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Cashman-Kadri S, Lagüe P, Fliss I, Beaulieu L. Assessing the Activity under Different Physico-Chemical Conditions, Digestibility, and Innocuity of a GAPDH-Related Fish Antimicrobial Peptide and Analogs Thereof. Antibiotics (Basel) 2023; 12:1410. [PMID: 37760707 PMCID: PMC10525732 DOI: 10.3390/antibiotics12091410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The antimicrobial activity of SJGAP (skipjack tuna GAPDH-related antimicrobial peptide) and four chemical analogs thereof was determined under different physicochemical conditions, including different pH values, the presence of monovalent and divalent cations, and after a heating treatment. The toxicity of these five peptides was also studied with hemolytic activity assays, while their stability under human gastrointestinal conditions was evaluated using a dynamic in vitro digestion model and chromatographic and mass spectrometric analyses. The antibacterial activity of all analogs was found to be inhibited by the presence of divalent cations, while monovalent cations had a much less pronounced impact, even promoting the activity of the native SJGAP. The peptides were also more active at acidic pH values, but they did not all show the same stability following a heat treatment. SJGAP and its analogs did not show significant hemolytic activity (except for one of the analogs at a concentration equivalent to 64 times that of its minimum inhibitory concentration), and the two analogs whose digestibility was studied degraded very rapidly once they entered the stomach compartment of the digestion model. This study highlights for the first time the characteristics of antimicrobial peptides from Scombridae or homologous to GAPDH that are directly related to their potential clinical or food applications.
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Affiliation(s)
- Samuel Cashman-Kadri
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC G1V 0A6, Canada; (S.C.-K.); (I.F.)
- Department of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada
- Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada
| | - Patrick Lagüe
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Quebec, QC G1V 0A6, Canada;
- Institute for Integrative Systems Biology, Department of Biochemistry, Microbiology and Bio-Informatics, Pavillon, Alexandre-Vachon, Université Laval, 1045 Avenue de la Medecine, Québec, QC G1V 0A6, Canada
- The Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), 1045 Avenue de la Medecine, Québec, QC G1V 0A6, Canada
| | - Ismail Fliss
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC G1V 0A6, Canada; (S.C.-K.); (I.F.)
- Department of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada
| | - Lucie Beaulieu
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC G1V 0A6, Canada; (S.C.-K.); (I.F.)
- Department of Food Science, Faculty of Agricultural and Food Sciences, Université Laval, Québec, QC G1V 0A6, Canada
- Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada
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2
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Stachowicz-Kuśnierz A, Korchowiec B, Korchowiec J. Nucleoside Analog Reverse-Transcriptase Inhibitors in Membrane Environment: Molecular Dynamics Simulations. Molecules 2023; 28:6273. [PMID: 37687102 PMCID: PMC10488468 DOI: 10.3390/molecules28176273] [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] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
The behavior of four drugs from the family of nucleoside analog reverse-transcriptase inhibitors (zalcitabine, stavudine, didanosine, and apricitabine) in a membrane environment was traced using molecular dynamics simulations. The simulation models included bilayers and monolayers composed of POPC and POPG phospholipids. It was demonstrated that the drugs have a higher affinity towards POPG membranes than POPC membranes due to attractive long-range electrostatic interactions. The results obtained for monolayers were consistent with those obtained for bilayers. The drugs accumulated in the phospholipid polar headgroup region. Two adsorption modes were distinguished. They differed in the degree of penetration of the hydrophilic headgroup region. Hydrogen bonds between drug molecules and phospholipid heads were responsible for adsorption. It was shown that apricitabine penetrated the hydrophilic part of the POPC and POPG membranes more effectively than the other drugs. Van der Waals interactions between S atoms and lipids were responsible for this.
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Affiliation(s)
| | | | - Jacek Korchowiec
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland; (A.S.-K.); (B.K.)
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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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New understanding of electrical activity brought by surface potential of cardiomyocytes. Sci Rep 2021; 11:6593. [PMID: 33758297 PMCID: PMC7988015 DOI: 10.1038/s41598-021-86138-w] [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] [Received: 09/21/2020] [Accepted: 03/11/2021] [Indexed: 11/15/2022] Open
Abstract
Aiming at the problem encountered in the previous research: during the electrical activity of cardiomyocytes, the influent ions do not seem to be directly derived from the extracellular fluid. We chose to cut in from the colloidal properties of the cells, follow the basic principles of physical chemistry, and establish hypotheses along the derivation of the structural characteristics of cardiomyocytes. Through the surface ion adsorption experiment and patch clamp experiment of living cells, under the condition of sequentially reducing the concentration of Na+ in the extracellular fluid, we observed the exchange and diffusion of adsorbed ions on the cell surface; the changes of inflow INa, ICa-L and action potential; and correlation between results. The results showed that the hypothesis is true. The observed parameter changes were consistent with the fact that during depolarization of cardiomyocytes, the ions of influx were derived from the inference of adsorbed ions on the cell surface; at the same time, it also provided an objective and realistic explanation for the generation of electrocardiogram.
