1
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Pacheco-Sangerman F, Gómez-Merino FC, Peralta-Sánchez MG, Trejo-Téllez LI. Sulfated Nutrition Modifies Nutrient Content and Photosynthetic Pigment Concentration in Cabbage under Salt Stress. PLANTS (BASEL, SWITZERLAND) 2024; 13:1337. [PMID: 38794408 PMCID: PMC11124958 DOI: 10.3390/plants13101337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/28/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Negative effects of salt stress may be counteracted by adequate management of sulfated nutrition. Herein, we applied 3.50, 4.25, and 5.00 mM SO42- in a nutrient solution to counteract salt stress induced by 75 and 150 mM NaCl in cabbage cv. Royal. The increase in NaCl concentration from 75 to 150 mM reduced the contents of macronutrients and micronutrients in the shoot. When increasing from 3.50 to 4.25 mM SO42-, the contents of nitrogen (N), phosphorous (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) in shoots were enhanced, at both concentrations of NaCl. Increasing from 3.50 to 4.25 mM SO42- enhanced iron (Fe), zinc (Zn), manganese (Mn), and sodium (Na) concentrations with 75 mM NaCl. With 150 mM NaCl, the increase from 3.50 to 4.25 mM SO42- enhanced the contents of Cu and Mn, but also those of Na. Chlorophylls a, b, and total decreased as the concentration of SO42- increased in plants treated with 150 mM NaCl. With 75 mM NaCl, carotenoid concentration had a positive relationship with SO42-. Hence, the 4.25 mM SO42- concentration increased the contents of macronutrients and micronutrients in the presence of 75 mM NaCl, while, with 150 mM NaCl, it improved the contents of macronutrients except K. The chlorophyll a/chlorophyll b ratio remained close to 3 when the plants were treated with 5.00 mM SO42-, regardless of NaCl. Similarly, this level of SO42- increased the concentration of carotenoids, which translated into reductions in the total chlorophyll/carotenoid ratios, indicating a protective effect of the photosynthetic apparatus. It is concluded that higher doses of sulfur favor the accumulation of nutrients and increase the concentration of carotenoids under salt stress.
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Affiliation(s)
- Fresia Pacheco-Sangerman
- Programa de Edafología, Colegio de Postgraduados Campus Montecillo, Carretera México-Texcoco km 36.5, Montecillo C. P. 56264, Estado de México, Mexico
| | - Fernando Carlos Gómez-Merino
- Programa de Recursos Genéticos y Productividad-Fisiología Vegetal, Colegio de Postgraduados Campus Montecillo, Carretera México-Texcoco km 36.5, Montecillo C. P. 56264, Estado de México, Mexico
| | - María Guadalupe Peralta-Sánchez
- Programa de Edafología, Colegio de Postgraduados Campus Montecillo, Carretera México-Texcoco km 36.5, Montecillo C. P. 56264, Estado de México, Mexico
| | - Libia I Trejo-Téllez
- Programa de Edafología, Colegio de Postgraduados Campus Montecillo, Carretera México-Texcoco km 36.5, Montecillo C. P. 56264, Estado de México, Mexico
- Programa de Recursos Genéticos y Productividad-Fisiología Vegetal, Colegio de Postgraduados Campus Montecillo, Carretera México-Texcoco km 36.5, Montecillo C. P. 56264, Estado de México, Mexico
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2
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Biriukov D, Javanainen M. Efficient Simulations of Solvent Asymmetry Across Lipid Membranes Using Flat-Bottom Restraints. J Chem Theory Comput 2023; 19:6332-6341. [PMID: 37651714 PMCID: PMC10537000 DOI: 10.1021/acs.jctc.3c00614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Indexed: 09/02/2023]
Abstract
The routinely employed periodic boundary conditions complicate molecular simulations of physiologically relevant asymmetric lipid membranes together with their distinct solvent environments. Therefore, separating the extracellular fluid from its cytosolic counterpart has often been performed using a costly double-bilayer setup. Here, we demonstrate that the lipid membrane and solvent asymmetry can be efficiently modeled with a single lipid bilayer by applying an inverted flat-bottom potential to ions and other solute molecules, thereby restraining them to only interact with the relevant leaflet. We carefully optimized the parameters of the suggested method so that the results obtained using the flat-bottom and double-bilayer approaches become mutually indistinguishable. Then, we apply the flat-bottom approach to lipid bilayers with various compositions and solvent environments, covering ions and cationic peptides to validate the approach in a realistic use case. We also discuss the possible limitations of the method as well as its computational efficiency and provide a step-by-step guide on how to set up such simulations in a straightforward manner.
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Affiliation(s)
- Denys Biriukov
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the
Czech Republic, Flemingovo
nam. 2, Prague 6 CZ-16610, Czech Republic
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, Brno CZ-62500, Czech Republic
| | - Matti Javanainen
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the
Czech Republic, Flemingovo
nam. 2, Prague 6 CZ-16610, Czech Republic
- Institute
of Biotechnology, University of Helsinki, Helsinki FI-00790, Finland
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3
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Németh LJ, Martinek TA, Jójárt B. Tilted State Population of Antimicrobial Peptide PGLa Is Coupled to the Transmembrane Potential. J Chem Inf Model 2022; 62:4963-4969. [PMID: 36190907 DOI: 10.1021/acs.jcim.2c00667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cationic antimicrobial peptide PGLa gets into close contact with the anionic bacterial cell membrane, facilitating cross-membrane transport phenomena and membrane disruption depending on the concentration. The mechanisms of action are closely associated with the tilted insertion geometry of PGLa. Therefore, we aimed to understand the interaction between the transmembrane potential (TMP) and the orientation of the membrane-bound PGLa helix. Molecular dynamics simulations were performed with TMP, and we found that the PGLa tilt angle relative to the membrane is coupled with the TMP. Elevated TMP increases the population of the tilted state. We observed positive feedback between the tilt angle and the TMP, which occurs due to the electrostatic interaction between the peptidic helix and the Na+ cations at the membrane-water interface. These TMP coupled phenomena can contribute to understanding the direct antimicrobial and adjuvant effects of PGLa in combination with regular antibiotics.
