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Sahu SN, Satpathy SS, Pattnaik S, Mohanty C, Pattanayak SK. Boerhavia diffusa plant extract can be a new potent therapeutics against mutant nephrin protein responsible for type1 nephrotic syndrome: Insight into hydrate-ligand docking interactions and molecular dynamics simulation study. J INDIAN CHEM SOC 2022. [DOI: 10.1016/j.jics.2022.100669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Hryc J, Szczelina R, Markiewicz M, Pasenkiewicz-Gierula M. Lipid/water interface of galactolipid bilayers in different lyotropic liquid-crystalline phases. Front Mol Biosci 2022; 9:958537. [PMID: 36046609 PMCID: PMC9423040 DOI: 10.3389/fmolb.2022.958537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, carried out using computational methods, the organisation of the lipid/water interface of bilayers composed of galactolipids with both α-linolenoyl acyl chains is analysed and compared in three different lyotropic liquid-crystalline phases. These systems include the monogalactosyldiglyceride (MGDG) and digalactosyldiglyceride (DGDG) bilayers in the lamellar phase, the MGDG double bilayer during stalk phase formation and the inverse hexagonal MGDG phase. For each system, lipid-water and direct and water-mediated lipid-lipid interactions between the lipids of one bilayer leaflet and those of two apposing leaflets at the onset of new phase (stalk) formation, are identified. A network of interactions between DGDG molecules and its topological properties are derived and compared to those for the MGDG bilayer.
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Affiliation(s)
- Jakub Hryc
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Robert Szczelina
- Faculty of Mathematics and Computer Science, Jagiellonian University, Krakow, Poland
| | - Michal Markiewicz
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- *Correspondence: Marta Pasenkiewicz-Gierula, ; Michal Markiewicz,
| | - Marta Pasenkiewicz-Gierula
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
- *Correspondence: Marta Pasenkiewicz-Gierula, ; Michal Markiewicz,
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Tourte M, Coffinet S, Wörmer L, Lipp JS, Hinrichs KU, Oger PM. The Exploration of the Thermococcus barophilus Lipidome Reveals the Widest Variety of Phosphoglycolipids in Thermococcales. Front Microbiol 2022; 13:869479. [PMID: 35865931 PMCID: PMC9294538 DOI: 10.3389/fmicb.2022.869479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
One of the most distinctive characteristics of archaea is their unique lipids. While the general nature of archaeal lipids has been linked to their tolerance to extreme conditions, little is known about the diversity of lipidic structures archaea are able to synthesize, which hinders the elucidation of the physicochemical properties of their cell membrane. In an effort to widen the known lipid repertoire of the piezophilic and hyperthermophilic model archaeon Thermococcus barophilus, we comprehensively characterized its intact polar lipid (IPL), core lipid (CL), and polar head group compositions using a combination of cutting-edge liquid chromatography and mass spectrometric ionization systems. We tentatively identified 82 different IPLs based on five distinct CLs and 10 polar head group derivatives of phosphatidylhexoses, including compounds reported here for the first time, e.g., di-N-acetylhexosamine phosphatidylhexose-bearing lipids. Despite having extended the knowledge on the lipidome, our results also indicate that the majority of T. barophilus lipids remain inaccessible to current analytical procedures and that improvements in lipid extraction and analysis are still required. This expanded yet incomplete lipidome nonetheless opens new avenues for understanding the physiology, physicochemical properties, and organization of the membrane in this archaeon as well as other archaea.
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Affiliation(s)
- Maxime Tourte
- Univ. Lyon, Univ. Lyon 1, CNRS, UMR 5240, Villeurbanne, France
- Univ. Lyon, INSA Lyon, CNRS, UMR 5240, Villeurbanne, France
| | - Sarah Coffinet
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Lars Wörmer
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Julius S. Lipp
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Nguan H, Ishak KA, Zahid NI, Martinez-Felipe A, Hashim R, Aripin NFK. Incommensurate lamellar phase from long chain Mannosides: Investigation by X-Ray scattering and replica exchange molecular dynamics (REMD). J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Charó N, Jerez H, Tatti S, Romero EL, Schattner M. The Anti-Inflammatory Effect of Nanoarchaeosomes on Human Endothelial Cells. Pharmaceutics 2022; 14:pharmaceutics14040736. [PMID: 35456570 PMCID: PMC9027062 DOI: 10.3390/pharmaceutics14040736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 01/14/2023] Open
Abstract
Archaebacterias are considered a unique source of novel biomaterials of interest for nanomedicine. In this perspective, the effects of nanoarchaeosomes (ARC), which are nanovesicles prepared from polar lipids extracted from the extreme halophilic Halorubrum tebenquinchense, on human umbilical vein endothelial cells (HUVEC) were investigated in physiological and under inflammatory static conditions. Upon incubation, ARC (170 nm mean size, −41 mV ζ) did not affect viability, cell proliferation, and expression of intercellular adhesion molecule-1 (ICAM-1) and E-selectin under basal conditions, but reduced expression of both molecules and secretion of IL-6 induced by lypopolysaccharide (LPS), Pam3CSK4 or Escherichia coli. Such effects were not observed with TNF-α or IL-1β stimulation. Interestingly, ARC significantly decreased basal levels of von Willebrand factor (vWF) and levels induced by all stimuli. None of these parameters was altered by liposomes of hydrogenated phosphatidylcholine and cholesterol of comparable size and concentration. Only ARC were endocytosed by HUVEC and reduced mRNA expression of ICAM-1 and vWF via NF-ĸB and ERK1/2 in LPS-stimulated cells. This is the first report of the anti-inflammatory effect of ARC on endothelial cells and our data suggest that its future use in vascular disease may hopefully be of particular interest.
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Affiliation(s)
- Nancy Charó
- Laboratory of Experimental Thrombosis and Immunobiology of Inflammation, Institute of Experimental Medicine, CONICET-National Academy of Medicine, Pacheco de Melo 3081, Buenos Aires 1425, Argentina;
| | - Horacio Jerez
- Center for Research and Development in Nanomedicines (CIDEN), National University of Quilmes, Roque Saenz Peña, Bernal 1876, Argentina;
| | - Silvio Tatti
- Department of Obstetrics and Gynecology, Clinical Hospital, Av. Córdoba 2351, Buenos Aires 1120, Argentina;
| | - Eder Lilia Romero
- Center for Research and Development in Nanomedicines (CIDEN), National University of Quilmes, Roque Saenz Peña, Bernal 1876, Argentina;
- Correspondence: (E.L.R.); (M.S.)
| | - Mirta Schattner
- Laboratory of Experimental Thrombosis and Immunobiology of Inflammation, Institute of Experimental Medicine, CONICET-National Academy of Medicine, Pacheco de Melo 3081, Buenos Aires 1425, Argentina;
- Correspondence: (E.L.R.); (M.S.)
