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Jaikishan S, Lavainne M, Ravald HK, Scobbie K, Dusa F, Maheswari R, Turpeinen J, Eikemans I, Chen R, Rantala J, Aseyev V, Maier NN, Wiedmer SK. Fragment-based approach to study fungicide-biomimetic membrane interactions. SOFT MATTER 2024. [PMID: 39012330 DOI: 10.1039/d4sm00648h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
In this study, the molecular interactions of the allylamine-type fungicide butenafine and a set of substructures ("fragments") with liposomes mimicking biological membranes were studied to gain a better understanding of the structural factors governing membrane affinity and perturbation. Specifically, drug/fragment-membrane interactions were investigated using an interdisciplinary approach involving micro differential scanning calorimetry, open-tubular capillary electrochromatography, nanoplasmonic sensing, and quartz crystal microbalance. By incubating the drug and the fragment compounds with liposomes with varying lipid composition or by externally adding the compounds to preformed liposomes, a detailed mechanistic picture on the underlying drug/fragment-membrane interactions was obtained. The nature and the degree of ionisation of polar head groups of the lipids had a major influence on the nature of drug-membrane interactions, and so had the presence and relative concentration of cholesterol within the membranes. The in-depth understanding of drug/fragment-membranes interactions established by the presented interdisciplinary fragment-based approach may be useful in guiding the design and early-stage evaluation of prospective antifungal drug candidates, and the discovery of agents with improved membrane penetrating characteristics in general.
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Affiliation(s)
- Shishir Jaikishan
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Marine Lavainne
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Henri K Ravald
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Kieran Scobbie
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Filip Dusa
- Institute of Analytical Chemistry, Czech Academy of Sciences, Veveří 97, Brno 60200, Czech Republic
| | - Rekha Maheswari
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Jenni Turpeinen
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Ian Eikemans
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Rui Chen
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Julia Rantala
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Vladimir Aseyev
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Norbert N Maier
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
| | - Susanne K Wiedmer
- Department of Chemistry, A.I. Virtasen aukio 1, POB 55, 00014 University of Helsinki, Finland.
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Moqadam M, Gartan P, Talandashti R, Chiapparino A, Titeca K, Gavin AC, Reuter N. A Membrane-Assisted Mechanism for the Release of Ceramide from the CERT START Domain. J Phys Chem B 2024; 128:6338-6351. [PMID: 38903016 PMCID: PMC11228987 DOI: 10.1021/acs.jpcb.4c02398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/26/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Ceramide transfer protein CERT is the mediator of nonvesicular transfer of ceramide from the ER to Golgi. In CERT, START is the domain responsible for the binding and transport of ceramide. A wealth of structural data has revealed a helix-grip fold surrounding a large hydrophobic cavity holding the ceramide. Yet, little is known about the mechanisms by which START releases the ceramide through the polar region and into the packed environment of cellular membranes. As such events do not lend themselves easily to experimental investigations, we used multiple unbiased microsecond-long molecular simulations. We propose a membrane-assisted mechanism in which the membrane acts as an allosteric effector initiating the release of ceramide and where the passage of the ceramide acyl chains is facilitated by the intercalation of a single phosphatidylcholine lipid in the cavity, practically greasing the ceramide way out. We verify using free energy calculation and experimental lipidomics data that CERT forms stable complexes with phosphatidylcholine lipids, in addition to ceramide, thus providing validation for the proposed mechanism.
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Affiliation(s)
- Mahmoud Moqadam
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Parveen Gartan
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Reza Talandashti
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Antonella Chiapparino
- European
Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
| | - Kevin Titeca
- European
Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
- Department
of Cell Physiology and Metabolism, University
of Geneva, CMU Rue Michel-Servet 1, Genève 4 1211, Switzerland
| | - Anne-Claude Gavin
- Department
of Cell Physiology and Metabolism, University
of Geneva, CMU Rue Michel-Servet 1, Genève 4 1211, Switzerland
| | - Nathalie Reuter
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
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3
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Sapia J, Vanni S. Molecular dynamics simulations of intracellular lipid droplets: a new tool in the toolbox. FEBS Lett 2024; 598:1143-1153. [PMID: 38627196 DOI: 10.1002/1873-3468.14879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/14/2024] [Accepted: 03/25/2024] [Indexed: 05/25/2024]
Abstract
Lipid droplets (LDs) are ubiquitous intracellular organelles with a central role in multiple lipid metabolic pathways. However, identifying correlations between their structural properties and their biological activity has proved challenging, owing to their unique physicochemical properties as compared with other cellular membranes. In recent years, molecular dynamics (MD) simulations, a computational methodology allowing the accurate description of molecular assemblies down to their individual components, have been demonstrated to be a useful and powerful approach for studying LD structural and dynamical properties. In this short review, we attempt to highlight, as comprehensively as possible, how MD simulations have contributed to our current understanding of multiple molecular mechanisms involved in LD biology.