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Affiliation(s)
- Lukács J Németh
- Institute of Food Engineering, University of Szeged, Mars tér 7, Szeged HU-6724, Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, Szeged HU-6720, Hungary.,ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network, Szeged H6720, Hungary
| | - Balázs Jójárt
- Institute of Food Engineering, University of Szeged, Mars tér 7, Szeged HU-6724, Hungary
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4
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Bignucolo O, Bernèche S. The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix. Front Mol Biosci 2020; 7:162. [PMID: 32850956 PMCID: PMC7403406 DOI: 10.3389/fmolb.2020.00162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/24/2020] [Indexed: 11/13/2022] Open
Abstract
Voltage-gated potassium channels (Kv) allow ion permeation upon changes of the membrane electrostatic potential (Vm). Each subunit of these tetrameric channels is composed of six transmembrane helices, of which the anti-parallel helix bundle S1-S4 constitutes the voltage-sensor domain (VSD) and S5-S6 forms the pore domain. Here, using 82 molecular dynamics (MD) simulations involving 266 replicated VSDs, we report novel responses of the archaebacterial potassium channel KvAP to membrane polarization. We show that the S4 α-helix, which is straight in the experimental crystal structure solved under depolarized conditions (Vm ∼ 0), breaks into two segments when the cell membrane is hyperpolarized (Vm << 0), and reversibly forms a single straight helix following depolarization (Vm = 0). The outermost segment of S4 translates along the normal to the membrane, bringing new perspective to previously paradoxical accessibility experiments that were initially thought to imply the displacement of the whole VSD across the membrane. The novel model is applied through steered and unbiased MD simulations to the recently solved whole structure of KvAP. The simulations show that the resting state involves a re-orientation of the S5 α-helix by ∼ 5-6 degrees in respect to the normal of the bilayer, which could result in the constriction and closure of the selectivity filter. Our findings support the idea that the breakage of S4 under (hyper)polarization is a general feature of Kv channels with a non-swapped topology.
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Affiliation(s)
- Olivier Bignucolo
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel/Lausanne, Switzerland
| | - Simon Bernèche
- Biozentrum, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel/Lausanne, Switzerland
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5
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De Mel JU, Gupta S, Perera RM, Ngo L, Zolnierczuk P, Bleuel M, Pingali SV, Schneider GJ. Influence of External NaCl Salt on Membrane Rigidity of Neutral DOPC Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:9356-9367. [PMID: 32672981 DOI: 10.1021/acs.langmuir.0c01004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sodium chloride (NaCl) is a very common molecule in biotic and abiotic aqueous environments. In both cases, variation of ionic strength is inevitable. In addition to the osmotic variation posed by such perturbations, the question of whether the interactions of monovalent ions Na+ and Cl-, especially with the neutral head groups of phospholipid membranes are impactful enough to change the membrane rigidity, is still not entirely understood. We investigated the dynamics of 1,2-di-(octadecenoyl)-sn-glycero-3-phosphocholine (DOPC) vesicles with zwitterionic neutral head groups in the fluid phase with increasing external salt concentration. At higher salt concentrations, we observe an increase in bending rigidity from neutron spin echo (NSE) spectroscopy and an increase in bilayer thickness from small-angle X-ray scattering (SAXS). We compared different models to distinguish membrane undulations, lipid tail motions, and the translational diffusion of the vesicles. All of the models indicate an increase in bending rigidity by a factor of 1.3-3.6. We demonstrate that even down to t > 10 ns and for Q > 0.07 Å-1, the observed NSE relaxation spectra are influenced by translational diffusion of the vesicles. For t < 5 ns, the lipid tail motion dominates the intermediate dynamic structure factor. As the salt concentration increases, this contribution diminishes. We introduced a time-dependent analysis for the bending rigidity that highlights only a limited Zilman-Granek time window in which the rigidity is physically meaningful.
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Affiliation(s)
- Judith U De Mel
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Sudipta Gupta
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Rasangi M Perera
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Ly Ngo
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Piotr Zolnierczuk
- Jülich Centre for Neutron Science (JCNS), Outstation at SNS, POB 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Markus Bleuel
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562, United States
| | - Sai Venkatesh Pingali
- Neutron Sciences Directorate, Oak Ridge National Laboratory (ORNL), POB 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Gerald J Schneider
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Department of Physics & Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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6
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Andoh Y, Hayakawa S, Okazaki S. Molecular dynamics study of lipid bilayers modeling outer and inner leaflets of plasma membranes of mouse hepatocytes. I. Differences in physicochemical properties between the two leaflets. J Chem Phys 2020; 153:035105. [PMID: 32716170 DOI: 10.1063/5.0012676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Outer and inner leaflets of plasma cell membranes have different lipid compositions, and the membrane properties of each leaflet can differ from each other significantly due to these composition differences. However, because of the experimental difficulty in measuring the membrane properties for each leaflet separately, the differences are not well understood at a molecular level. In this study, we constructed two lipid bilayer systems, modeling outer and inner leaflets of plasma membranes of mouse hepatocytes based on experimental composition data. The ion concentration in the interlamellar water phase was also set to match the concentration in extra- and intracellular fluids. The differences in physical properties between the outer and inner leaflets of mouse hepatocyte cell membrane models were investigated by performing 1.2 μs-long all-atomistic molecular dynamics calculations under physiological temperature and pressure conditions (310.15 K and 1 atm). The calculated electron density profiles along the bilayer normal for each model bilayer system captured well the asymmetric feature of the experimental electron density profile across actual cell plasma membranes, indicating that our procedure of modeling the outer and inner leaflets of the cell plasma membranes was satisfactory. We found that compared to the outer leaflet model, the inner leaflet model had a very bulky and soft structure in the lateral direction. To confirm the differences, membrane fluidity was measured from the lateral diffusivity and relaxation times. The fluidity was significantly higher in the inner leaflet model than in the outer leaflet model. We also discuss two topics that are of wide interest in biology, i.e., the interdigitation of acyl tails of lipid molecules between two monolayers and the lateral concentration fluctuation of lipid molecules in the bilayers.
