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Gandini R, Reichenbach T, Spadiut O, Tan TC, Kalyani DC, Divne C. A Transmembrane Crenarchaeal Mannosyltransferase Is Involved in N-Glycan Biosynthesis and Displays an Unexpected Minimal Cellulose-Synthase-like Fold. J Mol Biol 2020; 432:4658-4672. [PMID: 32569746 DOI: 10.1016/j.jmb.2020.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/13/2020] [Accepted: 06/16/2020] [Indexed: 11/30/2022]
Abstract
Protein glycosylation constitutes a critical post-translational modification that supports a vast number of biological functions in living organisms across all domains of life. A seemingly boundless number of enzymes, glycosyltransferases, are involved in the biosynthesis of these protein-linked glycans. Few glycan-biosynthetic glycosyltransferases have been characterized in vitro, mainly due to the majority being integral membrane proteins and the paucity of relevant acceptor substrates. The crenarchaeote Pyrobaculum calidifontis belongs to the TACK superphylum of archaea (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) that has been proposed as an eukaryotic ancestor. In archaea, N-glycans are mainly found on cell envelope surface-layer proteins, archaeal flagellins and pili. Archaeal N-glycans are distinct from those of eukaryotes, but one noteworthy exception is the high-mannose N-glycan produced by P. calidifontis, which is similar in sugar composition to the eukaryotic counterpart. Here, we present the characterization and crystal structure of the first member of a crenarchaeal membrane glycosyltransferase, PcManGT. We show that the enzyme is a GDP-, dolichylphosphate-, and manganese-dependent mannosyltransferase. The membrane domain of PcManGT includes three transmembrane helices that topologically coincide with "half" of the six-transmembrane helix cellulose-binding tunnel in Rhodobacter spheroides cellulose synthase BcsA. Conceivably, this "half tunnel" would be suitable for binding the dolichylphosphate-linked acceptor substrate. The PcManGT gene (Pcal_0472) is located in a large gene cluster comprising 14 genes of which 6 genes code for glycosyltransferases, and we hypothesize that this cluster may constitute a crenarchaeal N-glycosylation (PNG) gene cluster.
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Affiliation(s)
- Rosaria Gandini
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Tom Reichenbach
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Oliver Spadiut
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Tien-Chye Tan
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Dayanand C Kalyani
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
| | - Christina Divne
- School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden.
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Nikolaev A, Makarchuk I, Thesseling A, Hoeser J, Friedrich T, Melin F, Hellwig P. Stabilization of the Highly Hydrophobic Membrane Protein, Cytochrome bd Oxidase, on Metallic Surfaces for Direct Electrochemical Studies. Molecules 2020; 25:molecules25143240. [PMID: 32708635 PMCID: PMC7397230 DOI: 10.3390/molecules25143240] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 11/23/2022] Open
Abstract
The cytochrome bd oxidase catalyzes the reduction of oxygen to water in bacteria and it is thus an interesting target for electrocatalytic studies and biosensor applications. The bd oxidase is completely embedded in the phospholipid membrane. In this study, the variation of the surface charge of thiol-modified gold nanoparticles, the length of the thiols and the other crucial parameters including optimal phospholipid content and type, have been performed, giving insight into the role of these factors for the optimal interaction and direct electron transfer of an integral membrane protein. Importantly, all three tested factors, the lipid type, the electrode surface charge and the thiol length mutually influenced the stability of films of the cytochrome bd oxidase. The best electrocatalytic responses were obtained on the neutral gold surface when the negatively charged phosphatidylglycerol (PG) was used and on the charged gold surface when the zwitterionic phosphatidylethanolamine (PE) was used. The advantages of the covalent binding of the membrane protein to the electrode surface over the non-covalent binding are also discussed.
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Affiliation(s)
- Anton Nikolaev
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, 67081 Strasbourg, France; (A.N.); (I.M.)
| | - Iryna Makarchuk
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, 67081 Strasbourg, France; (A.N.); (I.M.)
| | - Alexander Thesseling
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany; (A.T.); (J.H.); (T.F.)
| | - Jo Hoeser
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany; (A.T.); (J.H.); (T.F.)
| | - Thorsten Friedrich
- Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany; (A.T.); (J.H.); (T.F.)
| | - Frédéric Melin
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, 67081 Strasbourg, France; (A.N.); (I.M.)