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Macrophage apoptosis using alendronate in targeted nanoarchaeosomes. Eur J Pharm Biopharm 2021; 160:42-54. [PMID: 33440242 DOI: 10.1016/j.ejpb.2021.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Abstract
Nanoarchaeosomes are non-hydrolysable nanovesicles made of archaeolipids, naturally functionalised with ligand for scavenger receptor class 1. We hypothesized that nitrogenate bisphosphonate alendronate (ALN) loaded nanoarchaeosomes (nanoarchaeosomes(ALN)) may constitute more efficient macrophage targeted apoptotic inducers than ALN loaded nanoliposomes (nanoliposomes (ALN)). To that aim, ALN was loaded in cholesterol containing (nanoARC-chol(ALN)) or not (nanoARC(ALN)) nanoarchaeosomes. Nanoarchaeosomes(ALN) (220-320 nm sized, ~ -40 mV ξ potential, 38-50 μg ALN/mg lipid ratio) displayed higher structural stability than nanoliposomes(ALN) of matching size and ξ potential, retaining most of ALN against a 1/200 folds dilution. The cytotoxicity of nanoARC(ALN) on J774A.1 cells, resulted > 30 folds higher than free ALN and nanoliposomes(ALN) and was reduced by cholesterol in nanoARC-chol(ALN). Devoid of ALN, nanoARC-chol was non-cytotoxic, exhibited pronounced anti-inflammatory activity on J774.1 cells, strongly reducing reactive oxygen species (ROS) and IL-6 induced by LPS. Nanoarchaeosomes bilayer extensively interacted with serum proteins but resulted refractory to phospholipases. Upon J774A.1 cells uptake, nanoarchaeosomes induced cytoplasmic acid vesicles, reduced the mitochondrial membrane potential by 20-40 % without consuming ATP neither damaging lysosomes and increasing pERK. Refractory to chemoenzymatic attacks, either void or drug loaded, nanoarchaeosomes induced either anti-inflammation or macrophages apoptosis, constituting promising targeted nanovesicles for multiple therapeutic purposes.
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Yee SM, Gillams RJ, McLain SE, Lorenz CD. Effects of lipid heterogeneity on model human brain lipid membranes. SOFT MATTER 2021; 17:126-135. [PMID: 33155582 DOI: 10.1039/d0sm01766c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cell membranes naturally contain a heterogeneous lipid distribution. However, homogeneous bilayers are commonly preferred and utilised in computer simulations due to their relative simplicity, and the availability of lipid force field parameters. Recently, experimental lipidomics data for the human brain cell membranes under healthy and Alzheimer's disease (AD) conditions were investigated, since disruption to the lipid composition has been implicated in neurodegenerative disorders, including AD [R. B. Chan et al., J. Biol. Chem., 2012, 287, 2678-2688]. In order to observe the effects of lipid complexity on the various bilayer properties, molecular dynamics simulations were used to study four membranes with increasing heterogeneity: a pure POPC membrane, a POPC and cholesterol membrane in a 1 : 1 ratio (POPC-CHOL), and to our knowledge, the first realistic models of a healthy brain membrane and an Alzheimer's diseased brain membrane. Numerous structural, interfacial, and dynamical properties, including the area per lipid, interdigitation, dipole potential, and lateral diffusion of the two simple models, POPC and POPC-CHOL, were analysed and compared to those of the complex brain models consisting of 27 lipid components. As the membranes gain heterogeneity, a number of alterations were found in the structural and dynamical properties, and more significant differences were observed in the lateral diffusion. Additionally, we observed snorkeling behaviour of the lipid tails that may play a role in the permeation of small molecules across biological membranes. In this work, atomistic description of realistic brain membrane models is provided, which can add insight towards the permeability and transport pathways of small molecules across these membrane barriers.
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Affiliation(s)
- Sze May Yee
- Department of Physics, King's College London, London WC2R 2LS, UK.
| | - Richard J Gillams
- School of Electronics and Computer Science, and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sylvia E McLain
- Department of Chemistry, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK
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Martins LS, Duarte EL, Lamy MT, Rozenfeld JHK. Supramolecular organization of α-galactosylceramide in pure dispersions and in cationic DODAB bilayers. Chem Phys Lipids 2020; 232:104963. [PMID: 32882224 DOI: 10.1016/j.chemphyslip.2020.104963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/01/2020] [Accepted: 08/20/2020] [Indexed: 11/30/2022]
Abstract
α-galactosylceramide (α-GalCer; KRN7000) strongly stimulates NKT cells. The structures of α-GalCer assemblies and of cationic DODAB bilayers containing α-GalCer were investigated by differential scanning calorimetry (DSC) and electron spin resonance (ESR) spectroscopy. Assemblies of α-GalCer have a very tightly packed gel phase, causing spin labels to cluster and display spin exchange interactions. An endothermic phase transition is observed by DSC, leading to a fluid phase. This phase transition peak disappears upon mixing with DODAB, showing that up to 9 mol% α-GalCer is miscible with the cationic lipid. ESR spectra show that α-GalCer decreases DODAB gel phase packing, resulting in a decrease of gel-fluid transition temperature and cooperativity in DSC thermograms of mixed bilayers. In contrast, α-GalCer increases the rigidity of the fluid phase. These effects are probably due to the conformation of the rigid amide bond that connects the phytosphingosine base of α-GalCer to its long and saturated acyl chain. Possibly, α-GalCer adopts a V-shaped conformation because of the perpendicular orientation of the amide bond towards the axes of the hydrocarbon chains. Apparently, the effect of the amide bond configuration is a key structural feature for the interaction between ceramide-based glycolipids and DODAB molecules, since we have previously reported a similar decrease of gel phase packing and increase in fluid phase rigidity for DODAB bilayers containing C24:1β-glucosylceramide. Since the structure of delivery systems is critical to the biological activity of α-GalCer, this work certainly contributes to the planning and development of novel immunotherapeutic tools.
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Affiliation(s)
- Letícia S Martins
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, R. Botucatu 862, 04023-062, São Paulo, SP, Brazil
| | - Evandro L Duarte
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508090, São Paulo, SP, Brazil
| | - M Teresa Lamy
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, 05508090, São Paulo, SP, Brazil
| | - Julio H K Rozenfeld
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, R. Botucatu 862, 04023-062, São Paulo, SP, Brazil.