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Affiliation(s)
- Yoshimichi Andoh
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Shiho Hayakawa
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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7
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Bilotto P, Lengauer M, Andersson J, Ramach U, Mears LLE, Valtiner M. Interaction Profiles and Stability of Rigid and Polymer-Tethered Lipid Bilayer Models at Highly Charged and Highly Adhesive Contacts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:15552-15563. [PMID: 31475831 DOI: 10.1021/acs.langmuir.9b01942] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Understanding interaction force versus distance profiles of supported lipid bilayers (SLBs) is relevant to a number of areas, which rely on these model systems, including, e.g., characterization of ligand/receptor interactions or bacterial adhesion. Here, the stability of 4 different SLB architectures was compared using the surface forces apparatus (SFA) and atomic force microscopy (AFM). Specifically, the outer envelope of the bilayer systems remained constant as 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). The inner layer was varied between DPPC and 1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP) both on mica, and self-assembled monolayers (SAMs) of hexadecanethiol and the polymer-tethered diphytanylglycerol-tetraethylene glycol-lipoid acid (DPhyTL) on smooth gold surfaces. In that same order these gave an increasing strength of interaction between the inner layer and the supporting substrate and hence improved stability under highly adhesive conditions. Detachment profiles from highly charged and highly adhesive contacts were characterized, and approach characteristics were fitted to DLVO models. We find increasing stability under highly adhesive loads, approaching the hydrophobic limit of the adhesive energy between the inner and outer layers for the SAM-based systems. For all four SLBs we further compare AFM surface topographies, which strongly depend on preparation conditions, and the DLVO fitting of the SFA approach curves finds a strong charge regulation behavior during interaction, dependent on the particular model system. In addition, we find undulation characteristics during approach and separation. The increased stability of the complex architectures on a gold support makes these model systems an ideal starting point for studying more complex strongly adhesive/interacting systems, including, for example, ligand/receptor interactions, biosensing interactions, or cell/surface interactions.
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Affiliation(s)
- Pierluigi Bilotto
- Institute of Applied Physics , Vienna University of Technology , Vienna 1040 , Austria
| | - Maximilian Lengauer
- Institute of Applied Physics , Vienna University of Technology , Vienna 1040 , Austria
| | | | - Ulrich Ramach
- Institute of Applied Physics , Vienna University of Technology , Vienna 1040 , Austria
- CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie , Wiener Neustadt 2700 , Austria
| | - Laura L E Mears
- Institute of Applied Physics , Vienna University of Technology , Vienna 1040 , Austria
| | - Markus Valtiner
- Institute of Applied Physics , Vienna University of Technology , Vienna 1040 , Austria
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8
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Kirsch SA, Böckmann RA. Coupling of Membrane Nanodomain Formation and Enhanced Electroporation near Phase Transition. Biophys J 2019; 116:2131-2148. [PMID: 31103234 PMCID: PMC6554532 DOI: 10.1016/j.bpj.2019.04.024] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/29/2022] Open
Abstract
Biological cells are enveloped by a heterogeneous lipid bilayer that prevents the uncontrolled exchange of substances between the cell interior and its environment. In particular, membranes act as a continuous barrier for salt and macromolecules to ensure proper physiological functions within the cell. However, it has been shown that membrane permeability strongly depends on temperature and, for phospholipid bilayers, displays a maximum at the transition between the gel and fluid phase. Here, extensive molecular dynamics simulations of dipalmitoylphosphatidylcholine bilayers were employed to characterize the membrane structure and dynamics close to phase transition, as well as its stability with respect to an external electric field. Atomistic simulations revealed the dynamic appearance and disappearance of spatially related nanometer-sized thick ordered and thin interdigitating domains in a fluid-like bilayer close to the phase transition temperature (Tm). These structures likely represent metastable precursors of the ripple phase that vanished at increased temperatures. Similarly, a two-phase bilayer with coexisting gel and fluid domains featured a thickness minimum at the interface because of splaying and interdigitating lipids. For all systems, application of an external electric field revealed a reduced bilayer stability with respect to pore formation for temperatures close to Tm. Pore formation occurred exclusively in thin interdigitating membrane nanodomains. These findings provide a link between the increased membrane permeability and the structural heterogeneity close to phase transition.
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Affiliation(s)
- Sonja A Kirsch
- Computational Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
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9
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Goossens K, De Winter H. Molecular Dynamics Simulations of Membrane Proteins: An Overview. J Chem Inf Model 2018; 58:2193-2202. [PMID: 30336018 DOI: 10.1021/acs.jcim.8b00639] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Simulations of membrane proteins have been rising in popularity in the past decade. Advancements in technology and force fields made it possible to simulate behavior of membrane proteins. Membrane protein simulations can now be used as supporting evidence for experimental findings, for elucidating protein mechanisms, and validating protein crystal structures. Unrelated to experimental data, these simulations can also serve to investigate larger scale processes like protein sorting, protein-membrane interactions, and more. In this review, the history as well as the state-of-the-art methodologies in membrane protein simulations will be summarized. An emphasis will be put on how to set up the system and on the current models for the different components of the simulation system. An overview of the available tools for membrane protein simulation will be given, and current limitations and prospects will also be discussed.
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Affiliation(s)
- Kenneth Goossens
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
| | - Hans De Winter
- Department of Pharmaceutical Sciences, Laboratory of Medicinal Chemistry , University of Antwerp , Universiteitsplein 1 , 2610 Wilrijk , Belgium
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10
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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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11
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Fuhs T, Klausen LH, Sønderskov SM, Han X, Dong M. Direct measurement of surface charge distribution in phase separating supported lipid bilayers. NANOSCALE 2018; 10:4538-4544. [PMID: 29461548 DOI: 10.1039/c7nr09522h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The local surface charge density of the cell membrane influences regulation and localization of membrane proteins. The local surface charge density could, until recently, not be measured directly under physiological conditions, and it was largely a hypothetical yet very important parameter. Here we use unsaturated lipids of a distinct charge (DOTAP, DOPC, and DOPG) and a neutral fully saturated lipid (DPPC) to create model membranes with phase separating domains of a defined charge. We then apply quantitative surface charge microscopy (QSCM) to investigate the local surface charge density; this is a technique based on a scanning ion conductance microscope (SICM) capable of measuring surface charge density with nanoscale lateral resolution. We are able to clearly distinguish lipid domains from charge and topography in all three model membranes. The measured surface charge densities furthermore reveal that disordered domains formed by charged lipids are in fact not only impure, but also incorporate uncharged saturated lipids. We estimate that at least 30% of disordered domains in DOPG : DPPC and DOTAP : DPPC will be DPPC. These ratios could present a limit for the formation of charged domains in lipid membranes.
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Affiliation(s)
- Thomas Fuhs
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin, 150001, China.