- Correspondence: (F.M.); (P.H.)
| | - Petra Hellwig
- Laboratoire de Bioelectrochimie et Spectroscopie, UMR 7140, Chimie de la Matière Complexe, Université de Strasbourg, CNRS, 67081 Strasbourg, France; (A.N.); (I.M.)
- Correspondence: (F.M.); (P.H.)
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53
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Buslaev P, Mustafin K, Gushchin I. Principal component analysis highlights the influence of temperature, curvature and cholesterol on conformational dynamics of lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183253. [PMID: 32142820 DOI: 10.1016/j.bbamem.2020.183253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/14/2020] [Accepted: 02/27/2020] [Indexed: 01/06/2023]
Abstract
Membrane lipids are inherently highly dynamic molecules. Currently, it is difficult to probe the structures of individual lipids experimentally at the timescales corresponding to atomic motions, and consequently molecular dynamics simulations are used widely. In our previous work, we have introduced the principal component analysis (PCA) as a convenient framework for comprehensive quantitative description of lipid motions. Here, we present a newly developed open source script, PCAlipids, which automates the analysis and allows us to refine the approach and test its limitations. We use PCAlipids to determine the influence of temperature, cholesterol and curvature on individual lipids, and show that the most prominent lipid tail scissoring motion is strongly affected by these factors and allows tracking of phase transition. Addition of cholesterol affects the conformations and selectively changes the dynamics of lipid molecules, impacting the large-amplitude motions. Introduction of curvature biases the conformational ensembles towards more extended structures. We hope that the developed approach will be useful for understanding the molecular basis of different processes occurring in lipid membrane systems and will stimulate development of complementary experimental techniques probing the conformations of individual lipid molecules.
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Affiliation(s)
- P Buslaev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - K Mustafin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - I Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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54
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Cannabidiol protects keratinocyte cell membranes following exposure to UVB and hydrogen peroxide. Redox Biol 2020; 36:101613. [PMID: 32863232 PMCID: PMC7327251 DOI: 10.1016/j.redox.2020.101613] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/09/2020] [Accepted: 06/18/2020] [Indexed: 12/16/2022] Open
Abstract
Keratinocytes, the major cell type of the epidermis, are particularly sensitive to environmental factors including exposure to sunlight and chemical agents. Since oxidative stress may arise as a result of these factors, compounds are actively sought that can act as protective agents. Recently, cannabidiol (CBD), a phytocannabinoid found in Cannabis Sativa L., has gained increased interest due to its anti-inflammatory and antioxidant properties, and absence of psychoactive effects. This prompted us to analyze the protective effects of CBD on keratinocytes exposed to UVB irradiation and hydrogen peroxide. Here we show, using liquid chromatography mass spectrometry, that CBD was able to penetrate keratinocytes, and accumulated within the cellular membrane. CBD reduced redox balance shift, towards oxidative stress, caused by exposure UVB/hydrogen peroxide, estimated by superoxide anion radical generation and total antioxidant status and consequently lipid peroxidation level. CBD was found to protect keratinocytes by preventing changes in the composition of the cellular membrane, associated with UVB/hydrogen peroxide damages which included reduced polyunsaturated fatty acid levels, increased sialic acid and lipid peroxidation products (malondialdehyde and 8-isoprostanes) levels. This maintains cell membranes integrity and prevents the release of lactate dehydrogenase. In addition, CBD prevented UVB/hydrogen peroxide-induced reduction of keratinocyte size and zeta potential, and also decreased activity of ATP-binding cassette membrane transporters. Together, these findings suggest that CBD could be a potential protective agent for keratinocytes against the harmful effects of irradiation and chemical environmental factors that cause oxidative stress. UVB/H2O2 stimulates keratinocytes membrane penetration by CBD. CBD protects cells against UVB/H2O2 induced redox imbalance. CBD maintains membrane integrity by preventing its component modifications. CBD decreases activity of ATP-binding cassette membrane transporters. CBD could be a potential keratinocytes protector against the harmful factors.