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Kim J, Jozic A, Sahay G. Naturally Derived Membrane Lipids Impact Nanoparticle-Based Messenger RNA Delivery. Cell Mol Bioeng 2020; 13:463-474. [PMID: 32837581 PMCID: PMC7250267 DOI: 10.1007/s12195-020-00619-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/16/2020] [Indexed: 02/08/2023] Open
Abstract
Introduction Lipid based nanoparticles (LNPs) are clinically successful vectors for hepatic delivery of nucleic acids. These systems are being developed for non-hepatic delivery of mRNA for the treatment of diseases like cystic fibrosis or retinal degeneration as well as infectious diseases. Localized delivery to the lungs requires aerosolization. We hypothesized that structural lipids within LNPs would provide features of integrity which can be tuned for attributes required for efficient hepatic and non-hepatic gene delivery. Herein, we explored whether naturally occurring lipids that originate from the cell membrane of plants and microorganisms enhance mRNA-based gene transfection in vitro and in vivo and whether they assist in maintaining mRNA activity after nebulization. Methods We substituted DSPC, a structural lipid used in a conventional LNP formulation, to a series of naturally occurring membrane lipids. We measured the effect of these membrane lipids on size, encapsulation efficiency and their impact on transfection efficiency. We further characterized LNPs after nebulization and measured whether they retained their transfection efficiency. Results One plant-derived structural lipid, DGTS, led to a significant improvement in liver transfection of mRNA. DGTS LNPs had similar transfection ability when administered in the nasal cavity to conventional LNPs. In contrast, we found that DGTS LNPs had reduced transfection efficiency in cells pre-and post-nebulization while maintaining size and encapsulation similar to DSPC LNPs. Conclusions We found that structural lipids provide differential mRNA-based activities in vitro and in vivo which also depend on the mode of administration. Understanding influence of structural lipids on nanoparticle morphology and structure can lead to engineering potent materials for mRNA-based gene therapy applications.
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Affiliation(s)
- Jeonghwan Kim
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Sciences Building, Portland, OR USA
| | - Antony Jozic
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Sciences Building, Portland, OR USA
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Sciences Building, Portland, OR USA.,Department of Biomedical Engineering, Oregon Health Science University, Robertson Life Sciences Building, Portland, OR USA
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Szczelina R, Baczynski K, Markiewicz M, Pasenkiewicz-Gierula M. Network of lipid interconnections at the interfaces of galactolipid and phospholipid bilayers. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Murakawa M, Ohta H, Shimojima M. Lipid remodeling under acidic conditions and its interplay with low Pi stress in Arabidopsis. PLANT MOLECULAR BIOLOGY 2019; 101:81-93. [PMID: 31201686 PMCID: PMC6695348 DOI: 10.1007/s11103-019-00891-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/06/2019] [Indexed: 06/09/2023]
Abstract
Here we show that accumulation of galactose-containing lipids in plastid membranes in shoots and the other membranes in roots maintains Arabidopsis growth under acidic stress and acidic phosphate deficiency. Soil acidification and phosphate deficiency are closely related to each other in natural environments. In addition to the toxicity of high proton concentrations, acid soil can lead to imbalances of ion availability and nutritional deficiencies, including inorganic phosphate (Pi). Among plants, activation of non-phosphorus-containing galactolipid, digalactosyldiacylglycerol (DGDG), synthesis concomitant with phospholipid degradation, namely membrane lipid remodeling, is crucial for coping with Pi starvation. However, regulation mechanisms of membrane lipid composition during acidic stress have not been clarified. Here, we investigated lipid metabolism in Arabidopsis thaliana grown under acidic stress with or without Pi. Under Pi-sufficient acidic conditions, DGDG was increased in shoot membranes, and some Pi starvation-responsive genes that are involved in lipid remodeling were upregulated without reducing Pi content in leaves. In contrast, under acidic Pi deficiency, membrane lipid remodeling in roots was partially repressed at a lower external pH. Nevertheless, phenotypic comparison between wild type and the double mutant of MGD2/3, which are responsible for DGDG accumulation during Pi starvation, indicated that the complete absence of lipid remodeling in roots resulted in a loss of tolerance to Pi deficiency rather specifically under acidic conditions. This result suggested important physiological roles of galactolipid-enriched membranes under acidic Pi deficiency.
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Affiliation(s)
- Masato Murakawa
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan
| | - Mie Shimojima
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-65 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8501, Japan.
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Martins LS, Nomura DA, Duarte EL, Riske KA, Lamy MT, Rozenfeld JHK. Structural characterization of cationic DODAB bilayers containing C24:1 β-glucosylceramide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:643-650. [PMID: 30611744 DOI: 10.1016/j.bbamem.2018.12.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/09/2018] [Accepted: 12/28/2018] [Indexed: 01/13/2023]
Abstract
The effect of 5 mol%, 9 mol%, and 16 mol% of C24:1 β-glucosylceramide (βGlcCer) on the structure of cationic DODAB bilayers was investigated by means of differential scanning calorimetry (DSC), electron spin resonance (ESR) spectroscopy and fluorescence microscopy. βGlcCer is completely miscible with DODAB at all fractions tested, since no domains were observed in fluorescence microscopy or ESR spectra. The latter showed that βGlcCer destabilized the gel phase of DODAB bilayers by decreasing the gel phase packing. As a consequence, βGlcCer induced a decrease in the phase transition temperature and cooperativity of DODAB bilayers, as seen in DSC thermograms. ESR spectra also showed that βGlcCer induced an increase in DODAB fluid phase order and/or rigidity. Despite their different structures, a similar effect of loosening the gel phase packing and turning the fluid phase more rigid/organized has also been observed when low molar fractions of cholesterol were incorporated in DODAB bilayers. The structural characterization of mixed membranes made of cationic lipids and glucosylceramides may be important for developing novel immunotherapeutic tools such as vaccine adjuvants.
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Affiliation(s)
- Letícia S Martins
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, R. Botucatu 862, 04023-062 São Paulo, SP, Brazil
| | - Daniela A Nomura
- Instituto de Física, Universidade de São Paulo, CP 66318, CEP 05315-970 São Paulo, SP, Brazil
| | - Evandro L Duarte
- Instituto de Física, Universidade de São Paulo, CP 66318, CEP 05315-970 São Paulo, SP, Brazil
| | - Karin A Riske
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, R. Botucatu 862, 04023-062 São Paulo, SP, Brazil
| | - M Teresa Lamy
- Instituto de Física, Universidade de São Paulo, CP 66318, CEP 05315-970 São Paulo, SP, Brazil
| | - Julio H K Rozenfeld
- Departamento de Biofísica, Escola Paulista de Medicina, Universidade Federal de São Paulo, R. Botucatu 862, 04023-062 São Paulo, SP, Brazil.
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Weng L, Stott SL, Toner M. Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation. Annu Rev Biomed Eng 2018; 21:1-31. [PMID: 30525930 DOI: 10.1146/annurev-bioeng-060418-052130] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.