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12
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Martí J. Free-energy surfaces of ionic adsorption in cholesterol-free and cholesterol-rich phospholipid membranes. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1391383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Jordi Martí
- Department of Physics, Technical University of Catalonia-Barcelona Tech, Barcelona, Spain
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13
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Abstract
The relationship between bilayer stability and lipid head group orientation is reported. In this work, molecular-dynamics simulations are performed to analyze the structure-property relationship of lipid biomembranes, taking into account coarse-grained model lipid interactions. The work explains the molecular scale mechanism of the phase behavior of lipid systems due to ion-lipid or anesthetic-lipid interactions, where reorientations of dipoles play a key role in modifying lipid phases and thereby alter biomembrane function. Our study demonstrates that simple dipolar reorientation is indeed sufficient in tuning a bilayer to a randomly flipped nonbilayer lamellar phase. This study may be used to assess the impact of changes in lipid phase characteristics on biomembrane structure due to the presence of anesthetics and ions.
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Affiliation(s)
- Tanay Paul
- Department of Physics, University of Calcutta,92, A. P. C. Road, Kolkata 700009, India
| | - Jayashree Saha
- Department of Physics, University of Calcutta,92, A. P. C. Road, Kolkata 700009, India
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14
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Gonzalez MA, Barriga HMG, Richens JL, Law RV, O'Shea P, Bresme F. How does ytterbium chloride interact with DMPC bilayers? A computational and experimental study. Phys Chem Chem Phys 2017; 19:9199-9209. [DOI: 10.1039/c7cp01400g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lanthanide salts have been studied for many years, primarily in Nuclear Magnetic Resonance (NMR) experiments of mixed lipid–protein systems and more recently to study lipid flip-flop in model membrane systems.
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Affiliation(s)
| | | | | | - Robert V. Law
- Department of Chemistry
- Imperial College London
- London
- UK
| | - Paul O'Shea
- Department of Chemistry
- Imperial College London
- London
- UK
- School of Life Sciences
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15
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Kostritskii AY, Kondinskaia DA, Nesterenko AM, Gurtovenko AA. Adsorption of Synthetic Cationic Polymers on Model Phospholipid Membranes: Insight from Atomic-Scale Molecular Dynamics Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10402-10414. [PMID: 27642663 DOI: 10.1021/acs.langmuir.6b02593] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Although synthetic cationic polymers represent a promising class of effective antibacterial agents, the molecular mechanisms behind their antimicrobial activity remain poorly understood. To this end, we employ atomic-scale molecular dynamics simulations to explore adsorption of several linear cationic polymers of different chemical structure and protonation (polyallylamine (PAA), polyethylenimine (PEI), polyvinylamine (PVA), and poly-l-lysine (PLL)) on model bacterial membranes (4:1 mixture of zwitterionic phosphatidylethanolamine (PE) and anionic phosphatidylglycerol (PG) lipids). Overall, our findings show that binding of polycations to the anionic membrane surface effectively neutralizes its charge, leading to the reorientation of water molecules close to the lipid/water interface and to the partial release of counterions to the water phase. In certain cases, one has even an overcharging of the membrane, which was shown to be a cooperative effect of polymer charges and lipid counterions. Protonated amine groups of polycations are found to interact preferably with head groups of anionic lipids, giving rise to formation of hydrogen bonds and to a noticeable lateral immobilization of the lipids. While all the above findings are mostly defined by the overall charge of a polymer, we found that the polymer architecture also matters. In particular, PVA and PEI are able to accumulate anionic PG lipids on the membrane surface, leading to lipid segregation. In turn, PLL whose charge twice exceeds charges of PVA/PEI does not induce such lipid segregation due to its considerably less compact architecture and relatively long side chains. We also show that partitioning of a polycation into the lipid/water interface is an interplay between its protonation level (the overall charge) and hydrophobicity of the backbone. Therefore, a possible strategy in creating highly efficient antimicrobial polymeric agents could be in tuning these polycation's properties through proper combination of protonated and hydrophobic blocks.
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Affiliation(s)
- Andrei Yu Kostritskii
- Faculty of Physics, St. Petersburg State University , Ulyanovskaya str. 3, Petrodvorets, St. Petersburg 198504 Russia
| | - Diana A Kondinskaia
- Faculty of Physics, St. Petersburg State University , Ulyanovskaya str. 3, Petrodvorets, St. Petersburg 198504 Russia
| | - Alexey M Nesterenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119991 Russia
| | - Andrey A Gurtovenko
- Faculty of Physics, St. Petersburg State University , Ulyanovskaya str. 3, Petrodvorets, St. Petersburg 198504 Russia
- Institute of Macromolecular Compounds, Russian Academy of Sciences , Bolshoi Prospect V.O. 31, St. Petersburg 199004 Russia
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16
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Eftaiha AF, Wanasundara SN, Paige MF, Bowles RK. Exploring the Impact of Tail Polarity on the Phase Behavior of Single Component and Mixed Lipid Monolayers Using a MARTINI Coarse-Grained Force Field. J Phys Chem B 2016; 120:7641-51. [DOI: 10.1021/acs.jpcb.6b03970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ala’a F. Eftaiha
- Department
of Chemistry, The Hashemite University, P.O. Box 150459, Zarqa 13115, Jordan
- Department
of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - Surajith N. Wanasundara
- Department
of Medical Imaging, University of Saskatchewan, 103 Hospital Drive, Saskatoon, SK S7N 0W8, Canada
| | - Matthew F. Paige
- Department
of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
| | - Richard K. Bowles
- Department
of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada
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17
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Sliozberg YR, Chantawansri TL. Mechanism resulting in chemical imbalance due to cellular damage associated with mechanoporation: A molecular dynamics study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.03.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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18
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Melcr J, Bonhenry D, Timr Š, Jungwirth P. Transmembrane Potential Modeling: Comparison between Methods of Constant Electric Field and Ion Imbalance. J Chem Theory Comput 2016; 12:2418-25. [DOI: 10.1021/acs.jctc.5b01202] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Josef Melcr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Daniel Bonhenry
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Štěpán Timr
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic
Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo
nám. 2, 16610 Prague 6, Czech Republic
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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19
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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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20
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Yang J, Bonomi M, Calero C, Martí J. Free energy landscapes of sodium ions bound to DMPC–cholesterol membrane surfaces at infinite dilution. Phys Chem Chem Phys 2016; 18:9036-41. [DOI: 10.1039/c5cp05527j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Typical configuration of two DMPC lipids and one cholesterol molecule solvating one sodium ion, together with two additional water molecules.
