stably expressed in HEK293 cells; functional significance and correlation with biophysical state of plasma membrane. Naunyn Schmiedebergs Arch Pharmacol 2014; 387:487-502. [PMID: 24577425 DOI: 10.1007/s00210-014-0962-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 02/10/2014] [Indexed: 12/31/2022]
Abstract
The effect of sodium, potassium, and lithium on δ-opioid receptor ligand binding parameters and coupling with the cognate G proteins was compared in model HEK293 cell line stably expressing PTX-insensitive δ-OR-Gi1α (Cys(351)-Ile(351)) fusion protein. Agonist [(3)H]DADLE binding was decreased in the order Na(+) ≫ Li(+) > K(+) > (+)NMDG. When plotted as a function of increasing NaCl concentrations, the binding was best-fitted with a two-phase exponential decay considering two Na(+)-responsive sites (r (2) = 0.99). High-affinity Na(+)-sites were characterized by Kd = 7.9 mM and represented 25 % of the basal level determined in the absence of ions. The remaining 75 % represented the low-affinity sites (Kd = 463 mM). Inhibition of [(3)H]DADLE binding by lithium, potassium, and (+)-NMDG proceeded in low-affinity manner only. Surprisingly, the affinity/potency of DADLE-stimulated [(35)S]GTPγS binding was increased in a reverse order: Na(+) < K(+) < Li(+). This result was demonstrated in PTX-treated as well as PTX-untreated cells. Therefore, it is not restricted to Gi1α(Cys(351)-Ile(351)) within the δ-OR-Gi1α fusion protein, but is also valid for stimulation of endogenous G proteins of Gi/Go family in HEK293 cells. Biophysical studies of interaction of ions with polar head-group region of lipids using Laurdan generalized polarization indicated the low-affinity type of interaction only proceeding in the order: Cs(+) < K(+) < Na(+) < Li(+). The results are discussed in terms of interaction of Na(+), K(+) and Li(+) with the high- and low-affinity sites located in water-accessible part of δ-OR binding pocket. We also consider the role of negatively charged Cl(-), Br(-), and I(-) counter anions in inhibition of both [(3)H]DADLE and [(35)S]GTPγS binding.
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Affiliation(s)
- Miroslava Vošahlíková
- Institute of Physiology, Academy of Sciences of the Czech Republic v.v.i., Vídeňská 1083, 14220, Prague 4, Czech Republic
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36
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Yu Y, Liu X, Gong W, Liu G, Cheng D, Bao H, Gao D. Adsorption of potentially toxic metals on negatively charged liposomes: equilibrium isotherms and quantitative modeling. RSC Adv 2014. [DOI: 10.1039/c4ra04775c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The adsorption data of ten metal ions on liposomes fit Freundlich equilibrium well. Covalent index of metal ions affect significantly the adsorption intensity (n). A quantitative model of KF with metal ionic properties were established by PLS.
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Affiliation(s)
- Yanjun Yu
- College of Chemistry
- Beijing Normal University
- Beijing, People's Republic of China
| | - Xinhui Liu
- State Key Laboratory of Water Environment Simulation
- School of Environment
- Beijing Normal University
- Beijing 100875, People's Republic of China
| | - Wenwen Gong
- State Key Laboratory of Water Environment Simulation
- School of Environment
- Beijing Normal University
- Beijing 100875, People's Republic of China
| | - Guannan Liu
- State Key Laboratory of Water Environment Simulation
- School of Environment
- Beijing Normal University
- Beijing 100875, People's Republic of China
| | - Dengmiao Cheng
- State Key Laboratory of Water Environment Simulation
- School of Environment
- Beijing Normal University
- Beijing 100875, People's Republic of China
| | - Huaying Bao
- College of Chemistry
- Beijing Normal University
- Beijing, People's Republic of China
| | - Ding Gao
- State Key Laboratory of Water Environment Simulation
- School of Environment
- Beijing Normal University
- Beijing 100875, People's Republic of China
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37
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Wachtel E, Bach D, Miller I. Room temperature ordering of dipalmitoyl phosphatidylserine bilayers induced by short chain alcohols. Chem Phys Lipids 2013; 175-176:20-6. [DOI: 10.1016/j.chemphyslip.2013.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 07/18/2013] [Accepted: 07/20/2013] [Indexed: 10/26/2022]
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38