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5
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Gehan P, Kulifaj S, Soule P, Bodin J, Amoura M, Walrant A, Sagan S, Thiam A, Ngo K, Vivier V, Cribier S, Rodriguez N. Penetratin translocation mechanism through asymmetric droplet interface bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183415. [DOI: 10.1016/j.bbamem.2020.183415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/06/2020] [Accepted: 07/11/2020] [Indexed: 01/15/2023]
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6
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Sahoo A, Matysiak S. Microscopic Picture of Calcium-Assisted Lipid Demixing and Membrane Remodeling Using Multiscale Simulations. J Phys Chem B 2020; 124:7327-7335. [PMID: 32786720 DOI: 10.1021/acs.jpcb.0c03067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The specificity of anionic phospholipids-calcium ion interaction and lipid demixing has been established as a key regulatory mechanism in several cellular signaling processes. The mechanism and implications of this calcium-assisted demixing have not been elucidated from a microscopic point of view. Here, we present an overview of atomic interactions between calcium and phospholipids that can drive nonideal mixing of lipid molecules in a model lipid bilayer composed of zwitterionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)) and anionic (1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-l-serine (POPS)) lipids with computer simulations at multiple resolutions. Lipid nanodomain formation and growth were driven by calcium-enabled lipid bridging of the charged phosphatidylserine (PS) headgroups, which were favored against inter-POPS dipole interactions. Consistent with several experimental studies of calcium-associated membrane sculpting, our analyses also suggest modifications in local membrane curvature and cross-leaflet couplings as a response to such induced lateral heterogeneity. In addition, reverse mapping to a complementary atomistic description revealed structural insights in the presence of anionic nanodomains, at timescales not accessed by previous computational studies. This work bridges information across multiple scales to reveal a mechanistic picture of calcium ion's impact on membrane biophysics.
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Affiliation(s)
- Abhilash Sahoo
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States
| | - Silvina Matysiak
- Biophysics Program, Institute of Physical Science and Technology, University of Maryland, College Park, Maryland 20742, United States.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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7
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The effect of monovalent (Na +, K +) and divalent (Ca 2+, Mg 2+) cations on rapeseed oleosome (oil body) extraction and stability at pH 7. Food Chem 2020; 306:125578. [PMID: 31622835 DOI: 10.1016/j.foodchem.2019.125578] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/11/2019] [Accepted: 09/22/2019] [Indexed: 11/21/2022]
Abstract
Oleosomes are storage vehicles of TAGs in plant seeds. They are protected with a phospholipid-protein monolayer and extracted with alkaline aqueous media; however, pH adjustment intensifies the extraction process. Therefore, the aim of this work was to investigate the extraction mechanism of rapeseed oleosomes at pH 7 and at the presence of monovalent and divalent cations (Na+, K+, Mg2+, and Ca+2). The oleosome yield at pH 9.5 was 64 wt%, while the yield at pH 7 with H2O was just 43 wt.%. The presence of cations at pH 7, significantly enhanced the yield, with K+ giving the highest yield (64 wt.%). The cations affected the oleosome interface and their interactions. The presence of monovalent cations resulted in aggregation and minor coalescence, while divalent cations resulted in extensive coalescence. These results help to understand the interactions of oleosomes in their native matrix and design simple extraction processes at neutral conditions.
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8
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Köksal ES, Liese S, Kantarci I, Olsson R, Carlson A, Gözen I. Nanotube-Mediated Path to Protocell Formation. ACS NANO 2019; 13:6867-6878. [PMID: 31177769 DOI: 10.1021/acsnano.9b01646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cellular compartments are membrane-enclosed, spatially distinct microenvironments that confine and protect biochemical reactions in the biological cell. On the early Earth, the autonomous formation of compartments is thought to have led to the encapsulation of nucleotides, thereby satisfying a starting condition for the emergence of life. Recently, surfaces have come into focus as potential platforms for the self-assembly of prebiotic compartments, as significantly enhanced vesicle formation was reported in the presence of solid interfaces. The detailed mechanism of such formation at the mesoscale is still under discussion. We report here on the spontaneous transformation of solid-surface-adhered lipid deposits to unilamellar membrane compartments through a straightforward sequence of topological changes, proceeding via a network of interconnected lipid nanotubes. We show that this transformation is entirely driven by surface-free energy minimization and does not require hydrolysis of organic molecules or external stimuli such as electrical currents or mechanical agitation. The vesicular structures take up and encapsulate their external environment during formation and can subsequently separate and migrate upon exposure to hydrodynamic flow. This may link the self-directed transition from weakly organized bioamphiphile assemblies on solid surfaces to protocells with secluded internal contents.