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55
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Bertero E, Kutschka I, Maack C, Dudek J. Cardiolipin remodeling in Barth syndrome and other hereditary cardiomyopathies. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165803. [PMID: 32348916 DOI: 10.1016/j.bbadis.2020.165803] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 12/19/2019] [Accepted: 04/13/2020] [Indexed: 12/18/2022]
Abstract
Mitochondria play a prominent role in cardiac energy metabolism, and their function is critically dependent on the integrity of mitochondrial membranes. Disorders characterized by mitochondrial dysfunction are commonly associated with cardiac disease. The mitochondrial phospholipid cardiolipin directly interacts with a number of essential protein complexes in the mitochondrial membranes including the respiratory chain, mitochondrial metabolite carriers, and proteins critical for mitochondrial morphology. Barth syndrome is an X-linked disorder caused by an inherited defect in the biogenesis of the mitochondrial phospholipid cardiolipin. How cardiolipin deficiency impacts on mitochondrial function and how mitochondrial dysfunction causes cardiomyopathy has been intensively studied in cellular and animal models of Barth syndrome. These findings may also have implications for the molecular mechanisms underlying other inherited disorders associated with defects in cardiolipin, such as Sengers syndrome and dilated cardiomyopathy with ataxia (DCMA).
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Affiliation(s)
- Edoardo Bertero
- Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, 97078 Würzburg, Germany
| | - Ilona Kutschka
- Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, 97078 Würzburg, Germany
| | - Christoph Maack
- Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, 97078 Würzburg, Germany
| | - Jan Dudek
- Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, 97078 Würzburg, Germany.
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56
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Zhang H, Ren P, Huang Y, Zeng W, Zhong K, Gao H, Cen X, Bu Q. Untargeted lipidomic analysis of human hippocampus for temporal lobe epilepsy with hippocampal sclerosis. Epilepsy Res 2020; 161:106299. [DOI: 10.1016/j.eplepsyres.2020.106299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/22/2020] [Accepted: 02/18/2020] [Indexed: 12/15/2022]
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El-Hafidi M, Correa F, Zazueta C. Mitochondrial dysfunction in metabolic and cardiovascular diseases associated with cardiolipin remodeling. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165744. [PMID: 32105822 DOI: 10.1016/j.bbadis.2020.165744] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/21/2020] [Accepted: 02/20/2020] [Indexed: 02/07/2023]
Abstract
Cardiolipin (CL) is an acidic phospholipid almost exclusively found in the inner mitochondrial membrane, that not only stabilizes the structure and function of individual components of the mitochondrial electron transport chain, but regulates relevant mitochondrial processes, like mitochondrial dynamics and cristae structure maintenance among others. Alterations in CL due to peroxidation, correlates with loss of such mitochondrial activities and disease progression. In this review it is recapitulated the current state of knowledge of the role of cardiolipin remodeling associated with mitochondrial dysfunction in metabolic and cardiovascular diseases.
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Affiliation(s)
- Mohammed El-Hafidi
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología I. Ch. 14080, Ciudad de México, México
| | - Francisco Correa
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología I. Ch. 14080, Ciudad de México, México
| | - Cecilia Zazueta
- Departamento de Biomedicina Cardiovascular, Instituto Nacional de Cardiología I. Ch. 14080, Ciudad de México, México.
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58
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Yao H, Cai H, Li D. Thermostabilization of Membrane Proteins by Consensus Mutation: A Case Study for a Fungal Δ8-7 Sterol Isomerase. J Mol Biol 2020; 432:5162-5183. [PMID: 32105736 DOI: 10.1016/j.jmb.2020.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 11/15/2022]
Abstract
Membrane proteins are generally challenging to work with because of their notorious instability. Protein engineering has been used increasingly to thermostabilize labile membrane proteins such as G-protein-coupled receptors for structural and functional studies in recent years. Two major strategies exist. Scanning mutagenesis systematically eliminates destabilizing residues, whereas the consensus approach assembles mutants with the most frequent residues among selected homologs, bridging sequence conservation with stability. Here, we applied the consensus concept to stabilize a fungal homolog of the human sterol Δ8-7 isomerase, a 26.4 kDa protein with five transmembrane helices. The isomerase is also called emopamil-binding protein (EBP), as it binds this anti-ischemic drug with high affinity. The wild-type had an apparent melting temperature (Tm) of 35.9 °C as measured by the fluorescence-detection size-exclusion chromatography-based thermostability assay. A total of 87 consensus mutations sourced from 22 homologs gained expression level and thermostability, increasing the apparent Tm to 69.9 °C at the cost of partial function loss. Assessing the stability and activity of several systematic chimeric constructs identified a construct with an apparent Tm of 79.8 °C and two regions for function rescue. Further back-mutations of the chimeric construct in the two target regions yielded the final construct with similar apparent activity to the wild-type and an elevated Tm of 88.8 °C, totaling an increase of 52.9 °C. The consensus approach is effective and efficient because it involves fewer constructs compared with scanning mutagenesis. Our results should encourage more use of the consensus strategy for membrane protein thermostabilization.