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Odinokov AV, Titov SV, Tikhomirov VA, Basilevsky MV, Alfimov MV. Inclusion complexes of β-cyclodextrine with organic ligands: molecular dynamics simulation of the thermodynamic stability in gas phase and in water solution. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.740636] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Nesterenko AM, Ermakov YA. Molecular-dynamic simulation of phospholipid bilayers: Ion distribution at the surface of neutral and charged bilayer in the liquid crystalline state. BIOCHEMISTRY MOSCOW SUPPLEMENT SERIES A-MEMBRANE AND CELL BIOLOGY 2013. [DOI: 10.1134/s1990747812050145] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Physicochemical characterization of a monorhamnolipid secreted by Pseudomonas aeruginosa MA01 in aqueous media. An experimental and molecular dynamics study. Colloids Surf B Biointerfaces 2013; 101:256-65. [DOI: 10.1016/j.colsurfb.2012.06.035] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 06/26/2012] [Accepted: 06/29/2012] [Indexed: 11/19/2022]
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41
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Picas L, Milhiet PE, Hernández-Borrell J. Atomic force microscopy: a versatile tool to probe the physical and chemical properties of supported membranes at the nanoscale. Chem Phys Lipids 2012. [PMID: 23194897 DOI: 10.1016/j.chemphyslip.2012.10.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Atomic force microscopy (AFM) was developed in the 1980s following the invention of its precursor, scanning tunneling microscopy (STM), earlier in the decade. Several modes of operation have evolved, demonstrating the extreme versatility of this method for measuring the physicochemical properties of samples at the nanoscopic scale. AFM has proved an invaluable technique for visualizing the topographic characteristics of phospholipid monolayers and bilayers, such as roughness, height or laterally segregated domains. Implemented modes such as phase imaging have also provided criteria for discriminating the viscoelastic properties of different supported lipid bilayer (SLB) regions. In this review, we focus on the AFM force spectroscopy (FS) mode, which enables determination of the nanomechanical properties of membrane models. The interpretation of force curves is presented, together with newly emerging techniques that provide complementary information on physicochemical properties that may contribute to our understanding of the structure and function of biomembranes. Since AFM is an imaging technique, some basic indications on how real-time AFM imaging is evolving are also presented at the end of this paper.
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Affiliation(s)
- Laura Picas
- Institut Curie, CNRS UMR 144, 26 rue d'Ulm, 75248 Paris, France
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42
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Pyrkova DV, Tarasova NK, Krylov NA, Nolde DE, Pentkovsky VM, Efremov RG. Dynamic clustering of lipids in hydrated two-component membranes: results of computer modeling and putative biological impact. J Biomol Struct Dyn 2012; 31:87-95. [PMID: 22804614 DOI: 10.1080/07391102.2012.691365] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Delineation and analysis of lateral clustering of lipids in model bilayers is an important step toward understanding of the physical processes underlying formation of lipid domains and rafts in cell membranes. Computer modeling methods represent a powerful tool to address the problem since they can detect clusters of only few lipid molecules - this issue still resists easy characterization with modern experimental techniques. In this work, we propose a computational method to detect and analyze parts of membrane with different packing densities and hydrogen bonding patterns. A series of one- and two-component fluid systems containing lipids with the same polar heads and different acyl chains, dioleoylphosphatidylcholine (18:1) and dipalmitoylphosphatidylcholine (16:0), or with same acyl chains and different polar heads, dioleoylphosphatidylserine (18:1) and dioleoylphosphatidylcholine (18:1), were studied via molecular dynamics simulations. Four criteria of clustering were considered. It was shown that the water-lipid interface of biomembranes represents a highly dynamic and "mosaic" picture, whose parameters depend on the bilayer composition. Some systems (e.g. with 20-30% of the anionic lipid) demonstrate unusual clustering properties and demand further investigation at molecular level. Lateral microheterogeneities in fluid lipid bilayers seem to be among the most important factors determining the nature of the membrane-water interface in a cell.