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Affiliation(s)
- Elif S Köksal
- Centre for Molecular Medicine Norway, Faculty of Medicine , University of Oslo , 0318 Oslo , Norway
| | - Susanne Liese
- Department of Chemistry, Faculty of Mathematics and Natural Sciences , University of Oslo , 0315 Oslo , Norway
| | - Ilayda Kantarci
- Centre for Molecular Medicine Norway, Faculty of Medicine , University of Oslo , 0318 Oslo , Norway
| | - Ragni Olsson
- Centre for Molecular Medicine Norway, Faculty of Medicine , University of Oslo , 0318 Oslo , Norway
| | - Andreas Carlson
- Department of Chemistry, Faculty of Mathematics and Natural Sciences , University of Oslo , 0315 Oslo , Norway
| | - Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine , University of Oslo , 0318 Oslo , Norway
- Department of Mathematics, Faculty of Mathematics and Natural Sciences , University of Oslo , 0315 Oslo , Norway
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , SE-412 96 Göteborg , Sweden
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9
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Deplazes E, White J, Murphy C, Cranfield CG, Garcia A. Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers. Biophys Rev 2019; 11:483-490. [PMID: 31115866 DOI: 10.1007/s12551-019-00541-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022] Open
Abstract
Maintaining gradients of solvated protons and alkali metal ions such as Na+ and K+ across membranes is critical for cellular function. Over the last few decades, both the interactions of protons and alkali metal ions with phospholipid membranes have been studied extensively and the reported interactions of these ions with phospholipid headgroups are very similar, yet few studies have investigated the potential interdependence between proton and alkali metal ion binding at the water-lipid interface. In this short review, we discuss the similarities between the proton-membrane and alkali ion-membrane interactions. Such interactions include cation attraction to the phosphate and carbonyl oxygens of the phospholipid headgroups that form strong lipid-ion and lipid-ion-water complexes. We also propose potential mechanisms that may modulate the affinities of these cationic species to the water-phospholipid interfacial oxygen moieties. This review aims to highlight the potential interdependence between protons and alkali metal ions at the membrane surface and encourage a more nuanced understanding of the complex nature of these biologically relevant processes.
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Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia. .,School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, 6845, Australia.
| | - Jacqueline White
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Christopher Murphy
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Charles G Cranfield
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Alvaro Garcia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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10
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Intramembrane ionic protein-lipid interaction regulates integrin structure and function. PLoS Biol 2018; 16:e2006525. [PMID: 30427828 PMCID: PMC6261646 DOI: 10.1371/journal.pbio.2006525] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 11/28/2018] [Accepted: 10/29/2018] [Indexed: 11/24/2022] Open
Abstract
Protein transmembrane domains (TMDs) are generally hydrophobic, but our bioinformatics analysis shows that many TMDs contain basic residues at terminal regions. Physiological functions of these membrane-snorkeling basic residues are largely unclear. Here, we show that a membrane-snorkeling Lys residue in integrin αLβ2 (also known as lymphocyte function-associated antigen 1 [LFA-1]) regulates transmembrane heterodimer formation and integrin adhesion through ionic interplay with acidic phospholipids and calcium ions (Ca2+) in T cells. The amino group of the conserved Lys ionically interacts with the phosphate group of acidic phospholipids to stabilize αLβ2 transmembrane association, thus keeping the integrin at low-affinity conformation. Intracellular Ca2+ uses its charge to directly disrupt this ionic interaction, leading to the transmembrane separation and the subsequent extracellular domain extension to increase adhesion activity. This Ca2+-mediated regulation is independent on the canonical Ca2+ signaling or integrin inside-out signaling. Our work therefore showcases the importance of intramembrane ionic protein–lipid interaction and provides a new mechanism of integrin activation. Integrin αLβ2 is the major integrin in T cells and plays a vital role in regulating T-cell activation, adhesion, and migration. The transmembrane association of αL and β2 is crucial for maintaining the integrin at low-affinity conformation. Here, we find that the conserved basic residue (K702) in the transmembrane domain of β2 contributes to transmembrane association through ternary ionic interaction with acidic phospholipid and αL cytoplasmic residue. Upon T-cell activation, influxed calcium ions (Ca2+) can directly disrupt the ionic K702–lipid interaction through its positive charges, which leads to transmembrane separation and subsequent extracellular domain extension to switch αLβ2 to high-affinity conformation. This Ca2+-mediated regulation is through the modulation of the ionic Lys–lipid interaction but not through the canonical Ca2+ signaling or integrin inside-out signaling. Our study thus reports a new regulatory mechanism of integrin activation and showcases the importance of intramembrane ionic protein–lipid interaction. This finding might have general relevance, as bioinformatics analysis shows the presence of membrane-snorkeling basic residue is a common feature of transmembrane proteins.
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11
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He Z, Feng G, Yang B, Yang L, Liu CW, Xu HG, Xu XL, Zheng WJ, Gao YQ. Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride. J Chem Phys 2018; 148:222839. [DOI: 10.1063/1.5024279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Zhili He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Gang Feng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Bin Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lijiang Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Cheng-Wen Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Hong-Guang Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xi-Ling Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Jun Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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12
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Jing R, Kjellerup BV. Biogeochemical cycling of metals impacting by microbial mobilization and immobilization. J Environ Sci (China) 2018; 66:146-154. [PMID: 29628081 DOI: 10.1016/j.jes.2017.04.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/09/2017] [Accepted: 04/19/2017] [Indexed: 06/08/2023]
Abstract
Microbial mobilization and immobilization processes can affect the bioavailability and mobility of metals thereby influencing their toxicity and can therefore be utilized to treat solid and liquid wastes contaminated by metals. However, the microbial mobilization and immobilization of metals depends on the microbial metabolism, the environment conditions. In this review, mobilization and immobilization of metals are discussed with regard to the presence and function of involved microorganisms and in relation to applications such as bioleaching. Furthermore, the biosorption process is evaluated as a possible approach for microbial immobilization of metal on the basis of four mechanisms: (1) physical adsorption, (2) ion exchange, (3) complexation, and (4) microprecipitation. In addition, sulfide precipitation by sulfate reducing bacteria was included as an example of an application of microbial immobilization. Based on the evaluation and recommendations in this paper, bioremediation strategies for metals can be improved thus increasing the opportunity for field applications.