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Affiliation(s)
- Jennifer Sapia
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
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Barbernitz MX, Devine LR, Cole RN, Raben DM. The role of N-terminal phosphorylation of DGK-θ. J Lipid Res 2024; 65:100506. [PMID: 38272356 PMCID: PMC10914586 DOI: 10.1016/j.jlr.2024.100506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Diacylglycerol kinases (DGKs) are lipid kinases that mediate the phosphorylation of diacylglycerol (DAG) leading to the production of phosphatidic acid (PtdOH). To examine the role of phosphorylation on DGK-θ, we first identified the phosphorylated sites on endogenous DGK-θ from mouse brain and found four sites: S15, S17, which we refer to phosphomotif-1 sites, and S22 and S26 which we refer to as phosphomotif-2 sites. This study focused on the role of these phosphorylated sites on enzyme activity, membrane binding, thermal stability, and cellular half-life of DGK-θ. After generating a construct devoid of all non-catalytic phosphorylation sites (4A), we also generated other constructs to mimic phosphorylation of these residues by mutating them to glutamate (E). Our data demonstrate that an increase in membrane affinity requires the phosphorylation of all four endogenous sites as the phosphomimetic 4E but not other phosphomimietics. Furthermore, 4E also shows an increase in basal activity as well as an increase in the Syt1-induced activity compared to 4A. It is noteworthy that these phosphorylations had no effect on the thermal stability or cellular half-life of this enzyme. Interestingly, when only one phosphorylation domain (phosphomotif-1 or phosphomotif-2) contained phosphomimetics (S15E/S17E or S22E/S26E), the basal activity was also increased but membrane binding affinity was not increased. Furthermore, when only one residue in each domain mimicked an endogenous phosphorylated serine (S15E/S22E or S17E/S26E), the Syt1-induced activity as well as membrane binding affinity decreased relative to 4A. These results indicate that these endogenous phosphorylation sites contribute differentially to membrane binding and enzymatic activity.
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Affiliation(s)
- Millie X Barbernitz
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lauren R Devine
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert N Cole
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel M Raben
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Physiology and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Papadopoulou P, van der Pol R, van Hilten N, van Os WL, Pattipeiluhu R, Arias-Alpizar G, Knol RA, Noteborn W, Moradi MA, Ferraz MJ, Aerts JMFG, Sommerdijk N, Campbell F, Risselada HJ, Sevink GJA, Kros A. Phase-Separated Lipid-Based Nanoparticles: Selective Behavior at the Nano-Bio Interface. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2310872. [PMID: 37988682 DOI: 10.1002/adma.202310872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Indexed: 11/23/2023]
Abstract
The membrane-protein interface on lipid-based nanoparticles influences their in vivo behavior. Better understanding may evolve current drug delivery methods toward effective targeted nanomedicine. Previously, the cell-selective accumulation of a liposome formulation in vivo is demonstrated, through the recognition of lipid phase-separation by triglyceride lipases. This exemplified how liposome morphology and composition can determine nanoparticle-protein interactions. Here, the lipase-induced compositional and morphological changes of phase-separated liposomes-which bear a lipid droplet in their bilayer- are investigated, and the mechanism upon which lipases recognize and bind to the particles is unravelled. The selective lipolytic degradation of the phase-separated lipid droplet is observed, while nanoparticle integrity remains intact. Next, the Tryptophan-rich loop of the lipase is identified as the region with which the enzymes bind to the particles. This preferential binding is due to lipid packing defects induced on the liposome surface by phase separation. In parallel, the existing knowledge that phase separation leads to in vivo selectivity, is utilized to generate phase-separated mRNA-LNPs that target cell-subsets in zebrafish embryos, with subsequent mRNA delivery and protein expression. Together, these findings can expand the current knowledge on selective nanoparticle-protein communications and in vivo behavior, aspects that will assist to gain control of lipid-based nanoparticles.