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Affiliation(s)
- Jing Yang
- Department of Physics
- Technical University of Catalonia-Barcelona Tech
- 08034 Barcelona
- Spain
| | | | - Carles Calero
- Center for Polymer Studies and Department of Physics
- Boston University
- Boston
- USA
| | - Jordi Martí
- Department of Physics
- Technical University of Catalonia-Barcelona Tech
- 08034 Barcelona
- Spain
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21
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Antipina AY, Gurtovenko AA. Molecular-level insight into the interactions of DNA with phospholipid bilayers: barriers and triggers. RSC Adv 2016. [DOI: 10.1039/c6ra05607e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A zwitterionic phospholipid bilayer represents a repulsive barrier for DNA binding; this barrier can be overcome through adsorption of divalent cations to the bilayer surface.
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Affiliation(s)
- A. Yu. Antipina
- Faculty of Physics
- St. Petersburg State University
- St. Petersburg 198504
- Russia
- Department of Photonics and Optical Information Technology
| | - A. A. Gurtovenko
- Faculty of Physics
- St. Petersburg State University
- St. Petersburg 198504
- Russia
- Institute of Macromolecular Compounds
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22
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Kirsch SA, Böckmann RA. Membrane pore formation in atomistic and coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:2266-2277. [PMID: 26748016 DOI: 10.1016/j.bbamem.2015.12.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022]
Abstract
Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sonja A Kirsch
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
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23
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Cordomí A, Edholm O, Perez JJ. Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers. J Chem Theory Comput 2015; 5:2125-34. [PMID: 26613152 DOI: 10.1021/ct9000763] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The behavior of electrolytes in molecular dynamics simulations of zwitterionic phospholipid bilayers is very sensitive to the force field parameters used. Here, several 200 ns molecular dynamics of simulations of dipalmitoyl phosphotidylcholine (PC) bilayers in 0.2 M sodium or potassium chloride using various common force field parameters for the cations are presented. All employed parameter sets give a larger number of Na(+) ions than K(+) ions that bind to the lipid heads, but depending on the parameter choice quite different results are seen. A wide range of coordination numbers for the Na(+) and K(+) ions is also observed. These findings have been analyzed and compared to published experimental data. Some simulations produce aggregates of potassium chloride, indicating (in accordance with published simulations) that these force fields do not reproduce the delicate balance between salt and solvated ions. The differences between the force fields can be characterized by one single parameter, the electrostatic radius of the ion, which is correlated to σMO (M represents Na(+)/K(+)), the Lennard-Jones radius. When this parameter exceeds a certain threshold, binding to the lipid heads is no longer observed. One would, however, need more accurate experimental data to judge or rank the different force fields precisely. Still, reasons for the poor performance of some of the parameter sets are clearly demonstrated, and a quality control procedure is provided.
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Affiliation(s)
- Arnau Cordomí
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
| | - Olle Edholm
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
| | - Juan J Perez
- Department d'Enginyeria Química, Technical University of Catalonia (UPC), Avenue Diagonal 647, 08028 Barcelona, Spain, and, Theoretical Biological Physics, Royal Institute of Technology (KTH), SE-10691 Stockholm, Sweden
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24
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Lee H, Kim SM, Jeon TJ. Effects of imidazolium-based ionic liquids on the stability and dynamics of gramicidin A and lipid bilayers at different salt concentrations. J Mol Graph Model 2015; 61:53-60. [DOI: 10.1016/j.jmgm.2015.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 05/19/2015] [Accepted: 06/29/2015] [Indexed: 10/23/2022]
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25
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Yang W, Tian K, Ye S. Interaction between Potassium Phosphate Buffer Solution and Modeling Cell Membrane Investigated by Sum Frequency Generation Vibrational Spectroscopy. CHINESE J CHEM PHYS 2015. [DOI: 10.1063/1674-0068/28/cjcp1504070] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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26
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Yang J, Calero C, Bonomi M, Martí J. Specific Ion Binding at Phospholipid Membrane Surfaces. J Chem Theory Comput 2015; 11:4495-9. [DOI: 10.1021/acs.jctc.5b00540] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Yang
- Department
of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
| | - Carles Calero
- Center
for Polymer Studies and Department of Physics, Boston University, 590
Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Massimiliano Bonomi
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jordi Martí
- Department
of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia, Spain
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27
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Stanishneva-Konovalova T, Sokolova O. Molecular dynamics simulations of negatively charged DPPC/DPPI lipid bilayers at two levels of resolution. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.04.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Li P, Song LF, Merz KM. Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model. J Chem Theory Comput 2015; 11:1645-57. [PMID: 26574374 DOI: 10.1021/ct500918t] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Monovalent ions play fundamental roles in many biological processes in organisms. Modeling these ions in molecular simulations continues to be a challenging problem. The 12-6 Lennard-Jones (LJ) nonbonded model is widely used to model monovalent ions in classical molecular dynamics simulations. A lot of parameterization efforts have been reported for these ions with a number of experimental end points. However, some reported parameter sets do not have a good balance between the two Lennard-Jones parameters (the van der Waals (VDW) radius and potential well depth), which affects their transferability. In the present work, via the use of a noble gas curve we fitted in former work (J. Chem. Theory Comput. 2013, 9, 2733), we reoptimized the 12-6 LJ parameters for 15 monovalent ions (11 positive and 4 negative ions) for three extensively used water models (TIP3P, SPC/E, and TIP4P(EW)). Since the 12-6 LJ nonbonded model performs poorly in some instances for these ions, we have also parameterized the 12-6-4 LJ-type nonbonded model (J. Chem. Theory Comput. 2014, 10, 289) using the same three water models. The three derived parameter sets focused on reproducing the hydration free energies (the HFE set) and the ion-oxygen distance (the IOD set) using the 12-6 LJ nonbonded model and the 12-6-4 LJ-type nonbonded model (the 12-6-4 set) overall give improved results. In particular, the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets.