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Affiliation(s)
- Ran Jing
- University of Maryland at College Park, Department of Civil and Environmental Engineering, 1147 Glenn L. Martin Hall, College Park, MD 20742, USA.
| | - Birthe V Kjellerup
- University of Maryland at College Park, Department of Civil and Environmental Engineering, 1147 Glenn L. Martin Hall, College Park, MD 20742, USA.
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13
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Laudadio E, Minnelli C, Amici A, Massaccesi L, Mobbili G, Galeazzi R. Liposomal Formulations for an Efficient Encapsulation of Epigallocatechin-3-gallate: An in- Silico/Experimental Approach. Molecules 2018; 23:molecules23020441. [PMID: 29462955 PMCID: PMC6017453 DOI: 10.3390/molecules23020441] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/07/2018] [Accepted: 02/13/2018] [Indexed: 01/29/2023] Open
Abstract
As a part of research project aimed to optimize antioxidant delivery, here we studied the influence of both salts and lipid matrix composition on the interaction of epigallocatechin-3-gallate (EGCG) with bilayer leaflets. Thus, we combined in silico and experimental methods to study the ability of neutral and anionic vesicles to encapsulate EGCG in the presence of Ca2+ and Mg2+ divalent salts. Experimental and in silico results show a very high correlation, thus confirming the efficiency of the developed methodology. In particular, we found out that the presence of calcium ions hinders the insertion of EGCG in the liposome bilayer in both neutral and anionic systems. On the contrary, the presence of MgCl2 improves the insertion degree of EGCG molecules respect to the liposomes without divalent salts. The best and most efficient salt concentration is that corresponding to a 5:1 molar ratio between Mg2+ and EGCG, in both neutral and anionic vesicles. Concerning the lipid matrix composition, the anionic one results in better promotion of the catechin insertion within the bilayer since experimentally we achieved 100% EGCG encapsulation in the lipid carrier in the presence of a 5:1 molar ratio of magnesium. Thus, the combination of this anionic liposomal formulation with magnesium chloride, avoids time-consuming separation steps of unentrapped active principle and appears particularly suitable for EGCG delivery applications.
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Affiliation(s)
- Emiliano Laudadio
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Cristina Minnelli
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Adolfo Amici
- Dipartimento Scienze Cliniche Specialistiche ed Odontostomatologiche, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Luca Massaccesi
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Giovanna Mobbili
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Roberta Galeazzi
- Dipartimento di Scienze della Vita e dell'Ambiente (DISVA), Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
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14
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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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15
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Zhang T, Qiu Y, Luo Q, Zhao L, Yan X, Ding Q, Jiang H, Yang H. The Mechanism by Which Luteolin Disrupts the Cytoplasmic Membrane of Methicillin-Resistant Staphylococcus aureus. J Phys Chem B 2018; 122:1427-1438. [PMID: 29309144 DOI: 10.1021/acs.jpcb.7b05766] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most versatile human pathogens. Luteolin (LUT) has anti-MRSA activity by disrupting the MRSA cytoplasmic membrane. However, the mechanism by which luteolin disrupts the membrane remains unclear. Here, we performed differential scanning calorimetry (DSC) and all-atomic molecular dynamics (AA-MD) simulations to investigate the interactions and effects of LUT on model membranes composed of phosphatidylcholine (PC) and phosphatidylglycerol (PG). We detected the transition thermodynamic parameters of dipalmitoylphosphatidylcholine (DPPC) liposomes, dipalmitoylphosphatidylglycerol (DPPG) liposomes, and liposomes composed of both DPPC and DPPG at different LUT concentrations and showed that LUT molecules were located between polar heads and the hydrophobic region of DPPC/DPPG. In the MD trajectories, LUT molecules ranging from 5 to 50 had different effects on the membranes thickness, fluidity and ordered property of lipids, and lateral pressure of lipid bilayers composed of dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylglycerol (DOPG). Also, most LUT molecules were distributed in the region between the phosphorus atoms and C9 atoms of DOPC and DOPG. On the basis of the combination of these results, we conclude that the distinct effects of LUT on lipid bilayers composed of PCs and PGs may elucidate the mechanism by which LUT disrupts the cytoplasmic membrane of MRSA.