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Affiliation(s)
- Panagiota Papadopoulou
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Rianne van der Pol
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Niek van Hilten
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Winant L van Os
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Roy Pattipeiluhu
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Gabriela Arias-Alpizar
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Renzo Aron Knol
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Willem Noteborn
- NeCEN, Leiden University, Einsteinweg 55, Leiden, 2333 AL, The Netherlands
| | - Mohammad-Amin Moradi
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P. O. Box 513, Eindhoven, 5600 MB, The Netherlands
| | - Maria Joao Ferraz
- Department of Medical Biochemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | | | - Nico Sommerdijk
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P. O. Box 513, Eindhoven, 5600 MB, The Netherlands
- Department of Medical BioSciences and Radboud Technology Center - Electron Microscopy, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Frederick Campbell
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Herre Jelger Risselada
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
- Department of Physics, Technical University Dortmund, 44221, Dortmund, Germany
| | - Geert Jan Agur Sevink
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
| | - Alexander Kros
- Department of Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry (LIC), Leiden University, P. O. Box 9502, Leiden, 2300 RA, The Netherlands
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6
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Fujimori ASS, Ribeiro APD, Pereira AG, Dias-Audibert FL, Tonon CR, dos Santos PP, Dantas D, Zanati SG, Catharino RR, Zornoff LAM, Azevedo PS, de Paiva SAR, Okoshi MP, Lima EO, Polegato BF. Effects of Pera Orange Juice and Moro Orange Juice in Healthy Rats: A Metabolomic Approach. Metabolites 2023; 13:902. [PMID: 37623846 PMCID: PMC10456557 DOI: 10.3390/metabo13080902] [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: 06/29/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Cardiovascular disease is a leading cause of death worldwide. Heart failure is a cardiovascular disease with high prevalence, morbidity, and mortality. Several natural compounds have been studied for attenuating pathological cardiac remodeling. Orange juice has been associated with cardiovascular disease prevention by attenuating oxidative stress. However, most studies have evaluated isolated phytochemicals rather than whole orange juice and usually under pathological conditions. In this study, we evaluated plasma metabolomics in healthy rats receiving Pera or Moro orange juice to identify possible metabolic pathways and their effects on the heart. METHODS Sixty male Wistar rats were allocated into 3 groups: control (C), Pera orange juice (PO), and Moro orange juice (MO). PO and MO groups received Pera orange juice or Moro orange juice, respectively, and C received water with maltodextrin (100 g/L). Echocardiogram and euthanasia were performed after 4 weeks. Plasma metabolomic analysis was performed by high-resolution mass spectrometry. Type I collagen was evaluated in picrosirius red-stained slides and matrix metalloproteinase (MMP)-2 activity by zymography. MMP-9, tissue inhibitor of metalloproteinase (TIMP)-2, TIMP-4, type I collagen, and TNF-α protein expression were evaluated by Western blotting. RESULTS We differentially identified three metabolites in PO (N-docosahexaenoyl-phenylalanine, diglyceride, and phosphatidylethanolamine) and six in MO (N-formylmaleamic acid, N2-acetyl-L-ornithine, casegravol isovalerate, abscisic alcohol 11-glucoside, cyclic phosphatidic acid, and torvoside C), compared to controls, which are recognized for their possible roles in cardiac remodeling, such as extracellular matrix regulation, inflammation, oxidative stress, and membrane integrity. Cardiac function, collagen level, MMP-2 activity, and MMP-9, TIMP-2, TIMP-4, type I collagen, and TNF-α protein expression did not differ between groups. CONCLUSION Ingestion of Pera and Moro orange juice induces changes in plasma metabolites related to the regulation of extracellular matrix, inflammation, oxidative stress, and membrane integrity in healthy rats. Moro orange juice induces a larger number of differentially expressed metabolites than Pera orange juice. Alterations in plasma metabolomics induced by both orange juice are not associated with modifications in cardiac extracellular matrix components. Our results allow us to postulate that orange juice may have beneficial effects on pathological cardiac remodeling.
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Affiliation(s)
- Anderson S. S. Fujimori
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Ana P. D. Ribeiro
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Amanda G. Pereira
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Flávia L. Dias-Audibert
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas 13083-970, Brazil; (F.L.D.-A.); (R.R.C.)
| | - Carolina R. Tonon
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Priscila P. dos Santos
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Danielle Dantas
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Silmeia G. Zanati
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Rodrigo R. Catharino
- Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas 13083-970, Brazil; (F.L.D.-A.); (R.R.C.)
| | - Leonardo A. M. Zornoff
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Paula S. Azevedo
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Sergio A. R. de Paiva
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Marina P. Okoshi
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Estela O. Lima
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
| | - Bertha F. Polegato
- Internal Medicine Department, Botucatu Medical School, São Paulo State University (UNESP), Botucatu 18618-687, Brazil; (A.S.S.F.); (A.P.D.R.); (A.G.P.); (C.R.T.); (P.P.d.S.); (D.D.); (S.G.Z.); (L.A.M.Z.); (P.S.A.); (S.A.R.d.P.); (M.P.O.); (E.O.L.)
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7
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Zhu X, Huang C, Li N, Ma X, Li Z, Fan J. Distinct roles of graphene and graphene oxide nanosheets in regulating phospholipid flip-flop. J Colloid Interface Sci 2023; 637:112-122. [PMID: 36689797 DOI: 10.1016/j.jcis.2023.01.080] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 12/30/2022] [Accepted: 01/15/2023] [Indexed: 01/19/2023]
Abstract
Two-dimensional (2D) nanomaterials, such as graphene nanosheets (GNs) and graphene oxide nanosheets (GOs), could adhere onto or insert into a biological membrane, leading to a change in membrane properties and biological activities. Consequently, GN and GO become potential candidates for mediating interleaflet phospholipid transfer. In this work, molecular dynamics (MD) simulations were employed to investigate the effects of GN and GO on lipid flip-flop behavior and the underlying molecular mechanisms. Of great interest is that GN and GO work in opposite directions. The inserted GN can induce the formation of an ordered nanodomain, which dramatically elevates the free energy barrier of flipping phospholipids from one leaflet to the other, thus leading to a decreased lipid flip-flop rate. In contrast, the embedded GO can catalyze the transport of phospholipids between membrane leaflets by facilitating the formation of water pores. These results suggest that GN may work as an inhibitor of the interleaflet lipid translocation, while GO may play the role of scramblases. These findings are expected to expand promising biomedical applications of 2D nanomaterials.