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Affiliation(s)
- Pengfei Li
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Lin Frank Song
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824-1322, United States
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29
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Ionic strength and composition govern the elasticity of biological membranes. A study of model DMPC bilayers by force- and transmission IR spectroscopy. Chem Phys Lipids 2014; 186:17-29. [PMID: 25447291 DOI: 10.1016/j.chemphyslip.2014.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 11/05/2014] [Accepted: 11/11/2014] [Indexed: 12/15/2022]
Abstract
Infrared (IR) spectroscopy was used to quantify the ion mixture effect of seawater (SW), particularly the contribution of Mg(2+) and Ca(2+) as dominant divalent cations, on the thermotropic phase behaviour of 1,2-dimyristoyl-sn-glycero-3-posphocholine (DMPC) bilayers. The changed character of the main transition at 24 °C from sharp to gradual in films and the 1 °C shift of the main transition temperature in dispersions reflect the interactions of lipid headgroups with the ions in SW. Force spectroscopy was used to quantify the nanomechanical hardness of a DMPC supported lipid bilayer (SLB). Considering the electrostatic and ion binding equilibrium contributions while systematically probing the SLB in various salt solutions, we showed that ionic strength had a decisive influence on its nanomechanics. The mechanical hardness of DMPC SLBs in the liquid crystalline phase linearly increases with the increasing fraction of all ion-bound lipids in a series of monovalent salt solutions. It also linearly increases in the gel phase but almost three times faster (the corresponding slopes are 4.9 nN/100 mM and 13.32 nN/100 mM, respectively). We also showed that in the presence of divalent ions (Ca(2+) and Mg(2+)) the bilayer mechanical hardness was unproportionally increased, and that was accompanied with the decrease of Na(+) ion and increase of Cl(-) ion bound lipids. The underlying process is a cooperative and competitive ion binding in both the gel and the liquid crystalline phase. Bilayer hardness thus turned out to be very sensitive to ionic strength as well as to ionic composition of the surrounding medium. In particular, the indicated correlation helped us to emphasize the colligative properties of SW as a naturally occurring complex ion mixture.
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30
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Redondo-Morata L, Giannotti MI, Sanz F. Structural impact of cations on lipid bilayer models: Nanomechanical properties by AFM-force spectroscopy. Mol Membr Biol 2013; 31:17-28. [DOI: 10.3109/09687688.2013.868940] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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31
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Siontorou CG, Batzias FA. A methodological combined framework for roadmapping biosensor research: a fault tree analysis approach within a strategic technology evaluation frame. Crit Rev Biotechnol 2013; 34:31-55. [PMID: 23919240 DOI: 10.3109/07388551.2013.790339] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Biosensor technology began in the 1960s to revolutionize instrumentation and measurement. Despite the glucose sensor market success that revolutionized medical diagnostics, and artificial pancreas promise currently the approval stage, the industry is reluctant to capitalize on other relevant university-produced knowledge and innovation. On the other hand, the scientific literature is extensive and persisting, while the number of university-hosted biosensor groups is growing. Considering the limited marketability of biosensors compared to the available research output, the biosensor field has been used by the present authors as a suitable paradigm for developing a methodological combined framework for "roadmapping" university research output in this discipline. This framework adopts the basic principles of the Analytic Hierarchy Process (AHP), replacing the lower level of technology alternatives with internal barriers (drawbacks, limitations, disadvantages), modeled through fault tree analysis (FTA) relying on fuzzy reasoning to count for uncertainty. The proposed methodology is validated retrospectively using ion selective field effect transistor (ISFET) - based biosensors as a case example, and then implemented prospectively membrane biosensors, putting an emphasis on the manufacturability issues. The analysis performed the trajectory of membrane platforms differently than the available market roadmaps that, considering the vast industrial experience in tailoring and handling crystallic forms, suggest the technology path of biomimetic and synthetic materials. The results presented herein indicate that future trajectories lie along with nanotechnology, and especially nanofabrication and nano-bioinformatics, and focused, more on the science-path, that is, on controlling the natural process of self-assembly and the thermodynamics of bioelement-lipid interaction. This retained the nature-derived sensitivity of the biosensor platform, pointing out the differences between the scope of academic research and the market viewpoint.
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Affiliation(s)
- Christina G Siontorou
- Department of Industrial Management and Technology, University of Piraeus , Karaoli and Dimitriou, Piraeus , Greece
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32
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Rabinovich AL, Lyubartsev AP. Computer simulation of lipid membranes: Methodology and achievements. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070060] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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33
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Knecht V, Klasczyk B, Dimova R. Macro- versus microscopic view on the electrokinetics of a water-membrane interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7939-7948. [PMID: 23697333 DOI: 10.1021/la400342m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Electrophoresis is an experimental method widely used to study electrostatic properties of interfaces. Here, we question the validity of the macroscopic theory for the planar geometry by Helmholtz and Smoluchowski by considering a POPC bilayer in an aqueous solution with 500 mM NaCl, using molecular dynamics simulations. We find that POPC shows positive electrophoretic mobility due to adsorption of sodium ions at the lipid headgroups. The theory assumes that the region in which the water density undergoes a transition from the bulk value to zero (interfacial width) is small compared to the Debye screening length. This separation of length scale is not fullfilled in the present case. Hence, contrasting the theory, we observe that the surface is not sharply defined, continuum hydrodynamics is not applicable, the effective viscosity in the double layer is increased compared to the bulk, and the zeta potential is dominated by the dipole potential. Our results might have widespread implications for interpretation of electrokinetic studies in general.
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Affiliation(s)
- Volker Knecht
- Theory & Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, D-14424 Potsdam, Germany.
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34
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Porasso RD, López Cascales JJ. A criterion to identify the equilibration time in lipid bilayer simulations. PAPERS IN PHYSICS 2012. [DOI: 10.4279/pip.040005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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35
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Maftouni N, Amininasab M, Vali M, Ejtehadi M, Kowsari F. A Molecular Dynamics Simulation Study of Nanomechanical Properties of Asymmetric Lipid Bilayer. J Membr Biol 2012; 246:67-73. [DOI: 10.1007/s00232-012-9505-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 09/19/2012] [Indexed: 11/30/2022]
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36
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Yang H, Gao Z, Li P, Yu K, Yu Y, Xu TL, Li M, Jiang H. A theoretical model for calculating voltage sensitivity of ion channels and the application on Kv1.2 potassium channel. Biophys J 2012; 102:1815-25. [PMID: 22768937 DOI: 10.1016/j.bpj.2012.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 02/11/2012] [Accepted: 03/15/2012] [Indexed: 01/03/2023] Open
Abstract
Voltage sensing confers conversion of a change in membrane potential to signaling activities underlying the physiological processes. For an ion channel, voltage sensitivity is usually experimentally measured by fitting electrophysiological data to Boltzmann distributions. In our study, a two-state model of the ion channel and equilibrium statistical mechanics principle were used to test the hypothesis of empirically calculating the overall voltage sensitivity of an ion channel on the basis of its closed and open conformations, and determine the contribution of individual residues to the voltage sensing. We examined the theoretical paradigm by performing experimental measurements with Kv1.2 channel and a series of mutants. The correlation between the calculated values and the experimental values is at respective level, R(2) = 0.73. Our report therefore provides in silico prediction of key conformations and has identified additional residues critical for voltage sensing.