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Affiliation(s)
- Tao Zhang
- School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237, China
| | - Yunguang Qiu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Qichao Luo
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Lifen Zhao
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xin Yan
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University , 393 Huaxiazhong Road, Shanghai 201210, China
| | - Qiaoce Ding
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai 200237, China.,Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
| | - Huaiyu Yang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences , No. 19A Yuquan Road, Beijing 100049, China
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16
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Wellen Rudd BA, Vidalis AS, Allen HC. Thermodynamic versus non-equilibrium stability of palmitic acid monolayers in calcium-enriched sea spray aerosol proxy systems. Phys Chem Chem Phys 2018; 20:16320-16332. [DOI: 10.1039/c8cp01188e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Calcium ions bind to palmitic acid monolayers at the air–aqueous interface resulting in changes of both thermodynamic and non-equilibrium stability.
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Affiliation(s)
| | - Andrew S. Vidalis
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus
- USA
| | - Heather C. Allen
- Department of Chemistry & Biochemistry
- The Ohio State University
- Columbus
- USA
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17
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Piantanida L, Bolt HL, Rozatian N, Cobb SL, Voïtchovsky K. Ions Modulate Stress-Induced Nanotexture in Supported Fluid Lipid Bilayers. Biophys J 2017; 113:426-439. [PMID: 28746853 PMCID: PMC5529180 DOI: 10.1016/j.bpj.2017.05.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 05/22/2017] [Accepted: 05/30/2017] [Indexed: 12/13/2022] Open
Abstract
Most plasma membranes comprise a large number of different molecules including lipids and proteins. In the standard fluid mosaic model, the membrane function is effected by proteins whereas lipids are largely passive and serve solely in the membrane cohesion. Here we show, using supported 1,2-dioleoyl-sn-glycero-3-phosphocholine lipid bilayers in different saline solutions, that ions can locally induce ordering of the lipid molecules within the otherwise fluid bilayer when the latter is supported. This nanoordering exhibits a characteristic length scale of ∼20 nm, and manifests itself clearly when mechanical stress is applied to the membrane. Atomic force microscopy (AFM) measurements in aqueous solutions containing NaCl, KCl, CaCl2, and Tris buffer show that the magnitude of the effect is strongly ion-specific, with Ca2+ and Tris, respectively, promoting and reducing stress-induced nanotexturing of the membrane. The AFM results are complemented by fluorescence recovery after photobleaching experiments, which reveal an inverse correlation between the tendency for molecular nanoordering and the diffusion coefficient within the bilayer. Control AFM experiments on other lipids and at different temperatures support the hypothesis that the nanotexturing is induced by reversible, localized gel-like solidification of the membrane. These results suggest that supported fluid phospholipid bilayers are not homogenous at the nanoscale, but specific ions are able to locally alter molecular organization and mobility, and spatially modulate the membrane’s properties on a length scale of ∼20 nm. To illustrate this point, AFM was used to follow the adsorption of the membrane-penetrating antimicrobial peptide Temporin L in different solutions. The results confirm that the peptides do not absorb randomly, but follow the ion-induced spatial modulation of the membrane. Our results suggest that ionic effects have a significant impact for passively modulating the local properties of biological membranes, when in contact with a support such as the cytoskeleton.
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Affiliation(s)
- Luca Piantanida
- Department of Physics, Durham University, Durham, United Kingdom
| | - Hannah L Bolt
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Neshat Rozatian
- Department of Chemistry, Durham University, Durham, United Kingdom
| | - Steven L Cobb
- Department of Chemistry, Durham University, Durham, United Kingdom
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18
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Bettanin F, Jurinovich S, Caprasecca S, Mennucci B, Homem-de-Mello P. A quantum chemical investigation of the solvatochromism of a phthalocyanine within a lipid bilayer: Comparison between continuum and atomistic models. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.04.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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19
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Maeshima K, Yoshimoto M. Preparation and characterization of carbonic anhydrase-conjugated liposomes for catalytic synthesis of calcium carbonate particles. Enzyme Microb Technol 2017; 105:9-17. [PMID: 28756864 DOI: 10.1016/j.enzmictec.2017.06.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 05/15/2017] [Accepted: 06/03/2017] [Indexed: 11/27/2022]
Abstract
The biomimetic approach using immobilized enzymes is useful for the synthesis of structurally defined inorganic materials. In this work, carbonic anhydrase (CA) from bovine erythrocytes was covalently conjugated at 25°C to the liposomes composed of 15mol% 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine-N-(glutaryl) (NG-POPE), and the zwitterionic and anionic phospholipids with the same acyl chains as NG-POPE. For the conjugation, the carboxyl groups of liposomal NG-POPE were activated with 11mM 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and 4.6mM N-hydroxysulfosuccinimide (sulfo-NHS). The carbonic anhydrase-conjugated liposomes (CALs) with the mean hydrodynamic diameter of 149nm showed the esterase activity corresponding to on average 5.5×102 free CA molecules per liposome. On the other hand, the intrinsic fluorescence and absorbance measurements consistently revealed that on average 1.4×103 CA molecules were conjugated to a liposome, suggesting that the molecular orientation of enzyme affected its activity. The formation of calcium carbonate particles was significantly accelerated by the CALs ([lipid]=50μ M) in the 0.3M Tris solution at 10-40°C with dissolved CO2 (≈17mM) and CaCl2 (46mM). The anionic CALs were adsorbed with calcium as revealed with the ζ-potential measurements. The CAL system offered the calcium-rich colloidal interface where the bicarbonate ions were catalytically produced by the liposome-conjugated CA molecules. The CALs also functioned in the external loop airlift bubble column operated with a model flue gas (10vol/vo% CO2), yielding partly agglomerated calcium carbonate particles as observed with the scanning electron microscopy (SEM).