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Affiliation(s)
- Xiaohong Zhu
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Changxiong Huang
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Na Li
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Xinyao Ma
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China; Center for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Hong Kong, China.
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8
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Insertion Depth Modulates Protein Kinase C-δ-C1b Domain Interactions with Membrane Cholesterol as Revealed by MD Simulations. Int J Mol Sci 2023; 24:ijms24054598. [PMID: 36902029 PMCID: PMC10002858 DOI: 10.3390/ijms24054598] [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: 01/12/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Protein kinase C delta (PKC-δ) is an important signaling molecule in human cells that has both proapoptotic as well as antiapoptotic functions. These conflicting activities can be modulated by two classes of ligands, phorbol esters and bryostatins. Phorbol esters are known tumor promoters, while bryostatins have anti-cancer properties. This is despite both ligands binding to the C1b domain of PKC-δ (δC1b) with a similar affinity. The molecular mechanism behind this discrepancy in cellular effects remains unknown. Here, we have used molecular dynamics simulations to investigate the structure and intermolecular interactions of these ligands bound to δC1b with heterogeneous membranes. We observed clear interactions between the δC1b-phorbol complex and membrane cholesterol, primarily through the backbone amide of L250 and through the K256 side-chain amine. In contrast, the δC1b-bryostatin complex did not exhibit interactions with cholesterol. Topological maps of the membrane insertion depth of the δC1b-ligand complexes suggest that insertion depth can modulate δC1b interactions with cholesterol. The lack of cholesterol interactions suggests that bryostatin-bound δC1b may not readily translocate to cholesterol-rich domains within the plasma membrane, which could significantly alter the substrate specificity of PKC-δ compared to δC1b-phorbol complexes.
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9
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Liu YD, Liu HJ, Gong GW. Monitoring diacylglycerols in biofluids by non-isotopically paired charge derivatization combined with LC-MS/MS. Front Chem 2022; 10:1062118. [DOI: 10.3389/fchem.2022.1062118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022] Open
Abstract
Diacylglycerols (DAGs) are important lipid mediators in cellular signaling transduction and metabolism. Imbalanced production or consumption of DAGs has a negative impact on the physiological functions of the body. However, comprehensive monitoring of structurally diverse DAGs remains a daunting task due to the rapid metabolism and ion suppression characteristics in biofluids. These bottlenecks call for developing a method that enables sensitive quantification of DAGs in biological sample. In this work, a straightforward charge derivatization strategy was developed to insert a series of structure analogs charge label, i.e., N, N-dimethylglycine (DMG) and N, N-dimethylalanine (DMA), on the free hydroxyl group of the DAGs. Owing to the existence of tertiary amino groups in charge label, the mass spectrometry ionization response of the derivatized DAGs was significantly increased in comparison with traditional metal ion adducts. After charge derivatization, the specific neutral loss diagnostic ions (DMG, 103 Da and DMA, 117 Da) were captured by mass spectrometry. Then, the DMG/DMA-oriented paired multiple reaction monitoring methods based on the characteristic diagnostic ions of the derivatized DAGs have been developed as sensitive methods for the detection (detection limit = 16 aM) and quantification (quantification limit = 62.5 aM) of DAGs in serum. Moreover, the tagged 1,2-DAGs and 1,3-DAGs sn-isomers have been well separated on the reversed-phase column in combination with ultra-performance liquid chromatography. Finally, metabolic characterizations of the tagged DAGs were further explored in L-Arginine-induced acute pancreatitis mice and resveratrol treated model mice. The results indicated that 1,2-DAGs were increased in the serum of model mice relative to normal controls and resveratrol significantly altered this metabolic abnormality. The currently established DMG/DMA-oriented paired charge derivatization strategy is promising for depicting DAGs changes more accurately in metabolic studies of lipid-related diseases and accurately evaluating drug treatment strategies.
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10
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Heinonen S, Lautala S, Koivuniemi A, Bunker A. Insights into the behavior of unsaturated diacylglycerols in mixed lipid bilayers in relation to protein kinase C activation-A molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183961. [PMID: 35568204 DOI: 10.1016/j.bbamem.2022.183961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The lipid second messenger diacylglycerol (DAG) is known for its involvement in many types of cellular signaling, especially as an endogenous agonist for protein kinase C (PKC). Evidence has emerged that the degree of saturation of the DAG molecules can affect PKC activation. DAG molecules with different acyl chain saturation have not only been observed to induce varying extents of PKC activation, but also to express selectivity towards different PKC isozymes. Both qualities are important for precise therapeutic activation of PKC; understanding DAG behavior at the molecular level in different environments has much potential in the development of drugs to target PKC. We used molecular dynamics simulations to study the behavior of two different unsaturated DAG species in lipid environments with varying degrees of unsaturation. We focus on phosphatidylethanolamine (PE) instead of phosphatidylcholine (PC) to more accurately model the relevant biomembranes. The effect of cholesterol (CHOL) on these systems was also explored. We found that both high level of unsaturation in the acyl chains of the DAG species and presence of CHOL in the surrounding membrane increase DAG molecule availability at the lipid-water interface. This can partially explain the previously observed differences in PKC activation strength and specificity, the complete mechanism is, however, likely to be more complex. Our simulations coupled with the current understanding of lipids highlight the need for more simulations of biologically accurate lipid environments in order to determine the correct correlations between molecular mechanisms and biological behavior when studying PKC activation.