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Affiliation(s)
- Lindong Weng
- Center for Engineering in Medicine and BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA; , , .,Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Shannon L Stott
- Center for Engineering in Medicine and BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA; , , .,Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts 02129, USA.,Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Mehmet Toner
- Center for Engineering in Medicine and BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA; , , .,Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Shriners Hospital for Children, Boston, Massachusetts 02114, USA
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Parra FL, Caimi AT, Altube MJ, Cargnelutti DE, Vermeulen ME, de Farias MA, Portugal RV, Morilla MJ, Romero EL. Make It Simple: (SR-A1+TLR7) Macrophage Targeted NANOarchaeosomes. Front Bioeng Biotechnol 2018; 6:163. [PMID: 30460231 PMCID: PMC6232313 DOI: 10.3389/fbioe.2018.00163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/17/2018] [Indexed: 11/13/2022] Open
Abstract
Hyperhalophilic archaebacteria exclusively produce sn2,3 diphytanylglycerol diether archaeolipids, unique structures absent in bacteria and eukaryotes. Nanovesicles made of archaeolipids known as nanoarchaeosomes (nanoARC), possess highly stable bilayers, some of them displaying specific targeting ability. Here we hypothesize that nanoARC made from Halorubrum tebenquichense archaebacteria, may constitute efficient carriers for the TLR7 agonist imiquimod (IMQ). NanoARC-IMQ takes advantage of the intense interaction between IMQ and the highly disordered, poorly fluid branched archaeolipid bilayers, rich in archaeol analog of methyl ester of phosphatidylglycerophosphate (PGP-Me), a natural ligand of scavenger receptor A1 (SR-A1). This approach lacks complex manufacture steps required for bilayers labeling, enabling future analytical characterization, batch reproducibility, and adaptation to higher scale production. SR-A1 mediated internalization of particulate material is mostly targeted to macrophages and is extensive because it is not submitted to a negative feedback. A massive and selective intracellular delivery of IMQ may concentrate its effect specifically into the endosomes, where the TLR7 is expressed, magnifying its immunogenicity, at the same time reducing its systemic bioavailability, and therefore it's in vivo adverse effects. NanoARC-IMQ (600-900 nm diameter oligolamellar vesicles of ~-43 mV Z potential) were heavily loaded with IMQ at ~44 μg IMQ/mg phospholipids [~20 folds higher than the non-SR-A1 ligand soyPC liposomes loaded with IMQ (LIPO-IMQ)]. In vitro, nanoARC-IMQ induced higher TNF-α and IL-6 secretion by J774A1 macrophages compared to same dose of IMQ and same lipid dose of LIPO-IMQ. In vivo, 3 subcutaneous doses of nanoARC-IMQ+ 10 μg total leishmania antigens (TLA) at 50 μg IMQ per Balb/C mice, induced more pronounced DTH response, accompanied by a nearly 2 orders higher antigen-specific systemic IgG titers than IMQ+TLA and LIPO-IMQ. The isotype ratio of nanoARC-IMQ+TLA remained ~0.5 indicating, the same as IMQ+TLA, a Th2 biased response distinguished by a pronounced increase in antibody titers, without negative effects on splenocytes lymphoproliferation, with a potential CD8+LT induction 10 days after the last dose. Overall, this first approach showed that highly SR-A1 mediated internalization of heavily loaded nanoARC-IMQ, magnified the effect of IMQ on TLR7 expressing macrophages, leading to a more intense in vivo immune response.
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Affiliation(s)
- Federico Leonel Parra
- Departamento de Ciencia y Tecnología, Nanomedicine Research & Development Center, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Ayelen Tatiana Caimi
- Departamento de Ciencia y Tecnología, Nanomedicine Research & Development Center, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Maria Julia Altube
- Departamento de Ciencia y Tecnología, Nanomedicine Research & Development Center, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego Esteban Cargnelutti
- Centro Científico y Tecnológico de Mendoza, Instituto de Medicina y Biología Experimental de Cuyo, Consejo Nacional de Investigaciones Científicas y Técnicas, Mendoza, Argentina
| | - Mónica Elba Vermeulen
- Instituto de Medicina Experimental—Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | | | | | - Maria Jose Morilla
- Departamento de Ciencia y Tecnología, Nanomedicine Research & Development Center, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Eder Lilia Romero
- Departamento de Ciencia y Tecnología, Nanomedicine Research & Development Center, Universidad Nacional de Quilmes, Bernal, Argentina
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Glucosylceramide modifies the LPS-induced inflammatory response in macrophages and the orientation of the LPS/TLR4 complex in silico. Sci Rep 2018; 8:13600. [PMID: 30206272 PMCID: PMC6134110 DOI: 10.1038/s41598-018-31926-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/29/2018] [Indexed: 12/31/2022] Open
Abstract
Toll-like receptor 4 (TLR4) is activated by bacterial lipopolysaccharide (LPS), which drives the production of proinflammatory cytokines. Earlier studies have indicated that cholesterol- and glycosphingolipid-rich subregions of the plasma membrane (lipid domains) are important for TLR4-mediated signaling. We report that inhibition of glucosylceramide (GluCer) synthase, which resulted in decreased concentrations of the glycosphingolipid GluCer in lipid domains, reduced the LPS-induced inflammatory response in both mouse and human macrophages. Atomistic molecular dynamics simulations of the TLR4 dimer complex (with and without LPS in its MD-2 binding pockets) in membranes (in the presence and absence of GluCer) showed that: (1) LPS induced a tilted orientation of TLR4 and increased dimer integrity; (2) GluCer did not affect the integrity of the LPS/TLR4 dimer but reduced the LPS-induced tilt; and (3) GluCer increased electrostatic interactions between the membrane and the TLR4 extracellular domain, which could potentially modulate the tilt. We also showed that GCS inhibition reduced the interaction between TLR4 and the intracellular adaptor protein Mal. We conclude that the GluCer-induced effects on LPS/TLR4 orientation may influence the signaling capabilities of the LPS/TLR4 complex by affecting its interaction with downstream signaling proteins.
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17
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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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18
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Baczynski K, Markiewicz M, Pasenkiewicz‐Gierula M. Is the tilt of the lipid head group correlated with the number of intermolecular interactions at the bilayer interface? FEBS Lett 2018; 592:1507-1515. [DOI: 10.1002/1873-3468.13048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 11/10/2022]
Affiliation(s)
- 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
| | - Marta Pasenkiewicz‐Gierula
- Department of Computational Biophysics and Bioinformatics Faculty of Biochemistry, Biophysics and Biotechnology Jagiellonian University Krakow Poland
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19
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Ahmadi S, ManickamAchari V, Hussain Z, Hashim R. Epimeric and anomeric relationship of octyl- α - d -gluco/galactosides: Insight from density functional theory and atom in molecules studies. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Ahmadi S, Heidelberg T. Modelling and molecular dynamics simulation studies on a hexagonal glycolipid assembly. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2016. [DOI: 10.1007/s13738-016-0958-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Liu D, Zhang J, Xu S, Liu H. Membrane property and biofunction of phospholiposome incorporated with anomeric galactolipids. SPRINGERPLUS 2016; 5:655. [PMID: 27330921 PMCID: PMC4870520 DOI: 10.1186/s40064-016-2236-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/26/2016] [Indexed: 11/21/2022]
Abstract
There has been increasing interest in the construction of liposomes containing a targeting reagent for target-specific drug delivery. Glycoconjugates that can be recognized by transmembrane glycoprotein receptors have been extensively used to form glyco-liposomal drug carriers. However, the impact of anomerism, which is a common identity of natural glycoconjugates, on the glyco-liposomal properties has been hardly probed in previous studies. Here we investigate the liposomal properties of phospholipid incorporated with a pair of anomeric galactolipids. The anomeric galacto-liposomes are characterized and their membrane fluidity, thermo-stability, DNA condensation efficiency and fluorescence leakage are comparatively tested. The in vitro cellular internalization effect of the galacto-liposomes is also demonstrated. This study suggests that anomerism might give distinct impact on the membrane properties and even biofunctions of glyco-liposomes.