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Affiliation(s)
- Huaiyu Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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37
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A Molecular Dynamics Study of DMPC Lipid Bilayers Interacting with Dimethylsulfoxide–Water Mixtures. J Membr Biol 2012; 245:807-14. [DOI: 10.1007/s00232-012-9483-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 06/30/2012] [Indexed: 11/26/2022]
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38
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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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39
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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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40
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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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41
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Valley CC, Perlmutter JD, Braun AR, Sachs JN. NaCl interactions with phosphatidylcholine bilayers do not alter membrane structure but induce long-range ordering of ions and water. J Membr Biol 2011; 244:35-42. [PMID: 22015614 DOI: 10.1007/s00232-011-9395-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 09/19/2011] [Indexed: 11/25/2022]
Abstract
It is generally accepted that ions interact directly with lipids in biological membranes. Decades of biophysical studies on pure lipid bilayer systems have shown that only certain types of ions, most significantly large anions and multivalent cations, can fundamentally alter the structure and dynamics of lipid bilayers. It has long been accepted that at physiological concentrations NaCl ions do not alter the physical behavior or structure of bilayers composed solely of zwitterionic phosphatidylcholine (PC) lipids. Recent X-ray scattering experiments have reaffirmed this dogma, showing that below 1 M concentration, NaCl does not significantly alter bilayer structure. However, despite this history, there is an ongoing controversy within the molecular dynamics (MD) simulation community regarding NaCl/PC interactions. In particular, the CHARMM and GROMOS force fields show dramatically different behavior, including the effect on bilayer structure, surface potential, and the ability to form stable, coordinated ion-lipid complexes. Here, using long-timescale, constant-pressure simulations under the newest version of the CHARMM force field, we find that Na⁺ and Cl⁻ associate with PC head groups in a POPC bilayer with approximately equal, though weak, affinity, and that the salt has a negligible effect on bilayer structure, consistent with earlier CHARMM results and more recent X-ray data. The results suggest that interpretation of simulations where lipids interact with charged groups of any sort, including charged proteins, must be carefully scrutinized.
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Affiliation(s)
- Christopher C Valley
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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42
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Interaction of salicylate and a terpenoid plant extract with model membranes: reconciling experiments and simulations. Biophys J 2011; 99:3887-94. [PMID: 21156130 DOI: 10.1016/j.bpj.2010.11.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 10/14/2010] [Accepted: 11/04/2010] [Indexed: 02/02/2023] Open
Abstract
We investigate the effects of two structurally similar small cyclic molecules: salicylic acid and perillic acid on a zwitterionic model lipid bilayer, and show that both molecules might have biological activity related to membrane thinning. Salicylic acid is a nonsteroidal antiinflammatory drug, some of the pharmacological properties of which arise from its interaction with the lipid bilayer component of the plasma membrane. Prior simulations show that salicylate orders zwitterionic lipid membranes. However, this is in conflict with Raman scattering and vesicle fluctuation analysis data, which suggest the opposite. We show using extensive molecular dynamics simulations, cumulatively >2.5 μs, that salicylic acid indeed disorders membranes with concomitant membrane thinning and that the conflict arose because prior simulations suffered from artifacts related to the sodium-ion induced condensation of zwitterionic lipids modeled by the Berger force field. Perillic acid is a terpenoid plant extract that has antiinfective and anticancer properties, and is extensively used in eastern medicine. We found that perillic acid causes large-scale membrane thinning and could therefore exert its antimicrobial properties via a membrane-lytic mechanism reminiscent of antimicrobial peptides. Being more amphipathic, perillic acid is more potent in disrupting lipid headgroup packing, and significantly modifies headgroup dipole orientation. Like salicylate, the membrane thinning effect of perillic acid is masked by the presence of sodium ions. As an alternative to sodium cations, we advocate the straightforward solution of using larger countercations like potassium or tetra-methyl-ammonium that will maintain electroneutrality but not interact strongly with, and thus not condense, the lipid bilayer.
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43
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Issa ZK, Manke CW, Jena BP, Potoff JJ. Ca(2+) bridging of apposed phospholipid bilayers. J Phys Chem B 2011; 114:13249-54. [PMID: 20836527 DOI: 10.1021/jp105781z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In an effort to provide insight into the mechanism of Ca(2+)-induced fusion of lipid vesicles, molecular dynamics simulations in the isobaric-isothermal ensemble are used to investigate interactions of Ca(2+) with apposed lipid bilayers in close proximity. Simulations reveal the formation of a Ca(2+)-phospholipid "anhydrous complex" between apposed bilayers, whereas similar calculations performed with Na(+) display only complexation between neighboring lipids within the same bilayer. The binding of Ca(2+) to apposed phospholipids brings large regions of the bilayers into close contact (<4 Å), displacing water from phospholipid head groups in the process and creating regions of local dehydration. Dehydration of the apposed bilayers leads to ordering of the phospholipid tails, which is partially disrupted by the presence of Ca(2+)-phospholipid bridges.
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Affiliation(s)
- Zeena K Issa
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, Michigan 48202, USA
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44
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Ferber UM, Kaggwa G, Jarvis SP. Direct imaging of salt effects on lipid bilayer ordering at sub-molecular resolution. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 40:329-38. [PMID: 21153636 DOI: 10.1007/s00249-010-0650-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/21/2010] [Accepted: 11/23/2010] [Indexed: 11/29/2022]
Abstract
The interactions of salts with lipid bilayers are known to alter the properties of membranes and therefore influence their structure and dynamics. Sodium and calcium cations penetrate deeply into the headgroup region and bind to the lipids, whereas potassium ions only loosely associate with lipid molecules and mostly remain outside of the headgroup region. We investigated a dipalmitoylphosphatidylcholine (DPPC) bilayer in the gel phase in the presence of all three cations with a concentration of Ca²+ ions an order of magnitude smaller than the Na+ and K+ ions. Our findings indicate that the area per unit cell does not significantly change in these three salt solutions. However the lipid molecules do re-order non-isotropically under the influence of the three different cations. We attribute this reordering to a change in the highly directional intermolecular interactions caused by a variation in the dipole-dipole bonding arising from a tilt of the headgroup out of the membrane plane. Measurements in different NaCl concentrations also show a non-isotropic re-ordering of the lipid molecules.