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Affiliation(s)
- Keisuke Maeshima
- Department of Applied Molecular Bioscience, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan
| | - Makoto Yoshimoto
- Department of Applied Molecular Bioscience, Yamaguchi University, Tokiwadai 2-16-1, Ube 755-8611, Japan.
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20
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Zhang T, Luo Q, Yang L, Jiang H, Yang H. Characterizing the interactions of two lipid modifications with lipid rafts: farnesyl anchors vs. palmitoyl anchors. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:19-30. [PMID: 28585042 DOI: 10.1007/s00249-017-1217-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/27/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022]
Abstract
Farnesyl (Far) and palmitoyl (Pal) anchors play important roles in the traffic of many lipidated proteins. Herein, we show the distinctive interactions and influences of the two lipid modifications on lipid rafts (LRs) and non-raft-like membranes using molecular dynamics simulations. Palmitoyl anchors behave in a more ordered fashion, pack tighter with the lipids of LRs and diffuse at a slower rate than farnesyl anchors in LRs. When interacting with non-raft-like membranes these two types of anchors become less ordered, pack more loosely with lipids, and diffuse at a higher rate. By calculating both the number of contacts per chain and the number of contact atoms per carbon of the two anchors with the lipid components, we found that the palmitoyl chains preferred to associate with the saturated chains of lipids and cholesterol molecules in LRs, while farnesyl chains favored association with saturated chains and unsaturated chains. For non-raft-like membranes, these two lipid anchors had roughly the same preference for the three types of contact lipid chains. Additionally, palmitoyl anchors caused cholesterol to orient more perpendicular to the membrane surface, surrounding lipids to become more ordered, and lipid lateral fluidity to reduce significantly, compared to farnesyl anchors in LRs. By contrast, the POPE and DSPC became much less ordered, cholesterol became more tilted, and lipids became more fluid, when the two types lipid anchors were inserted in non-raft-like membranes. These findings are useful for understanding the traffic mechanisms of lipidated proteins with farnesyl and palmitoyl modifications in cell membranes.
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Affiliation(s)
- Tao Zhang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Qichao Luo
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linlin Yang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, 100 Science Avenue, Zhengzhou, 450001, China
| | - Hualiang Jiang
- School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaiyu Yang
- State Key Laboratory of Drug Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Science, 555 Zuchongzhi Road, Shanghai, 201203, China.
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21
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Das A, Adhikari C, Chakraborty A. Interaction of Different Divalent Metal Ions with Lipid Bilayer: Impact on the Encapsulation of Doxorubicin by Lipid Bilayer and Lipoplex Mediated Deintercalation. J Phys Chem B 2017; 121:1854-1865. [DOI: 10.1021/acs.jpcb.6b11443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Anupam Das
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh 452020, India
| | - Chandan Adhikari
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh 452020, India
| | - Anjan Chakraborty
- Discipline of Chemistry, Indian Institute of Technology Indore, Indore, Madhya Pradesh 452020, India
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22
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Selladurai SL, Miclette Lamarche R, Schmidt R, DeWolf CE. Model Lung Surfactant Films: Why Composition Matters. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:10767-10775. [PMID: 27641759 DOI: 10.1021/acs.langmuir.6b02945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Lung surfactant replacement therapies, Survanta and Infasurf, and two lipid-only systems both containing saturated and unsaturated phospholipids and one containing additional palmitic acid were used to study the impact of buffered saline on the surface activity, morphology, rheology, and structure of Langmuir monolayer model membranes. Isotherms and Brewster angle microscopy show that buffered saline subphases induce a film expansion, except when the cationic protein, SP-B, is present in sufficient quantities to already screen electrostatic repulsion, thus limiting the effect of changing pH and adding counterions. Grazing incidence X-ray diffraction results indicate an expansion not only of the liquid expanded phase but also an expansion of the lattice of the condensed phase. The film expansion corresponded in all cases with a significant reduction in the viscosity and elasticity of the films. The viscoelastic parameters are dominated by liquid expanded phase properties and do not appear to be dependent on the structure of the condensed phase domains in a phase separated film. The results highlight that the choice of subphase and film composition is important for meaningful interpretations of measurements using model systems.