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Affiliation(s)
- Danyang Liu
- />Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237 People’s Republic of China
| | - Junqi Zhang
- />Key Laboratory of Medical Molecular Virology (Ministry of Health and Ministry of Education), School of Basic Medical Sciences, Fudan University, 138 Yixueyuan Rd, Shanghai, 200032 People’s Republic of China
| | - Shouhong Xu
- />Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237 People’s Republic of China
| | - Honglai Liu
- />Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd, Shanghai, 200237 People’s Republic of China
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22
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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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23
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Molecular simulations of glycolipids: Towards mammalian cell membrane models. Biochimie 2015; 120:105-9. [PMID: 26427555 PMCID: PMC4710579 DOI: 10.1016/j.biochi.2015.09.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 09/25/2015] [Indexed: 12/19/2022]
Abstract
Glycolipids are key components of mammalian cell membranes, influencing a diverse range of cellular functions. For example, a number of receptor tyrosine kinases, including the epidermal growth factor receptor (EGFR), are allosterically regulated by the glycolipid monosialodihexosylganglioside (GM3). Recent advances in molecular dynamics methods, especially the development of coarse-grained models, have enabled simulations of increasingly complex models of cell membranes. We demonstrate these methodological developments via a case study of a coarse-grained model for the ganglioside GM3. This glycolipid is included in simulations of a mixed lipid bilayer model reflecting the compositional complexity of a mammalian cell membrane. The resultant membrane model is used to simulate the interactions of GM3 with the transmembrane domain of the EGFR. We review recent progress in molecular dynamics simulations of glycolipids. A coarse-grained model of the ganglioside GM3 is described. The GM3 model is used in coarse-grained simulations of a mammalian cell membrane. We describe the interactions of GM3 with the transmembrane domain of the EGFR.
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24
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Baczynski K, Markiewicz M, Pasenkiewicz-Gierula M. A computer model of a polyunsaturated monogalactolipid bilayer. Biochimie 2015; 118:129-40. [PMID: 26348551 DOI: 10.1016/j.biochi.2015.09.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 09/02/2015] [Indexed: 12/21/2022]
Abstract
1,2-di-O-acyl-3-O-β-D-galactopyranosyl-sn-glycerol (MGDG) is the main lipid component of thylakoid membranes of higher plants and algae. This monogalactolipid is thought of as a non-bilayer lipid but actually it can form both lamellar and nonlamellar phases. In this study, molecular dynamics (MD) simulations of the fully hydrated di-18:3 MGDG bilayer in the lamellar phase were carried out at 310 and 295 K for 200 and 450 ns, respectively, using the GROMACS 4 software package and OPLS-AA force field. At both temperatures, the lamellar phase of the systems was stable. The pure di-18:3 MGDG bilayer is the first step towards creating a computer model of the lipid matrix of the thylakoid membrane and the main aim of this study was to validate the computer model of di-18:3 MGDG in the bilayer and also to assess the properties of the bilayer. However, only a few of the predicted properties could be compared with those derived experimentally and in other MD simulations because of insufficient amount of such data. Thus, direct validation of the MGDG bilayer proved difficult. Therefore, in the validation process also an indirect approach was used, in which a computer model of the 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) bilayer simulated at the same temperatures using the same force field as the MGDG bilayer was assessed. Successful validation of the DOPC bilayer parameterized in the OPLS-AA force field and similar properties of the MGDG molecules in the pure 18:3 MGDG and in binary 18:3 MGDG-PC bilayers indicate that the computer model of the MDGD molecule is faithful and the MGDG bilayer is representative on the time scales covered in these MD simulations.
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Affiliation(s)
- 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
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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25
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Kociurzynski R, Pannuzzo M, Böckmann RA. Phase Transition of Glycolipid Membranes Studied by Coarse-Grained Simulations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:9379-9387. [PMID: 26267673 DOI: 10.1021/acs.langmuir.5b01617] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Glycolipids are important components of biological membranes. High concentrations of glycolipids are particularly found in lipid rafts, which take part in many physiological phenomena. This different partitioning and interaction pattern of glycolipids in the membrane as compared to those of phospholipids are likely due to their different chemical structures: the polar regions of glycosphingolipids can be even larger than for their hydrophobic moieties, giving rise to a rich conformational landscape. Here we study the influence of glycosphingolipids galactosylceramide (GCER) and monosialotetrahexosylganglioside (GM1) on the structural and thermodynamic properties of a phospholipid (DPPC) bilayer. Using the method of coarse-grained molecular dynamics simulation we show that both glycolipids increase the phase-transition temperature of phospholipid membranes and that the extent of this increase depends on the headgroup size and structure. GM1 shows a strong tendency to form mixed clusters with phospholipids, thereby stabilizing the membrane. In contrast, GCER is dispersed in the membrane. By occupying the interstitial space between phospholipids it causes a tighter packing of the lipids in the membrane.
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Affiliation(s)
- Raisa Kociurzynski
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg , Staudtstr. 5, 91058 Erlangen, Germany
| | - Martina Pannuzzo
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg , Staudtstr. 5, 91058 Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg , Staudtstr. 5, 91058 Erlangen, Germany
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26
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Lewis DD, Villarreal FD, Wu F, Tan C. Synthetic biology outside the cell: linking computational tools to cell-free systems. Front Bioeng Biotechnol 2014; 2:66. [PMID: 25538941 PMCID: PMC4260521 DOI: 10.3389/fbioe.2014.00066] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 11/23/2014] [Indexed: 12/22/2022] Open
Abstract
As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.