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Affiliation(s)
- Urs M Ferber
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
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45
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Lee SJ, Olsen B, Schlesinger PH, Baker NA. Characterization of perfluorooctylbromide-based nanoemulsion particles using atomistic molecular dynamics simulations. J Phys Chem B 2010; 114:10086-96. [PMID: 20684632 DOI: 10.1021/jp103228c] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Perfluorocarbon-based nanoemulsion particles have arisen as promising platforms for the cellular delivery of imaging and therapeutic agents to specific targets. However, current knowledge of the agent delivery mechanism is limited to qualitative and phenomenological models. Lack of detail at the molecular level has hence delayed optimizing or customizing nanoemulsion particles for therapeutic and imaging applications. Here we report the first atomistic structural details of a perfluorooctylbromide-based (PFOB-based) nanoemulsion particle (NEP) with a 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) lipid emulsifier. Newly developed PFOB force-field parameters were used in molecular dynamics simulations to model the PFOB-NEP interface in a planar configuration. These PFOB force field parameters were developed and tested to reproduce the characteristics of bulk PFOB as well as PFOB at interfaces with water and emulsifying phospholipids. The modeled PFOB-NEP interface demonstrated significant intercalation of PFOB into the emulsifying lipid monolayer and consequent changes in the structural, electrostatic, and mechanical properties of the POPC monolayer and PFOB. This intercalation provides an explanation for experimental data demonstrating melittin tryptophan fluorescence quenching upon binding to the nanoemulsion particles through the observation of direct contact between the melittin tryptophan and the PFOB bromine. Additionally, the atomistic details of the PFOB-NEP interface structure provided by our simulations are used to suggest the influence of each component on PFOB-NEP delivery function which will be tested in future coarse-grained simulations.
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Affiliation(s)
- Sun-Joo Lee
- Department of Biochemistry and Molecular Biophysics, Computational and Molecular Biophysics Graduate Program, Washington University in St. Louis, Missouri 63110, USA
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46
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Klasczyk B, Panzner S, Lipowsky R, Knecht V. Fusion-Relevant Changes in Lipid Shape of Hydrated Cholesterol Hemisuccinate Induced by pH and Counterion Species. J Phys Chem B 2010; 114:14941-6. [DOI: 10.1021/jp1043943] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benjamin Klasczyk
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany, and Novosom AG, Weinbergweg 22, 06120 Halle, Germany
| | - Steffen Panzner
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany, and Novosom AG, Weinbergweg 22, 06120 Halle, Germany
| | - Reinhard Lipowsky
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany, and Novosom AG, Weinbergweg 22, 06120 Halle, Germany
| | - Volker Knecht
- Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany, and Novosom AG, Weinbergweg 22, 06120 Halle, Germany
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47
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A molecular dynamics study on heat conduction characteristics in DPPC lipid bilayer. J Chem Phys 2010; 133:154705. [DOI: 10.1063/1.3481650] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Gurtovenko AA, Anwar J, Vattulainen I. Defect-Mediated Trafficking across Cell Membranes: Insights from in Silico Modeling. Chem Rev 2010; 110:6077-103. [DOI: 10.1021/cr1000783] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Andrey A. Gurtovenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Jamshed Anwar
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
| | - Ilpo Vattulainen
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., St. Petersburg, 199004 Russia, Computational Laboratory, Institute of Pharmaceutical Innovation, University of Bradford, Bradford, West Yorkshire BD7 1DP, U.K., Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Aalto University, School of Science and Technology, Finland, and MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
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49
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Gentilcore AN, Michaud-Agrawal N, Crozier PS, Stevens MJ, Woolf TB. Examining the origins of the hydration force between lipid bilayers using all-atom simulations. J Membr Biol 2010; 235:1-15. [PMID: 20387061 DOI: 10.1007/s00232-010-9249-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 03/11/2010] [Indexed: 11/26/2022]
Abstract
Using 237 all-atom double bilayer simulations, we examined the thermodynamic and structural changes that occur as a phosphatidylcholine lipid bilayer stack is dehydrated. The simulated system represents a micropatch of lipid multilayer systems that are studied experimentally using surface force apparatus, atomic force microscopy and osmotic pressure studies. In these experiments, the hydration level of the system is varied, changing the separation between the bilayers, in order to understand the forces that the bilayers feel as they are brought together. These studies have found a curious, strongly repulsive force when the bilayers are very close to each other, which has been termed the "hydration force," though the origins of this force are not clearly understood. We computationally reproduce this repulsive, relatively free energy change as bilayers come together and make qualitative conclusions as to the enthalpic and entropic origins of the free energy change. This analysis is supported by data showing structural changes in the waters, lipids and salts that have also been seen in experimental work. Increases in solvent ordering as the bilayers are dehydrated are found to be essential in causing the repulsion as the bilayers come together.
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Affiliation(s)
- Anastasia N Gentilcore
- Department of Physiology, Johns Hopkins University, School of Medicine, Baltimore, MD, USA
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50
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Lonez C, Lensink MF, Kleiren E, Vanderwinden JM, Ruysschaert JM, Vandenbranden M. Fusogenic activity of cationic lipids and lipid shape distribution. Cell Mol Life Sci 2010; 67:483-94. [PMID: 19924382 PMCID: PMC11115757 DOI: 10.1007/s00018-009-0197-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/20/2009] [Accepted: 10/29/2009] [Indexed: 10/20/2022]
Abstract
Addition of co-lipids into cationic lipid formulations is considered as promoting cell delivery of DNA by enhancing fusion processes with cell membranes. Here, by combining FRET and confocal microscopy, we demonstrate that some cationic lipids do not require a co-lipid to fuse efficiently with cells. These cationic lipids are able to self-organize into bilayers that are stable enough to form liposomes, while presenting some destabilizing properties reminiscent of the conically shaped fusogenic co-lipid, DOPE. We therefore analyzed the resident lipid structures in cationic bilayers by molecular dynamics simulations, clustering the individual lipid structures into populations of similarly shaped molecules, as opposed to the classical approach of using the static packing parameter to define the lipid shapes. Comparison of fusogenic properties with these lipid populations suggests that the ratio of cylindrical versus conical lipid populations correlates with the ability to fuse with cell membranes.
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Affiliation(s)
- Caroline Lonez
- Laboratory for Structure and Function of Biological Membranes, Centre for Structural Biology and Bioinformatics, Faculté des Sciences, Université Libre de Bruxelles, CP 206/2, Campus Plaine, Blvd. du Triomphe, 1050 Brussels, Belgium.
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