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Affiliation(s)
- Darya V Pyrkova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, 16/10, Moscow, 117997, Russia
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43
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Liu J, Tourdot R, Ramanan V, Agrawal NJ, Radhakrishanan R. Mesoscale simulations of curvature-inducing protein partitioning on lipid bilayer membranes in the presence of mean curvature fields. Mol Phys 2012; 110:1127-1137. [PMID: 26500377 PMCID: PMC4613783 DOI: 10.1080/00268976.2012.664661] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The membrane-surface migration of curvature-inducing proteins in response to membrane curvature gradients has been investigated using Monte Carlo simulations of a curvilinear membrane model based on the Helfrich Hamiltonian. Consistent with theoretical and experimental data, we find the proteins that generate curvature can also sense the background membrane curvature, wherein they preferentially partition to the high curvature regions. The partitioning strength depends linearly on local membrane curvature and the slope (or the coupling constant) of the partitioning probability versus mean curvature depends on the membrane bending rigidity and instantaneous curvature field caused by different proteins. Our simulation study allows us to quantitatively characterize and identify the important factors affecting the coupling constant (slope), which may be difficult to determine in experiments. Furthermore, the membrane model is used to study budding of vesicles where it is found that in order to stabilize a mature vesicle with a stable 'neck-region' (or stable membrane overhangs), the area (extent) of the intrinsic curvature region needs to exceed a threshold-critical value. The migration and partitioning of curvature-inducing proteins in a budding vesicle with a stable neck (with a characteristic negative value of the Gaussian curvature) is investigated.
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Affiliation(s)
- Jin Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Richard Tourdot
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vyas Ramanan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Neeraj J. Agrawal
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ravi Radhakrishanan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
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44
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Molecular Dynamics Simulations of Lipid Membrane Electroporation. J Membr Biol 2012; 245:531-43. [DOI: 10.1007/s00232-012-9434-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/30/2012] [Indexed: 10/28/2022]
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45
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Structure, dynamics, and hydration of POPC/POPS bilayers suspended in NaCl, KCl, and CsCl solutions. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:609-16. [DOI: 10.1016/j.bbamem.2011.11.033] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/09/2011] [Accepted: 11/28/2011] [Indexed: 11/24/2022]
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46
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Lucas TR, Bauer BA, Davis JE, Patel S. Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields. J Comput Chem 2012; 33:141-52. [PMID: 21997857 PMCID: PMC3488352 DOI: 10.1002/jcc.21927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 06/24/2011] [Accepted: 07/30/2011] [Indexed: 12/21/2022]
Abstract
We present results of molecular dynamics simulations of a model DPPC-water monolayer using charge equilibration (CHEQ) force fields, which explicitly account for electronic polarization in a classical treatment of intermolecular interactions. The surface pressure, determined as the difference between the monolayer and pure water surface tensions at 323 K, is predicted to be 22.92 ±1.29 dyne/cm, just slightly below the broad range of experimental values reported for this system. The surface tension for the DPPC-water monolayer is predicted to be 42.35 ±1.16 dyne/cm, in close agreement with the experimentally determined value of 40.9 dyne/cm. This surface tension is also consistent with the value obtained from DPPC monolayer simulations using state-of-the-art nonpolarizable force fields. The current results of simulations predict a monolayer-water potential difference relative to the pure water-air interface of 0.64 ±0.02 Volts, an improved prediction compared to the fixed-charge CHARMM27 force field, yet still overestimating the experimental range of 0.3 to 0.45 Volts. As the charge equilibration model is a purely charge-based model for polarization, the current results suggest that explicitly modeled polarization effects can offer improvements in describing interfacial electrostatics in such systems.
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Affiliation(s)
- Timothy R. Lucas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Brad A. Bauer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Joseph E. Davis
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Sandeep Patel
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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47
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Redondo-Morata L, Oncins G, Sanz F. Force spectroscopy reveals the effect of different ions in the nanomechanical behavior of phospholipid model membranes: the case of potassium cation. Biophys J 2012; 102:66-74. [PMID: 22225799 DOI: 10.1016/j.bpj.2011.10.051] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 10/06/2011] [Accepted: 10/24/2011] [Indexed: 10/14/2022] Open
Abstract
How do metal cations affect the stability and structure of phospholipid bilayers? What role does ion binding play in the insertion of proteins and the overall mechanical stability of biological membranes? Investigators have used different theoretical and microscopic approaches to study the mechanical properties of lipid bilayers. Although they are crucial for such studies, molecular-dynamics simulations cannot yet span the complexity of biological membranes. In addition, there are still some experimental difficulties when it comes to testing the ion binding to lipid bilayers in an accurate way. Hence, there is a need to establish a new approach from the perspective of the nanometric scale, where most of the specific molecular phenomena take place. Atomic force microscopy has become an essential tool for examining the structure and behavior of lipid bilayers. In this work, we used force spectroscopy to quantitatively characterize nanomechanical resistance as a function of the electrolyte composition by means of a reliable molecular fingerprint that reveals itself as a repetitive jump in the approaching force curve. By systematically probing a set of bilayers of different composition immersed in electrolytes composed of a variety of monovalent and divalent metal cations, we were able to obtain a wealth of information showing that each ion makes an independent and important contribution to the gross mechanical resistance and its plastic properties. This work addresses the need to assess the effects of different ions on the structure of phospholipid membranes, and opens new avenues for characterizing the (nano)mechanical stability of membranes.