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Affiliation(s)
- Hebang Yao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Hongmin Cai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China
| | - Dianfan Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.
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59
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Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass‐Spectrometry‐Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jani Reddy Bolla
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Robin A. Corey
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
- Department of BiologyUniversity of Copenhagen Copenhagen N 2200 Denmark
| | - Joseph Gault
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Alissa Hummer
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
| | - Jonathan T. S. Hopper
- OMass Therapeutics The Oxford Science Park, The Schrödinger Building Kidlington OX4 4GE UK
| | - David P. Lane
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm University 10691 Stockholm Sweden
| | - Timothy M. Allison
- Biomolecular Interaction Centre and School of Physical and Chemical SciencesUniversity of Canterbury Christchurch 8140 New Zealand
| | - Phillip J. Stansfeld
- Department of BiochemistryUniversity of Oxford South Parks Road Oxford OX1 3QU UK
- School of Life Sciences & Department of ChemistryUniversity of Warwick Coventry CV4 7AL UK
| | - Carol V. Robinson
- Department of ChemistryUniversity of Oxford South Parks Road Oxford OX1 3QZ UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet 17165 Solna Sweden
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60
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Bolla JR, Corey RA, Sahin C, Gault J, Hummer A, Hopper JTS, Lane DP, Drew D, Allison TM, Stansfeld PJ, Robinson CV, Landreh M. A Mass-Spectrometry-Based Approach to Distinguish Annular and Specific Lipid Binding to Membrane Proteins. Angew Chem Int Ed Engl 2020; 59:3523-3528. [PMID: 31886601 PMCID: PMC7065234 DOI: 10.1002/anie.201914411] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/29/2019] [Indexed: 01/21/2023]
Abstract
Membrane proteins engage in a variety of contacts with their surrounding lipids, but distinguishing between specifically bound lipids, and non-specific, annular interactions is a challenging problem. Applying native mass spectrometry to three membrane protein complexes with different lipid-binding properties, we explore the ability of detergents to compete with lipids bound in different environments. We show that lipids in annular positions on the presenilin homologue protease are subject to constant exchange with detergent. By contrast, detergent-resistant lipids bound at the dimer interface in the leucine transporter show decreased koff rates in molecular dynamics simulations. Turning to the lipid flippase MurJ, we find that addition of the natural substrate lipid-II results in the formation of a 1:1 protein-lipid complex, where the lipid cannot be displaced by detergent from the highly protected active site. In summary, we distinguish annular from non-annular lipids based on their exchange rates in solution.
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Affiliation(s)
- Jani Reddy Bolla
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Robin A. Corey
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet17165SolnaSweden
- Department of BiologyUniversity of CopenhagenCopenhagen N2200Denmark
| | - Joseph Gault
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Alissa Hummer
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Jonathan T. S. Hopper
- OMass TherapeuticsThe Oxford Science Park, The Schrödinger BuildingKidlingtonOX4 4GEUK
| | - David P. Lane
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet17165SolnaSweden
| | - David Drew
- Department of Biochemistry and BiophysicsStockholm University10691StockholmSweden
| | - Timothy M. Allison
- Biomolecular Interaction Centre and School of Physical and Chemical SciencesUniversity of CanterburyChristchurch8140New Zealand
| | - Phillip J. Stansfeld
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
- School of Life Sciences & Department of ChemistryUniversity of WarwickCoventryCV4 7ALUK
| | - Carol V. Robinson
- Department of ChemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QZUK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell BiologyKarolinska Institutet17165SolnaSweden
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61
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Bloch M, Santiveri M, Taylor NMI. Membrane Protein Cryo-EM: Cryo-Grid Optimization and Data Collection with Protein in Detergent. Methods Mol Biol 2020; 2127:227-244. [PMID: 32112326 DOI: 10.1007/978-1-0716-0373-4_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cryo-electron microscopy (cryo-EM) is a powerful tool for investigating the structure of macromolecules under near-native conditions. Especially in the context of membrane proteins, this technique has allowed researchers to obtain structural information at a previously unattainable level of detail. Specimen preparation remains the bottleneck of most cryo-EM research projects, with membrane proteins representing particularly challenging targets of investigation due to their universal requirement for detergents or other solubilizing agents. Here we describe preparation of negative staining and cryo-EM grids and downstream data collection of membrane proteins in detergent, by far the most common solubilization agent. This protocol outlines a quick and straightforward procedure for screening and determining the structure of a membrane protein of interest under biologically relevant conditions.