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Affiliation(s)
- Suvi Heinonen
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Saara Lautala
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Artturi Koivuniemi
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
| | - Alex Bunker
- Drug Research Program, Division of Pharmaceutical Biosciences, University of Helsinki, FI-00014, Helsinki, Finland
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11
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Molecular-dynamics-simulation-guided membrane engineering allows the increase of membrane fatty acid chain length in Saccharomyces cerevisiae. Sci Rep 2021; 11:17333. [PMID: 34462478 PMCID: PMC8405694 DOI: 10.1038/s41598-021-96757-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 08/05/2021] [Indexed: 11/08/2022] Open
Abstract
The use of lignocellulosic-based fermentation media will be a necessary part of the transition to a circular bio-economy. These media contain many inhibitors to microbial growth, including acetic acid. Under industrially relevant conditions, acetic acid enters the cell predominantly through passive diffusion across the plasma membrane. The lipid composition of the membrane determines the rate of uptake of acetic acid, and thicker, more rigid membranes impede passive diffusion. We hypothesized that the elongation of glycerophospholipid fatty acids would lead to thicker and more rigid membranes, reducing the influx of acetic acid. Molecular dynamics simulations were used to predict the changes in membrane properties. Heterologous expression of Arabidopsis thaliana genes fatty acid elongase 1 (FAE1) and glycerol-3-phosphate acyltransferase 5 (GPAT5) increased the average fatty acid chain length. However, this did not lead to a reduction in the net uptake rate of acetic acid. Despite successful strain engineering, the net uptake rate of acetic acid did not decrease. We suggest that changes in the relative abundance of certain membrane lipid headgroups could mitigate the effect of longer fatty acid chains, resulting in a higher net uptake rate of acetic acid.
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12
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Lipidomic and in-gel analysis of maleic acid co-polymer nanodiscs reveals differences in composition of solubilized membranes. Commun Biol 2021; 4:218. [PMID: 33594255 PMCID: PMC7886889 DOI: 10.1038/s42003-021-01711-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
Membrane proteins are key in a large number of physiological and pathological processes. Their study often involves a prior detergent solubilization step, which strips away the membrane and can jeopardize membrane protein integrity. A recent alternative to detergents encompasses maleic acid based copolymers (xMAs), which disrupt the lipid bilayer and form lipid protein nanodiscs (xMALPs) soluble in aqueous buffer. Although xMALPs are often referred to as native nanodiscs, little is known about the resemblance of their lipid and protein content to the native bilayer. Here we have analyzed prokaryotic and eukaryotic xMALPs using lipidomics and in-gel analysis. Our results show that the xMALPs content varies with the chemical properties of the used xMA.
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13
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Zewe JP, Miller AM, Sangappa S, Wills RC, Goulden BD, Hammond GRV. Probing the subcellular distribution of phosphatidylinositol reveals a surprising lack at the plasma membrane. J Cell Biol 2020; 219:133808. [PMID: 32211893 PMCID: PMC7054989 DOI: 10.1083/jcb.201906127] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/14/2019] [Accepted: 11/19/2019] [Indexed: 12/16/2022] Open
Abstract
The polyphosphoinositides (PPIn) are central regulatory lipids that direct membrane function in eukaryotic cells. Understanding how their synthesis is regulated is crucial to revealing these lipids’ role in health and disease. PPIn are derived from the major structural lipid, phosphatidylinositol (PI). However, although the distribution of most PPIn has been characterized, the subcellular localization of PI available for PPIn synthesis is not known. Here, we used several orthogonal approaches to map the subcellular distribution of PI, including localizing exogenous fluorescent PI, as well as detecting lipid conversion products of endogenous PI after acute chemogenetic activation of PI-specific phospholipase and 4-kinase. We report that PI is broadly distributed throughout intracellular membrane compartments. However, there is a surprising lack of PI in the plasma membrane compared with the PPIn. These experiments implicate regulation of PI supply to the plasma membrane, as opposed to regulation of PPIn-kinases, as crucial to the control of PPIn synthesis and function at the PM.