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Affiliation(s)
- Daniel D. Lewis
- Integrative Genetics and Genomics, University of California Davis, Davis, CA, USA
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | | | - Fan Wu
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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27
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Róg T, Vattulainen I. Cholesterol, sphingolipids, and glycolipids: what do we know about their role in raft-like membranes? Chem Phys Lipids 2014; 184:82-104. [PMID: 25444976 DOI: 10.1016/j.chemphyslip.2014.10.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 10/24/2014] [Accepted: 10/25/2014] [Indexed: 12/14/2022]
Abstract
Lipids rafts are considered to be functional nanoscale membrane domains enriched in cholesterol and sphingolipids, characteristic in particular of the external leaflet of cell membranes. Lipids, together with membrane-associated proteins, are therefore considered to form nanoscale units with potential specific functions. Although the understanding of the structure of rafts in living cells is quite limited, the possible functions of rafts are widely discussed in the literature, highlighting their importance in cellular functions. In this review, we discuss the understanding of rafts that has emerged based on recent atomistic and coarse-grained molecular dynamics simulation studies on the key lipid raft components, which include cholesterol, sphingolipids, glycolipids, and the proteins interacting with these classes of lipids. The simulation results are compared to experiments when possible.
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, Tampere, Finland; MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark.
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28
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The challenges of understanding glycolipid functions: An open outlook based on molecular simulations. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1130-45. [DOI: 10.1016/j.bbalip.2013.12.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 11/20/2022]
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29
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ManickamAchari V, Bryce RA, Hashim R. Conformational dynamics of dry lamellar crystals of sugar based lipids: an atomistic simulation study. PLoS One 2014; 9:e101110. [PMID: 24978205 PMCID: PMC4076255 DOI: 10.1371/journal.pone.0101110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 06/03/2014] [Indexed: 11/18/2022] Open
Abstract
The rational design of a glycolipid application (e.g. drug delivery) with a tailored property depends on the detailed understanding of its structure and dynamics. Because of the complexity of sugar stereochemistry, we have undertaken a simulation study on the conformational dynamics of a set of synthetic glycosides with different sugar groups and chain design, namely dodecyl β-maltoside, dodecyl β-cellobioside, dodecyl β-isomaltoside and a C12C10 branched β-maltoside under anhydrous conditions. We examined the chain structure in detail, including the chain packing, gauche/trans conformations and chain tilting. In addition, we also investigated the rotational dynamics of the headgroup and alkyl chains. Monoalkylated glycosides possess a small amount of gauche conformers (∼20%) in the hydrophobic region of the lamellar crystal (LC) phase. In contrast, the branched chain glycolipid in the fluid Lα phase has a high gauche population of up to ∼40%. Rotational diffusion analysis reveals that the carbons closest to the headgroup have the highest correlation times. Furthermore, its value depends on sugar type, where the rotational dynamics of an isomaltose was found to be 11-15% and more restrained near the sugar, possibly due to the chain disorder and partial inter-digitation compared to the other monoalkylated lipids. Intriguingly, the present simulation demonstrates the chain from the branched glycolipid bilayer has the ability to enter into the hydrophilic region. This interesting feature of the anhydrous glycolipid bilayer simulation appears to arise from a combination of lipid crowding and the amphoteric nature of the sugar headgroups.
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Affiliation(s)
- Vijayan ManickamAchari
- Department of Chemistry, University of Malaya, Kuala Lumpur, Malaysia
- Kavli Institute of Theoretical Physics China, Chinese Academy of Sciences, Beijing, China
| | - Richard A. Bryce
- Manchester Pharmacy School, University of Manchester, Manchester, United Kingdom
| | - Rauzah Hashim
- Department of Chemistry, University of Malaya, Kuala Lumpur, Malaysia
- Kavli Institute of Theoretical Physics China, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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30
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Maciejewski A, Pasenkiewicz-Gierula M, Cramariuc O, Vattulainen I, Rog T. Refined OPLS all-atom force field for saturated phosphatidylcholine bilayers at full hydration. J Phys Chem B 2014; 118:4571-81. [PMID: 24745688 DOI: 10.1021/jp5016627] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report parametrization of dipalmitoyl-phosphatidylcholine (DPPC) in the framework of the Optimized Parameters for Liquid Simulations all-atom (OPLS-AA) force field. We chose DPPC as it is one of the most studied phospholipid species and thus has plenty of experimental data necessary for model validation, and it is also one of the highly important and abundant lipid types, e.g., in lung surfactant. Overall, PCs have not been previously parametrized in the OPLS-AA force field; thus, there is a need to derive its bonding and nonbonding parameters for both the polar and nonpolar parts of the molecule. In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Møller-Plesset perturbation theory (MP2), and (3) density functional theory (DFT). We also tested the effect of the polar environment by using the polarizable continuum model (PCM), and for acyl chains the van der Waals parameters were also adjusted. In effect, six parameter sets were generated and tested on a DPPC bilayer. Out of these six sets, only one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM).
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Affiliation(s)
- Arkadiusz Maciejewski
- Department of Physics, Tampere University of Technology , PO Box 692, FI-33101 Tampere, Finland
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31
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Atomistic simulation studies of the α/β-glucoside and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations. J Mol Model 2014; 20:2165. [DOI: 10.1007/s00894-014-2165-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
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32
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Misran O, Timimi BA, Heidelberg T, Sugimura A, Hashim R. Deuterium NMR Investigation of the lyotropic phases of alkyl β-glycoside/D2O systems. J Phys Chem B 2013; 117:7335-44. [PMID: 23718628 DOI: 10.1021/jp401787b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We have investigated the phase behavior of four glycosides (βC8OGlc, βC8SGlc, βC10OGlc, βC8OGal) in water and D2O by optical polarizing microscopy and deuterium NMR. Previously published phase diagrams were evaluated by deuterium NMR, via monitoring D2O spectra, and confirmed the presence of the hexagonal, bicontinuous cubic, and lamellar phases in these glycosides. We have also shown the presence of the gel phase in (βC10OGlc) and observed the extensive supercooling of the lamellar phase to temperatures well below the Kraft line. While the main features of the phase diagrams were confirmed, some phase boundaries were found to be slightly different. Magnetically aligned spectra were also observed for relatively dilute samples for the hexagonal phase (βC8OGlc and βC8OGal) and the lamellar phase (βC8SGlc and βC10OGlc). The average number of bound water molecules per headgroup in the lamellar phase for the glycosides was determined by the systematic measurement of the quadrupolar splitting of D2O over a wide range of values of the (glycoside/water) molar ratio. The number of water molecules bound to the headgroup was found on average to be about 1.6-1.7 water molecules with no significant differences in this value for the different glycosides (and over the temperature range investigated), indicating that the bound water content is predominately influenced by the number of hydroxyl groups of the headgroup only. However, this bound water content of only 1.6-1.7 water molecules per sugar headgroup is surprisingly low, suggesting strong intermolecular interactions of the OH groups of headgroup sugars. The results are in line with computational results reported earlier for the octyl-β-glucoside and β-galactoside, which show the presence of strong intralayer hydrogen bonding.