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Affiliation(s)
- Magnus Bloch
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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62
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Sacchetto C, Sequeira V, Bertero E, Dudek J, Maack C, Calore M. Metabolic Alterations in Inherited Cardiomyopathies. J Clin Med 2019; 8:E2195. [PMID: 31842377 PMCID: PMC6947282 DOI: 10.3390/jcm8122195] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/06/2019] [Accepted: 12/09/2019] [Indexed: 12/12/2022] Open
Abstract
The normal function of the heart relies on a series of complex metabolic processes orchestrating the proper generation and use of energy. In this context, mitochondria serve a crucial role as a platform for energy transduction by supplying ATP to the varying demand of cardiomyocytes, involving an intricate network of pathways regulating the metabolic flux of substrates. The failure of these processes results in structural and functional deficiencies of the cardiac muscle, including inherited cardiomyopathies. These genetic diseases are characterized by cardiac structural and functional anomalies in the absence of abnormal conditions that can explain the observed myocardial abnormality, and are frequently associated with heart failure. Since their original description, major advances have been achieved in the genetic and phenotype knowledge, highlighting the involvement of metabolic abnormalities in their pathogenesis. This review provides a brief overview of the role of mitochondria in the energy metabolism in the heart and focuses on metabolic abnormalities, mitochondrial dysfunction, and storage diseases associated with inherited cardiomyopathies.
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Affiliation(s)
- Claudia Sacchetto
- IMAiA—Institute for Molecular Biology and RNA Technology, Faculty of Health, Universiteitssingel 50, 6229ER Maastricht, The Netherlands;
- Medicine and Life Sciences, Faculty of Science and Engineering, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
- Department of Biology, University of Padova, via Ugo Bassi 58B, 35121 Padova, Italy
| | - Vasco Sequeira
- Department of Translational Science, Comprehensive Heart Failure Center, University Clinic Würzburg, Am Schwarzenberg 15, 9708 Würzburg, Germany; (V.S.); (E.B.); (J.D.)
| | - Edoardo Bertero
- Department of Translational Science, Comprehensive Heart Failure Center, University Clinic Würzburg, Am Schwarzenberg 15, 9708 Würzburg, Germany; (V.S.); (E.B.); (J.D.)
| | - Jan Dudek
- Department of Translational Science, Comprehensive Heart Failure Center, University Clinic Würzburg, Am Schwarzenberg 15, 9708 Würzburg, Germany; (V.S.); (E.B.); (J.D.)
| | - Christoph Maack
- Department of Translational Science, Comprehensive Heart Failure Center, University Clinic Würzburg, Am Schwarzenberg 15, 9708 Würzburg, Germany; (V.S.); (E.B.); (J.D.)
| | - Martina Calore
- IMAiA—Institute for Molecular Biology and RNA Technology, Faculty of Health, Universiteitssingel 50, 6229ER Maastricht, The Netherlands;
- Medicine and Life Sciences, Faculty of Science and Engineering, Universiteitssingel 50, 6229ER Maastricht, The Netherlands
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63
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Fakhree MAA, Blum C, Claessens MMAE. Shaping membranes with disordered proteins. Arch Biochem Biophys 2019; 677:108163. [PMID: 31672499 DOI: 10.1016/j.abb.2019.108163] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/23/2019] [Accepted: 10/27/2019] [Indexed: 12/15/2022]
Abstract
Membrane proteins control and shape membrane trafficking processes. The role of protein structure in shaping cellular membranes is well established. However, a significant fraction of membrane proteins is disordered or contains long disordered regions. It becomes more and more clear that these disordered regions contribute to the function of membrane proteins. While the fold of a structured protein is essential for its function, being disordered seems to be a crucial feature of membrane bound intrinsically disordered proteins and protein regions. Here we outline the motifs that encode function in disordered proteins and discuss how these functional motifs enable disordered proteins to modulate membrane properties. These changes in membrane properties facilitate and regulate membrane trafficking processes which are highly abundant in eukaryotes.