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Affiliation(s)
- James P Zewe
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - April M Miller
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Sahana Sangappa
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Rachel C Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Brady D Goulden
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Gerald R V Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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14
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Unraveling the complex enzymatic machinery making a key galactolipid in chloroplast membrane: a multiscale computer simulation. Sci Rep 2020; 10:13514. [PMID: 32782311 PMCID: PMC7419546 DOI: 10.1038/s41598-020-70425-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022] Open
Abstract
Chloroplast membranes have a high content of the uncharged galactolipids monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG). These galactolipids are essential for the biogenesis of plastids and functioning of the photosynthetic machinery. A monotopic glycosyltransferase, monogalactosyldiacylglycerol synthase synthesizes the bulk of MGDG. It is embedded in the outer leaflet of the inner envelope membrane of chloroplasts. The protein transfers a galactose residue from UDP-galactose to diacylglycerol (DAG); it needs anionic lipids such as phosphatidylglycerol (PG) to be active. The intricacy of the organization and the process of active complex assembly and synthesis have been investigated at the Coarse-Grained and All-Atom of computer simulation levels to cover large spatial and temporal scales. The following self-assembly process and catalytic events can be drawn; (1) in the membrane, in the absence of protein, there is a spontaneous formation of PG clusters to which DAG molecules associate, (2) a reorganization of the clusters occurs in the vicinity of the protein once inserted in the membrane, (3) an accompanying motion of the catalytic domain of the protein brings DAG in the proper position for the formation of the active complex MGD1/UDP-Gal/DAG/PG for which an atomistic model of interaction is proposed.
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15
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Adams KJ, Pratt B, Bose N, Dubois LG, St John-Williams L, Perrott KM, Ky K, Kapahi P, Sharma V, MacCoss MJ, Moseley MA, Colton CA, MacLean BX, Schilling B, Thompson JW. Skyline for Small Molecules: A Unifying Software Package for Quantitative Metabolomics. J Proteome Res 2020; 19:1447-1458. [PMID: 31984744 DOI: 10.1021/acs.jproteome.9b00640] [Citation(s) in RCA: 216] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Vendor-independent software tools for quantification of small molecules and metabolites are lacking, especially for targeted analysis workflows. Skyline is a freely available, open-source software tool for targeted quantitative mass spectrometry method development and data processing with a 10 year history supporting six major instrument vendors. Designed initially for proteomics analysis, we describe the expansion of Skyline to data for small molecule analysis, including selected reaction monitoring, high-resolution mass spectrometry, and calibrated quantification. This fundamental expansion of Skyline from a peptide-sequence-centric tool to a molecule-centric tool makes it agnostic to the source of the molecule while retaining Skyline features critical for workflows in both peptide and more general biomolecular research. The data visualization and interrogation features already available in Skyline, such as peak picking, chromatographic alignment, and transition selection, have been adapted to support small molecule data, including metabolomics. Herein, we explain the conceptual workflow for small molecule analysis using Skyline, demonstrate Skyline performance benchmarked against a comparable instrument vendor software tool, and present additional real-world applications. Further, we include step-by-step instructions on using Skyline for small molecule quantitative method development and data analysis on data acquired with a variety of mass spectrometers from multiple instrument vendors.
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Affiliation(s)
- Kendra J Adams
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States.,Department of Neurology, Duke University, Durham, North Carolina 27710, United States
| | - Brian Pratt
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Neelanjan Bose
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Laura G Dubois
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States
| | - Lisa St John-Williams
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States
| | - Kevin M Perrott
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Karina Ky
- University of California San Francisco, San Francisco, California 94143, United States
| | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States
| | - Carol A Colton
- Department of Neurology, Duke University, Durham, North Carolina 27710, United States
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina 27701, United States.,Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710, United States
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16
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Fong WK, Sánchez-Ferrer A, Rappolt M, Boyd BJ, Mezzenga R. Structural Transformation in Vesicles upon Hydrolysis of Phosphatidylethanolamine and Phosphatidylcholine with Phospholipase C. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:14949-14958. [PMID: 31642682 DOI: 10.1021/acs.langmuir.9b02288] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This study provides insights into dynamic nanostructural changes in phospholipid systems during hydrolysis with phospholipase C, the fate of the hydrolysis products, and the kinetics of lipolysis. The effect of lipid restructuring of the vesicle was investigated using small-angle X-ray scattering and cryogenic scanning electron microscopy. The rate and extent of phospholipid hydrolysis were quantified using nuclear magnetic resonance. Hydrolysis of two phospholipids, phosphatidylethanolamine (PE) and phosphatidylcholine (PC), results in the cleavage of the molecular headgroup, causing two strikingly different changes in lipid self-assembly. The diacylglycerol product of PC escapes the lipid bilayer, whereas the diacylglycerol product adopts a different configuration within the lipid bilayer of the PE vesicles. These results are then discussed concerning the change of the lipid configuration upon the lipid membrane and its potential implications in vivo, which is of significant importance for the detailed understanding of the fate of lipidic particles and the rational design of enzyme-responsive lipid-based drug delivery systems.