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Affiliation(s)
- Lorena Redondo-Morata
- Institute for Bioengineering of Catalonia, University of Barcelona, Barcelona, Spain
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48
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Concentration dependence of NaCl ion distributions around DPPC lipid bilayers. Interdiscip Sci 2011; 3:272-82. [PMID: 22179761 DOI: 10.1007/s12539-011-0107-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/04/2011] [Accepted: 04/08/2011] [Indexed: 10/14/2022]
Abstract
We study the coordination of excess NaCl to zwitterionic DPPC lipid bilayers using molecular dynamics simulations. We find that Na ions directly coordinate with the DPPC lipid carbonyl groups. As the number of excess ions increases, the number of coordinated ions increases, until it reaches a plateau at a ratio near 1 ion per every four lipids at 310 K, and 1 ion per every six lipids at 323 K. The area per lipid decreases as the number of excess ions is increased. For low number of ions per lipids (1:16 and 1:8), most Na ions are bound to the lipid carbonyls, while the Cl form an ionic cloud around the lipid choline groups. As a result of the Na binding, the lipid has an effective positive charge density. The residence time of Na ions bound to the lipid is longer than 40 ns, while Cl ions exchange faster than the nanoseconds timescale. We find that the bound Na ions replace ordered water around the carbonyls. The net linear charge density near the carbonyl groups stays positive, regardless of the presence of excess salt in the solution.
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49
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Ganesan N, Bauer BA, Lucas TR, Patel S, Taufer M. Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs). J Comput Chem 2011; 32:2958-73. [PMID: 21793003 DOI: 10.1002/jcc.21871] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 04/25/2011] [Accepted: 05/21/2011] [Indexed: 01/19/2023]
Abstract
We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.
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Affiliation(s)
- Narayan Ganesan
- Department of Computer and Information Science, University of Delaware, Newark, Delaware 19716, USA
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50
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Luna C, Stroka KM, Bermudez H, Aranda-Espinoza H. Thermodynamics of monolayers formed by mixtures of phosphatidylcholine/phosphatidylserine. Colloids Surf B Biointerfaces 2011; 85:293-300. [PMID: 21440423 PMCID: PMC3081974 DOI: 10.1016/j.colsurfb.2011.02.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 01/26/2011] [Accepted: 02/28/2011] [Indexed: 10/18/2022]
Abstract
In this work we obtain the thermodynamic properties of mixed (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) PC and (1-stearoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (sodium salt)) PS monolayers. Measurements of compressibility (isotherms, bulk modulus, and excess area per molecule) and surface potential show that the properties of monolayers at the air-water interface depend on the concentration of ions (Na(+) and K(+)) and the proportion of PS in the mixture. The dependence on PS arises because the molecule is originally bound to a Na(+) counterion; by increasing the concentration of ions the entropy changes, creating a favorable system for the bound counterions of PS to join the bulk, leaving a negatively charged molecule. This change leads to an increase in electrostatic repulsions which is reflected by the increase in area per molecule versus surface pressure and a higher surface potential. The results lead to the conclusion that this mixture of phospholipids follows a non ideal behavior and can help to understand the thermodynamic behavior of membranes made of binary mixtures of a zwitterionic and an anionic phospholipid with a bound counterion.
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Affiliation(s)
- Carlos Luna
- Fischell Department of Bioengineering, University of Maryland at College Park, College Park, MD 20740
| | - Kimberly M. Stroka
- Fischell Department of Bioengineering, University of Maryland at College Park, College Park, MD 20740
| | - Harry Bermudez
- Department of Polymer Science and Engineering, University of Massachusetts Amherst, 120 Governors Drive, Amherst, MA 01003
| | - Helim Aranda-Espinoza
- Fischell Department of Bioengineering, University of Maryland at College Park, College Park, MD 20740
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