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Affiliation(s)
| | - Christian Blum
- Nanobiophysics Group, University of Twente, 7522, NB, Enschede, the Netherlands
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64
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Bhaduri S, Zhang H, Erramilli S, Cramer WA. Structural and functional contributions of lipids to the stability and activity of the photosynthetic cytochrome b 6 f lipoprotein complex. J Biol Chem 2019; 294:17758-17767. [PMID: 31597701 DOI: 10.1074/jbc.ra119.009331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 10/08/2019] [Indexed: 11/06/2022] Open
Abstract
The photosynthetic cytochrome b 6 f complex, a homodimer containing eight distinct subunits and 26 transmembrane helices per monomer, catalyzes proton-coupled electron transfer across the thylakoid membrane. The 2.5-Å-resolution structure of the complex from the cyanobacterium Nostoc sp. revealed the presence of 23 lipid-binding sites per monomer. Although the crystal structure of the cytochrome b 6 f from a plant source has not yet been solved, the identities of the lipids present in a plant b 6 f complex have previously been determined, indicating that the predominant lipid species are monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), phosphatidylglycerol (PG), and sulfoquinovosyldiacylglycerol (SQDG). Despite the extensive structural analyses of b 6 f-lipid interactions, the basis of the stabilization by lipids remains poorly understood. In the present study, we report on the effect of individual lipids on the structural and functional integrity of the b 6 f complex, purified from Spinacea oleracea It was found that (i) galactolipids (MGDG, DGDG, and SQDG) and phospholipids dilinolenoyl-phosphatidylglycerol (DLPG), 1,2-dioleoylphosphatidylglycerol (DOPG), and 1,2-dioleoyl-sn-glycerol-3-phosphatidylcholine (DOPC) structurally stabilize the complex to varying degrees; (ii) SQDG has a major role in stabilizing the dimeric complex; (iii) the b 6 f complex is stabilized by incorporation into nanodiscs or bicelles; (iv) removal of bound phospholipid by phospholipase A2 inactivates the cytochrome complex; and (v) activity can be restored significantly by the addition of the anionic lipid PG, which is attributed to stabilization of the quinone portal and the hinge region of the iron-sulfur protein.
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Affiliation(s)
- Satarupa Bhaduri
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47906
| | - Huamin Zhang
- SSCI, a Division of Albany Molecular Research Inc., West Lafayette, Indiana 47906
| | - Satchal Erramilli
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, Illinois 60637
| | - William A Cramer
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47906
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Frick M, Schmidt C. Mass spectrometry—A versatile tool for characterising the lipid environment of membrane protein assemblies. Chem Phys Lipids 2019; 221:145-157. [DOI: 10.1016/j.chemphyslip.2019.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 01/02/2023]
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66
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Exterkate M, Driessen AJM. Synthetic Minimal Cell: Self-Reproduction of the Boundary Layer. ACS OMEGA 2019; 4:5293-5303. [PMID: 30949617 PMCID: PMC6443216 DOI: 10.1021/acsomega.8b02955] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/01/2019] [Indexed: 05/09/2023]
Abstract
A critical aspect in the bottom-up construction of a synthetic minimal cell is to develop an entity that is capable of self-reproduction. A key role in this process is the expansion and division of the boundary layer that surrounds the compartment, a process in which content loss has to be avoided and the barrier function maintained. Here, we describe the latest developments regarding self-reproduction of a boundary layer with a focus on the growth and division of phospholipid-based membranes in the context of a synthetic minimal cell.