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Affiliation(s)
- Omar Misran
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
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33
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López CA, Sovova Z, van Eerden FJ, de Vries AH, Marrink SJ. Martini Force Field Parameters for Glycolipids. J Chem Theory Comput 2013; 9:1694-708. [DOI: 10.1021/ct3009655] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- César A. López
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Zofie Sovova
- Faculty
of Science, University
of South Bohemia, Czech Republic, and Institute of Nanobiology and
Structural Biology GCRC ASCR, v.v.i. Nove Hrady, Czech Republic
| | - Floris J. van Eerden
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Alex H. de Vries
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences
and Biotechnology (GBB) Institute and Zernike Institute for Advanced
Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
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34
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Cramariuc O, Rog T, Javanainen M, Monticelli L, Polishchuk AV, Vattulainen I. Mechanism for translocation of fluoroquinolones across lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2563-71. [DOI: 10.1016/j.bbamem.2012.05.027] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 05/21/2012] [Accepted: 05/25/2012] [Indexed: 11/24/2022]
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35
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Manickam Achari V, Nguan HS, Heidelberg T, Bryce RA, Hashim R. Molecular Dynamics Study of Anhydrous Lamellar Structures of Synthetic Glycolipids: Effects of Chain Branching and Disaccharide Headgroup. J Phys Chem B 2012; 116:11626-34. [DOI: 10.1021/jp302292s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Hock Seng Nguan
- Department
of Chemistry, University of Malaya, 50603
Kuala Lumpur, Malaysia
| | | | - Richard A. Bryce
- School of Pharmacy and Pharmaceutical
Sciences, University of Manchester, Manchester,
M13 9PT, U.K
| | - Rauzah Hashim
- Department
of Chemistry, University of Malaya, 50603
Kuala Lumpur, Malaysia
- Kavli Institute
of Theoretical
Physics China, Chinese Academy of Sciences, Beijing 100190, China
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36
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DeMarco ML. Three-Dimensional Structure of Glycolipids in Biological Membranes. Biochemistry 2012; 51:5725-32. [DOI: 10.1021/bi3003633] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mari L. DeMarco
- Division of Laboratory
and Genomic Medicine, Washington University School of Medicine, 660 South
Euclid Avenue, St. Louis, Missouri 63110, United States
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37
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Lehtinen J, Magarkar A, Stepniewski M, Hakola S, Bergman M, Róg T, Yliperttula M, Urtti A, Bunker A. Analysis of cause of failure of new targeting peptide in PEGylated liposome: Molecular modeling as rational design tool for nanomedicine. Eur J Pharm Sci 2012; 46:121-30. [DOI: 10.1016/j.ejps.2012.02.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 02/02/2012] [Accepted: 02/12/2012] [Indexed: 10/28/2022]
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38
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Stępniewski M, Kepczynski M, Jamróz D, Nowakowska M, Rissanen S, Vattulainen I, Róg T. Interaction of Hematoporphyrin with Lipid Membranes. J Phys Chem B 2012; 116:4889-97. [DOI: 10.1021/jp300899b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Michał Stępniewski
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków,
Poland
| | - Mariusz Kepczynski
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków,
Poland
| | - Dorota Jamróz
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków,
Poland
| | - Maria Nowakowska
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków,
Poland
| | - Sami Rissanen
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101
Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101
Tampere, Finland
- MEMPHYS-Center
for Biomembrane
Physics, University of Southern Denmark, Odense, Denmark
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, PO Box 692, FI-33101
Tampere, Finland
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39
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Magarkar A, Karakas E, Stepniewski M, Róg T, Bunker A. Molecular Dynamics Simulation of PEGylated Bilayer Interacting with Salt Ions: A Model of the Liposome Surface in the Bloodstream. J Phys Chem B 2012; 116:4212-9. [DOI: 10.1021/jp300184z] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Aniket Magarkar
- Centre for Drug Research,
Faculty
of Pharmacy, University of Helsinki, Helsinki,
Finland
| | - Esra Karakas
- Centre for Drug Research,
Faculty
of Pharmacy, University of Helsinki, Helsinki,
Finland
| | - Michał Stepniewski
- Centre for Drug Research,
Faculty
of Pharmacy, University of Helsinki, Helsinki,
Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, Tampere, Finland
| | - Alex Bunker
- Centre for Drug Research,
Faculty
of Pharmacy, University of Helsinki, Helsinki,
Finland
- Department of Chemistry, Aalto University, Espoo, Finland
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40
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Kapla J, Stevensson B, Dahlberg M, Maliniak A. Molecular dynamics simulations of membranes composed of glycolipids and phospholipids. J Phys Chem B 2011; 116:244-52. [PMID: 22122018 DOI: 10.1021/jp209268p] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipid membranes composed of 1,2-di-(9Z,12Z,15Z)-octadecatrienoyl-3-O-β-D-galactosyl-sn-glycerol or monogalactosyldiacylglycerol (MGDG) and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) were studied by means of molecular dynamics (MD) computer simulations. Three lipid compositions were considered: 0%, 20%, and 45% MGDG (by mole) denoted as MG-0, MG-20, and MG-45, respectively. The article is focused on the calculation of NMR dipolar interactions, which were confronted with previously reported experimental couplings. Dynamical processes and orientational distributions relevant for the averaging of dipolar interactions were evaluated. Furthermore, several parameters important for characterization of the bilayer structure, molecular organization, and dynamics were investigated. In general, only a minor change in DMPC properties was observed upon the increased MGDG/DMPC ratio, whereas properties related to MGDG undergo a more pronounced change. This effect was ascribed to the fact that DMPC is a bilayer (L(α)) forming lipid, whereas MGDG prefers a reverse hexagonal (H(II)) arrangement.