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Affiliation(s)
- Wye-Khay Fong
- Department of Health Sciences & Technology , ETH Zürich , 8092 Zürich , Switzerland
- Drug Delivery, Disposition and Dynamics, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences , Monash University , Parkville Campus, 381 Royal Parade , Parkville , 3052 Victoria , Australia
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , 1700 Fribourg , Switzerland
| | | | - Michael Rappolt
- School of Food Science and Nutrition , University of Leeds , LS2 9JT Leeds , Yorkshire , U.K
| | - Ben J Boyd
- Drug Delivery, Disposition and Dynamics, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences , Monash University , Parkville Campus, 381 Royal Parade , Parkville , 3052 Victoria , Australia
| | - Raffaele Mezzenga
- Department of Health Sciences & Technology , ETH Zürich , 8092 Zürich , Switzerland
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17
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Nomura K, Yamaguchi T, Mori S, Fujikawa K, Nishiyama KI, Shimanouchi T, Tanimoto Y, Morigaki K, Shimamoto K. Alteration of Membrane Physicochemical Properties by Two Factors for Membrane Protein Integration. Biophys J 2019; 117:99-110. [PMID: 31164197 PMCID: PMC6626835 DOI: 10.1016/j.bpj.2019.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 12/01/2022] Open
Abstract
After a nascent chain of a membrane protein emerges from the ribosomal tunnel, the protein is integrated into the cell membrane. This process is controlled by a series of proteinaceous molecular devices, such as signal recognition particles and Sec translocons. In addition to these proteins, we discovered two endogenous components regulating membrane protein integration in the inner membrane of Escherichia coli. The integration is blocked by diacylglycerol (DAG), whereas the blocking is relieved by a glycolipid named membrane protein integrase (MPIase). Here, we investigated the influence of these integration-blocking and integration-promoting factors on the physicochemical properties of membrane lipids via solid-state NMR and fluorescence measurements. These factors did not have destructive effects on membrane morphology because the membrane maintained its lamellar structure and did not fuse in the presence of DAG and/or MPIase at their effective concentrations. We next focused on membrane flexibility. DAG did not affect the mobility of the membrane surface, whereas the sugar chain in MPIase was highly mobile and enhanced the flexibility of membrane lipid headgroups. Comparison with a synthetic MPIase analog revealed the effects of the long sugar chain on membrane properties. The acyl chain order inside the membrane was increased by DAG, whereas the increase was cancelled by the addition of MPIase. MPIase also loosened the membrane lipid packing. Focusing on the transbilayer movement, MPIase reduced the rapid flip-flop motion of DAG. On the other hand, MPIase could not compensate for the diminished lateral diffusion by DAG. These results suggest that by manipulating the membrane lipids dynamics, DAG inhibits the protein from contacting the inner membrane, whereas the flexible long sugar chain of MPIase increases the opportunity for interaction between the membrane and the protein, leading to membrane integration of the newly formed protein.
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Affiliation(s)
- Kaoru Nomura
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan.
| | - Toshiyuki Yamaguchi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Shoko Mori
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Kohki Fujikawa
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Ken-Ichi Nishiyama
- Department of Biological Chemistry and Food Sciences, Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
| | | | - Yasushi Tanimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | | | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan.
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18
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Biophysical characterization of mycobacterial model membranes and their interaction with rifabutin: Towards lipid-guided drug screening in tuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1213-1227. [PMID: 31002767 DOI: 10.1016/j.bbamem.2019.04.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/12/2019] [Accepted: 04/08/2019] [Indexed: 01/31/2023]
Abstract
Lipid structure critically dictates the molecular interactions of drugs with membranes influencing passive diffusion, drug partitioning and accumulation, thereby underpinning a lipid-composition specific interplay. Spurring selective passive drug diffusion and uptake through membranes is an obvious solution to combat growing antibiotic resistance with minimized toxicities. However, the spectrum of complex mycobacterial lipids and lack thereof of suitable membrane platforms limits the understanding of mechanisms underlying drug-membrane interactions in tuberculosis. Herein, we developed membrane scaffolds specific to mycobacterial outer membrane and demonstrate them as improvised research platforms for investigating anti-tubercular drug interactions. Combined spectroscopy and microscopy results reveal an enhanced partitioning of model drug Rifabutin in trehalose dimycolate-containing mycobacterial membrane systems. These effects are apportioned to specific changes in membrane structure, order and fluidity leading to enhanced drug interaction. These findings on the membrane biophysical consequences of drug interactions will offer valuable insights for guiding the design of more effective antibiotic drugs coupled with tuned toxicity profiles.