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Affiliation(s)
- Sahana L Selladurai
- Department of Chemistry and Biochemistry and Centre for NanoScience Research, Concordia University , 7141 Sherbrooke Street West, Montreal, Canada H4B 1R6
| | - Renaud Miclette Lamarche
- Department of Chemistry and Biochemistry and Centre for NanoScience Research, Concordia University , 7141 Sherbrooke Street West, Montreal, Canada H4B 1R6
| | - Rolf Schmidt
- Department of Chemistry and Biochemistry and Centre for NanoScience Research, Concordia University , 7141 Sherbrooke Street West, Montreal, Canada H4B 1R6
| | - Christine E DeWolf
- Department of Chemistry and Biochemistry and Centre for NanoScience Research, Concordia University , 7141 Sherbrooke Street West, Montreal, Canada H4B 1R6
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23
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Kellermann MY, Yoshinaga MY, Valentine RC, Wörmer L, Valentine DL. Important roles for membrane lipids in haloarchaeal bioenergetics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2940-2956. [PMID: 27565574 DOI: 10.1016/j.bbamem.2016.08.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 08/11/2016] [Accepted: 08/19/2016] [Indexed: 10/21/2022]
Abstract
Recent advances in lipidomic analysis in combination with various physiological experiments set the stage for deciphering the structure-function of haloarchaeal membrane lipids. Here we focused primarily on changes in lipid composition of Haloferax volcanii, but also performed a comparative analysis with four other haloarchaeal species (Halobacterium salinarum, Halorubrum lacusprofundi, Halorubrum sodomense and Haloplanus natans) all representing distinctive cell morphologies and behaviors (i.e., rod shape vs. pleomorphic behavior). Common to all five haloarchaea, our data reveal an extraordinary high level of menaquinone, reaching up to 72% of the total lipids. This ubiquity suggests that menaquinones may function beyond their ordinary role as electron and proton transporter, acting simultaneously as ion permeability barriers and as powerful shield against oxidative stress. In addition, we aimed at understanding the role of cations interacting with the characteristic negatively charged surface of haloarchaeal membranes. We propose for instance that by bridging the negative charges of adjacent anionic phospholipids, Mg2+ acts as surrogate for cardiolipin, a molecule that is known to control curvature stress of membranes. This study further provides a bioenergetic perspective as to how haloarchaea evolved following oxygenation of Earth's atmosphere. The success of the aerobic lifestyle of haloarchaea includes multiple membrane-based strategies that successfully balance the need for a robust bilayer structure with the need for high rates of electron transport - collectively representing the molecular basis to inhabit hypersaline water bodies around the planet.
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Affiliation(s)
- Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
| | - Marcos Y Yoshinaga
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Leobener Strasse, D-28359 Bremen, Germany
| | | | - Lars Wörmer
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Leobener Strasse, D-28359 Bremen, Germany
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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24
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Mukherjee I, Barlowe C. Overexpression of Sly41 suppresses COPII vesicle-tethering deficiencies by elevating intracellular calcium levels. Mol Biol Cell 2016; 27:1635-49. [PMID: 27030673 PMCID: PMC4865320 DOI: 10.1091/mbc.e15-10-0704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/22/2016] [Indexed: 11/29/2022] Open
Abstract
SLY41 is a multicopy suppressor of mutations in the essential Ypt1 GTPase. Overexpression of Sly41 elevates cytosolic Ca2+ concentration, which stimulates SNARE-dependent fusion of COPII vesicles with Golgi membranes and suppresses deficiencies in Ypt1-dependent vesicle tethering. Thus Ca2+ positively regulates vesicle fusion with Golgi membranes. SLY41 was identified as a multicopy suppressor of loss of Ypt1, a Rab GTPase essential for COPII vesicle tethering at the Golgi complex. SLY41 encodes a polytopic membrane protein with homology to a class of solute transporter proteins, but how overexpression suppresses vesicle-tethering deficiencies is not known. Here we show that Sly41 is efficiently packaged into COPII vesicles and actively cycles between the ER and Golgi compartments. SLY41 displays synthetic negative genetic interactions with PMR1, which encodes the major Golgi-localized Ca2+/Mn2+ transporter and suggests that Sly41 influences cellular Ca2+ and Mn2+ homeostasis. Experiments using the calcium probe aequorin to measure intracellular Ca2+ concentrations in live cells reveal that Sly41 overexpression significantly increases cytosolic calcium levels. Although specific substrates of the Sly41 transporter were not identified, our findings indicate that localized overexpression of Sly41 to the early secretory pathway elevates cytosolic calcium levels to suppress vesicle-tethering mutants. In vitro SNARE cross-linking assays were used to directly monitor the influence of Ca2+ on tethering and fusion of COPII vesicles with Golgi membranes. Strikingly, calcium at suppressive concentrations stimulated SNARE-dependent membrane fusion when vesicle-tethering activity was reduced. These results show that calcium positively regulates the SNARE-dependent fusion stage of ER–Golgi transport.