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Affiliation(s)
- Jon Kapla
- Department of Materials and Environmental Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
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41
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Hashim R, Mirzadeh SM, Heidelberg T, Minamikawa H, Yoshiaki T, Sugimura A. A reevaluation of the epimeric and anomeric relationship of glucosides and galactosides in thermotropic liquid crystal self-assemblies. Carbohydr Res 2011; 346:2948-56. [DOI: 10.1016/j.carres.2011.10.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 10/18/2011] [Accepted: 10/20/2011] [Indexed: 11/25/2022]
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42
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Hall A, Róg T, Vattulainen I. Effect of Galactosylceramide on the Dynamics of Cholesterol-Rich Lipid Membranes. J Phys Chem B 2011; 115:14424-34. [DOI: 10.1021/jp203234n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Anette Hall
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
- Department of Applied Physics, Aalto University School of Science, Espoo, Finland
- MEMPHYS—Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
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43
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Parthasarathi R, Tian J, Redondo A, Gnanakaran S. Quantum Chemical Study of Carbohydrate–Phospholipid Interactions. J Phys Chem A 2011; 115:12826-40. [DOI: 10.1021/jp204015j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- R. Parthasarathi
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jianhui Tian
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Antonio Redondo
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - S. Gnanakaran
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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44
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Stepniewski M, Pasenkiewicz-Gierula M, Róg T, Danne R, Orlowski A, Karttunen M, Urtti A, Yliperttula M, Vuorimaa E, Bunker A. Study of PEGylated lipid layers as a model for PEGylated liposome surfaces: molecular dynamics simulation and Langmuir monolayer studies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:7788-7798. [PMID: 21604684 DOI: 10.1021/la200003n] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We have combined Langmuir monolayer film experiments and all-atom molecular dynamics (MD) simulation of a bilayer to study the surface structure of a PEGylated liposome and its interaction with the ionic environment present under physiological conditions. Lipids that form both gel and liquid-crystalline membranes have been used in our study. By varying the salt concentration in the Langmuir film experiment and including salt at the physiological level in the simulation, we have studied the effect of salt ions present in the blood plasma on the structure of the poly(ethylene glycol) (PEG) layer. We have also studied the interaction between the PEG layer and the lipid bilayer in both the liquid-crystalline and gel states. The MD simulation shows two clear results: (a) The Na(+) ions form close interactions with the PEG oxygens, with the PEG chains forming loops around them and (b) PEG penetrates the lipid core of the membrane for the case of a liquid-crystalline membrane but is excluded from the tighter structure of the gel membrane. The Langmuir monolayer results indicate that the salt concentration affects the PEGylated lipid system, and these results can be interpreted in a fashion that is in agreement with the results of our MD simulation. We conclude that the currently accepted picture of the PEG surface layer acting as a generic neutral hydrophilic polymer entirely outside the membrane, with its effect explained through steric interactions, is not sufficient. The phenomena we have observed may affect both the interaction between the liposome and bloodstream proteins and the liquid-crystalline-gel transition and is thus relevant to nanotechnological drug delivery device design.
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Affiliation(s)
- Michał Stepniewski
- Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
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45
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Structure and Dynamics of Glycosphingolipids in Lipid Bilayers: Insights from Molecular Dynamics Simulations. ACTA ACUST UNITED AC 2011. [DOI: 10.1155/2011/950256] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Glycolipids are important constituents of biological membranes, and understanding their structure and dynamics in lipid bilayers provides insights into their physiological and pathological roles. Experimental techniques have provided details into their behavior at model and biological membranes; however, computer simulations are needed to gain atomic level insights. This paper summarizes the insights obtained from MD simulations into the conformational and orientational dynamics of glycosphingolipids and their exposure, hydration, and hydrogen-bonding interactions in membrane environment. The organization of glycosphingolipids in raft-like membranes and their modulation of lipid membrane structure are also reviewed.
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46
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Horta BA, Perić-Hassler L, Hünenberger PH. Interaction of the disaccharides trehalose and gentiobiose with lipid bilayers: A comparative molecular dynamics study. J Mol Graph Model 2010; 29:331-46. [DOI: 10.1016/j.jmgm.2010.09.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/24/2010] [Accepted: 09/30/2010] [Indexed: 11/29/2022]
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47
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Stȩpniewski M, Bunker A, Pasenkiewicz-Gierula M, Karttunen M, Róg T. Effects of the Lipid Bilayer Phase State on the Water Membrane Interface. J Phys Chem B 2010; 114:11784-92. [DOI: 10.1021/jp104739a] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michał Stȩpniewski
- Department of Computational Biophysics and Bioinformatics, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Gronostajowa 7, Poland, Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Departments of Chemistry and Applied Physics, Aalto University, P.O. Box-16100, FI-00076 AALTO, Finland, Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street North, London, Ontario,
| | - Alex Bunker
- Department of Computational Biophysics and Bioinformatics, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Gronostajowa 7, Poland, Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Departments of Chemistry and Applied Physics, Aalto University, P.O. Box-16100, FI-00076 AALTO, Finland, Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street North, London, Ontario,
| | - Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Gronostajowa 7, Poland, Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Departments of Chemistry and Applied Physics, Aalto University, P.O. Box-16100, FI-00076 AALTO, Finland, Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street North, London, Ontario,
| | - Mikko Karttunen
- Department of Computational Biophysics and Bioinformatics, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Gronostajowa 7, Poland, Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Departments of Chemistry and Applied Physics, Aalto University, P.O. Box-16100, FI-00076 AALTO, Finland, Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street North, London, Ontario,
| | - Tomasz Róg
- Department of Computational Biophysics and Bioinformatics, Faculty of Biotechnology, Biochemistry and Biophysics, Jagiellonian University, Gronostajowa 7, Poland, Centre for Drug Research, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, FI-00014, University of Helsinki, Finland, Departments of Chemistry and Applied Physics, Aalto University, P.O. Box-16100, FI-00076 AALTO, Finland, Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street North, London, Ontario,
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48
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Hall A, Róg T, Karttunen M, Vattulainen I. Role of Glycolipids in Lipid Rafts: A View through Atomistic Molecular Dynamics Simulations with Galactosylceramide. J Phys Chem B 2010; 114:7797-807. [DOI: 10.1021/jp912175d] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Anette Hall
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, Middlesex College, 1151 Richmond St. N., London (ON), Canada N6A 5B7
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland, Department of Applied Physics, Aalto University School of Science and Engineering, P.O. Box 11100, FI-00076 Aalto, Finland, and MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
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49
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Pöyry S, Róg T, Karttunen M, Vattulainen I. Mitochondrial membranes with mono- and divalent salt: changes induced by salt ions on structure and dynamics. J Phys Chem B 2010; 113:15513-21. [PMID: 19886603 DOI: 10.1021/jp905915m] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We employ atomistic simulations to consider how mono- (NaCl) and divalent (CaCl(2)) salt affects properties of inner and outer membranes of mitochondria. We find that the influence of salt on structural properties is rather minute, only weakly affecting lipid packing, conformational ordering, and membrane electrostatic potential. The changes induced by salt are more prominent in dynamical properties related to ion binding and formation of ion-lipid complexes and lipid aggregates, as rotational diffusion of lipids is slowed down by ions, especially in the case of CaCl(2). In the same spirit, lateral diffusion of lipids is slowed down rather considerably for increasing concentration of CaCl(2). Both findings for dynamic properties can be traced to the binding of ions with lipid head groups and the related changes in interaction patterns in the headgroup region, where the binding of Na(+) and Ca(2+) ions is clearly different. The role of cardiolipins in these phenomena turns out to be important.
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Affiliation(s)
- Sanja Pöyry
- Department of Physics, Tampere University of Technology, Finland
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50
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Farrow B, Kamat PV. CdSe Quantum Dot Sensitized Solar Cells. Shuttling Electrons Through Stacked Carbon Nanocups. J Am Chem Soc 2009; 131:11124-31. [DOI: 10.1021/ja903337c] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Blake Farrow
- Radiation Laboratory, Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Prashant V. Kamat
- Radiation Laboratory, Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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