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19
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Sarkar S, Tran N, Rashid MH, Le TC, Yarovsky I, Conn CE, Drummond CJ. Toward Cell Membrane Biomimetic Lipidic Cubic Phases: A High-Throughput Exploration of Lipid Compositional Space. ACS APPLIED BIO MATERIALS 2018; 2:182-195. [DOI: 10.1021/acsabm.8b00539] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Sampa Sarkar
- School of Science, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Nhiem Tran
- School of Science, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Md Harunur Rashid
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Tu C. Le
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Charlotte E. Conn
- School of Science, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Calum J. Drummond
- School of Science, College of Science, Engineering and Health, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
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20
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Holme M, Rashid MH, Thomas MR, Barriga HMG, Herpoldt K, Heenan RK, Dreiss CA, Bañuelos JL, Xie HN, Yarovsky I, Stevens MM. Fate of Liposomes in the Presence of Phospholipase C and D: From Atomic to Supramolecular Lipid Arrangement. ACS CENTRAL SCIENCE 2018; 4:1023-1030. [PMID: 30159399 PMCID: PMC6107861 DOI: 10.1021/acscentsci.8b00286] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Indexed: 05/04/2023]
Abstract
Understanding the origins of lipid membrane bilayer rearrangement in response to external stimuli is an essential component of cell biology and the bottom-up design of liposomes for biomedical applications. The enzymes phospholipase C and D (PLC and PLD) both cleave the phosphorus-oxygen bonds of phosphate esters in phosphatidylcholine (PC) lipids. The atomic position of this hydrolysis reaction has huge implications for the stability of PC-containing self-assembled structures, such as the cell wall and lipid-based vesicle drug delivery vectors. While PLC converts PC to diacylglycerol (DAG), the interaction of PC with PLD produces phosphatidic acid (PA). Here we present a combination of small-angle scattering data and all-atom molecular dynamics simulations, providing insights into the effects of atomic-scale reorganization on the supramolecular assembly of PC membrane bilayers upon enzyme-mediated incorporation of DAG or PA. We observed that PC liposomes completely disintegrate in the presence of PLC, as conversion of PC to DAG progresses. At lower concentrations, DAG molecules within fluid PC bilayers form hydrogen bonds with backbone carbonyl oxygens in neighboring PC molecules and burrow into the hydrophobic region. This leads initially to membrane thinning followed by a swelling of the lamellar phase with increased DAG. At higher DAG concentrations, localized membrane tension causes a change in lipid phase from lamellar to the hexagonal and micellar cubic phases. Molecular dynamics simulations show that this destabilization is also caused in part by the decreased ability of DAG-containing PC membranes to coordinate sodium ions. Conversely, PLD-treated PC liposomes remain stable up to extremely high conversions to PA. Here, the negatively charged PA headgroup attracts significant amounts of sodium ions from the bulk solution to the membrane surface, leading to a swelling of the coordinated water layer. These findings are a vital step toward a fundamental understanding of the degradation behavior of PC lipid membranes in the presence of these clinically relevant enzymes, and toward the rational design of diagnostic and drug delivery technologies for phospholipase-dysregulation-based diseases.
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Affiliation(s)
- Margaret
N. Holme
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - M. Harunur Rashid
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
| | - Michael R. Thomas
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hanna M. G. Barriga
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Karla−Luise Herpoldt
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Richard K. Heenan
- STFC ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Cécile A. Dreiss
- School
of Cancer and Pharmaceutical Sciences, King’s
College London, London SE1 9NH, United Kingdom
| | - José Leobardo Bañuelos
- STFC ISIS
Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
- Department
of Physics, The University of Texas at El
Paso, El Paso, Texas 79968, United States
| | - Hai-nan Xie
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Irene Yarovsky
- School
of Engineering, RMIT University, Melbourne, Victoria 3001, Australia
- E-mail:
| | - Molly M. Stevens
- Department
of Materials, Imperial College London, London SW7 2AZ, United Kingdom
- Department of Bioengineering and Institute of Biomedical
Engineering, Imperial College London, London SW7 2AZ, United Kingdom
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- E-mail:
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21
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Wen PC, Mahinthichaichan P, Trebesch N, Jiang T, Zhao Z, Shinn E, Wang Y, Shekhar M, Kapoor K, Chan CK, Tajkhorshid E. Microscopic view of lipids and their diverse biological functions. Curr Opin Struct Biol 2018; 51:177-186. [PMID: 30048836 DOI: 10.1016/j.sbi.2018.07.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/27/2018] [Accepted: 07/05/2018] [Indexed: 12/21/2022]
Abstract
Biological membranes and their diverse lipid constituents play key roles in a broad spectrum of cellular and physiological processes. Characterization of membrane-associated phenomena at a microscopic level is therefore essential to our fundamental understanding of such processes. Due to the semi-fluid and dynamic nature of lipid bilayers, and their complex compositions, detailed characterization of biological membranes at an atomic scale has been refractory to experimental approaches. Computational modeling and simulation offer a highly complementary toolset with sufficient spatial and temporal resolutions to fill this gap. Here, we review recent molecular dynamics studies focusing on the diversity of lipid composition of biological membranes, or aiming at the characterization of lipid-protein interaction, with the overall goal of dissecting how lipids impact biological roles of the cellular membranes.
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Affiliation(s)
- Po-Chao Wen
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Paween Mahinthichaichan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Noah Trebesch
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Tao Jiang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Zhiyu Zhao
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Eric Shinn
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuhang Wang
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mrinal Shekhar
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Karan Kapoor
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chun Kit Chan
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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