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Affiliation(s)
- Indrani Mukherjee
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Charles Barlowe
- Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
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25
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Mahendran V, Philip J. Macromolecular conformation changes at oil-water interface in the presence of cations. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.02.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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26
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Pöyry S, Vattulainen I. Role of charged lipids in membrane structures - Insight given by simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2322-2333. [PMID: 27003126 DOI: 10.1016/j.bbamem.2016.03.016] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/09/2016] [Accepted: 03/11/2016] [Indexed: 01/28/2023]
Abstract
Lipids and proteins are the main components of cell membranes. It is becoming increasingly clear that lipids, in addition to providing an environment for proteins to work in, are in many cases also able to modulate the structure and function of those proteins. Particularly charged lipids such as phosphatidylinositols and phosphatidylserines are involved in several examples of such effects. Molecular dynamics simulations have proved an invaluable tool in exploring these aspects. This so-called computational microscope can provide both complementing explanations for the experimental results and guide experiments to fruitful directions. In this paper, we review studies that have utilized molecular dynamics simulations to unravel the roles of charged lipids in membrane structures. We focus on lipids as active constituents of the membranes, affecting both general membrane properties as well as non-lipid membrane components, mainly proteins. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sanja Pöyry
- Department of Physics, Tampere University of Technology, POB 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, POB 692, FI-33101 Tampere, Finland; MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark; Department of Physics, University of Helsinki, POB 64, FI-00014 Helsinki, Finland.
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27
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Neale C, Pomès R. Sampling errors in free energy simulations of small molecules in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2539-2548. [PMID: 26952019 DOI: 10.1016/j.bbamem.2016.03.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/14/2022]
Abstract
Free energy simulations are a powerful tool for evaluating the interactions of molecular solutes with lipid bilayers as mimetics of cellular membranes. However, these simulations are frequently hindered by systematic sampling errors. This review highlights recent progress in computing free energy profiles for inserting molecular solutes into lipid bilayers. Particular emphasis is placed on a systematic analysis of the free energy profiles, identifying the sources of sampling errors that reduce computational efficiency, and highlighting methodological advances that may alleviate sampling deficiencies. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180-3590, USA
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada; Department of Biochemistry, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
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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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Gang H, Liu J, Mu B. Binding structure and kinetics of surfactin monolayer formed at the air/water interface to counterions: A molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1955-62. [DOI: 10.1016/j.bbamem.2015.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 05/09/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
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30
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Wu W, Yan C, Shi X, Li L, Liu W, Xu C. Lipid in T-cell receptor transmembrane signaling. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 118:130-8. [DOI: 10.1016/j.pbiomolbio.2015.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 12/18/2022]
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31
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Wolf MG, Grubmüller H, Groenhof G. Anomalous surface diffusion of protons on lipid membranes. Biophys J 2015; 107:76-87. [PMID: 24988343 DOI: 10.1016/j.bpj.2014.04.062] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/06/2014] [Accepted: 04/07/2014] [Indexed: 11/30/2022] Open
Abstract
The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery.
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Affiliation(s)
- Maarten G Wolf
- Computational Biomolecular Chemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Gerrit Groenhof
- Computational Biomolecular Chemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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Antipina AY, Gurtovenko AA. Molecular Mechanism of Calcium-Induced Adsorption of DNA on Zwitterionic Phospholipid Membranes. J Phys Chem B 2015; 119:6638-45. [DOI: 10.1021/acs.jpcb.5b01256] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandra Yu. Antipina
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi
Prospect V.O. 31, St. Petersburg 199004, Russia
- Faculty
of Physics, St. Petersburg State University, Ulyanovskaya str. 1, Petrodvorets, St. Petersburg 198504, Russia
| | - Andrey A. Gurtovenko
- Institute
of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi
Prospect V.O. 31, St. Petersburg 199004, Russia
- Faculty
of Physics, St. Petersburg State University, Ulyanovskaya str. 1, Petrodvorets, St. Petersburg 198504, Russia
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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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Przybyło M, Drabik D, Łukawski M, Langner M. Effect of Monovalent Anions on Water Transmembrane Transport. J Phys Chem B 2014; 118:11470-9. [DOI: 10.1021/jp505687d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Magda Przybyło
- Laboratory for Biophysics of Macromolecular Aggregates,
Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-370 Wroclaw, Poland
| | - Dominik Drabik
- Laboratory for Biophysics of Macromolecular Aggregates,
Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-370 Wroclaw, Poland
| | - Maciej Łukawski
- Laboratory for Biophysics of Macromolecular Aggregates,
Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-370 Wroclaw, Poland
| | - Marek Langner
- Laboratory for Biophysics of Macromolecular Aggregates,
Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Pl. Grunwaldzki 13, 50-370 Wroclaw, Poland
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35
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Kohagen M, Mason PE, Jungwirth P. Accurate Description of Calcium Solvation in Concentrated Aqueous Solutions. J Phys Chem B 2014; 118:7902-9. [DOI: 10.1021/jp5005693] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Miriam Kohagen
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 16610 Prague
6, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 16610 Prague
6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo
nam. 2, 16610 Prague
6, Czech Republic
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36
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Pannuzzo M, De Jong DH, Raudino A, Marrink SJ. Simulation of polyethylene glycol and calcium-mediated membrane fusion. J Chem Phys 2014; 140:124905. [DOI: 10.1063/1.4869176] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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37
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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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38
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Liposome clusters with shear stress-induced membrane permeability. Chem Phys Lipids 2013; 174:8-16. [DOI: 10.1016/j.chemphyslip.2013.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/15/2013] [Accepted: 06/03/2013] [Indexed: 11/18/2022]
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