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Affiliation(s)
- Marten Exterkate
- Department of Molecular Microbiology,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747
AG Groningen, The Netherlands
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67
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Angladon MA, Fossépré M, Leherte L, Vercauteren DP. Interaction of POPC, DPPC, and POPE with the μ opioid receptor: A coarse-grained molecular dynamics study. PLoS One 2019; 14:e0213646. [PMID: 30870466 PMCID: PMC6417715 DOI: 10.1371/journal.pone.0213646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 02/26/2019] [Indexed: 11/18/2022] Open
Abstract
The μ opioid receptor (μOR), which is part of the G protein-coupled receptors family, is a membrane protein that is modulated by its lipid environment. In the present work, we model μOR in three different membrane systems: POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine), POPE (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine), and DPPC (1, 2-dipalmitoyl-sn-glycero-3-phosphocholine) through 45 μs molecular dynamics (MD) simulations at the coarse-grained level. Our theoretical studies provide new insights to the lipid-induced modulation of the receptor. Particularly, to characterize how μOR interacts with each lipid, we analyze the tilt of the protein, the number of contacts occurring between the lipids and each amino acid of the receptor, and the μOR-lipid interface described as a network graph. We also analyze the variations in the number and the nature of the protein contacts that are induced by the lipid structure. We show that POPC interacts preferentially with helix 1 (H1) and helices H5-H6, POPE, with H5-H6 and H6-H7, and DPPC, with H4 and H6. We demonstrate how each of the three lipids shape the structure of the μOR.
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Affiliation(s)
- Marie-Ange Angladon
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, Namur Medecine and Drug Innovation Center (NAMEDIC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
- * E-mail:
| | - Mathieu Fossépré
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, Namur Medecine and Drug Innovation Center (NAMEDIC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Laurence Leherte
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, Namur Medecine and Drug Innovation Center (NAMEDIC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
| | - Daniel P. Vercauteren
- Laboratoire de Physico-Chimie Informatique, Unité de Chimie Physique Théorique et Structurale, Namur Medecine and Drug Innovation Center (NAMEDIC), Namur Research Institute for Life Sciences (NARILIS), University of Namur (UNamur), Namur, Belgium
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68
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Cramer WA. Structure-function of the cytochrome b 6f lipoprotein complex: a scientific odyssey and personal perspective. PHOTOSYNTHESIS RESEARCH 2019; 139:53-65. [PMID: 30311133 PMCID: PMC6510485 DOI: 10.1007/s11120-018-0585-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 09/15/2018] [Indexed: 05/04/2023]
Abstract
Structure-function studies of the cytochrome b6f complex, the central hetero-oligomeric membrane protein complex in the electron transport chain of oxygenic photosynthesis, which formed the basis for a high-resolution (2.5 Å) crystallographic solution of the complex, are described. Structure-function differences between the structure of subunits of the bc complexes, b6f, and bc1 from mitochondria and photosynthetic bacteria, which are often assumed to function identically, are discussed. Major differences which suggest that quinone-dependent electron transport pathways can vary in b6f and bc1 complexes are as follows: (a) an additional c-type heme, cn, and bound single copies of chlorophyll a and β-carotene in the b6f complex; and (b) a cyclic electron transport pathway that encompasses the b6f and PSI reaction center complexes. The importance of including lipid in crystallization of the cytochrome complex, or with any hetero-oligomeric membrane protein complex, is emphasized, and consequences to structure-function of b6f being a lipoprotein complex discussed, including intra-protein dielectric heterogeneity and resultant pathways of trans-membrane electron transport. The role of the b6f complex in trans-membrane signal transduction from reductant generated on the p-side of the electron transport chain to the regulation of light energy to the two photosystems by trans-side phosphorylation of the light-harvesting chlorophyll protein is presented. Regarding structure aspects relevant to plastoquinol-quinone entrance-egress: (i) modification of the p-side channel for plastoquinone access to the iron-sulfur protein would change the rate-limiting step in electron transport; (ii) the narrow niche for entry of plastoquinol into b6f from the PSII reaction center complex would seem to require close proximity between the complexes.
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Affiliation(s)
- William A Cramer
- Department of Biological Sciences, Purdue University, Hockmeyer Building for Structural Biology, West Lafayette, IN, 47907, USA.
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69
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Das AK, Kudlacek O, Baumgart F, Jaentsch K, Stockner T, Sitte HH, Schütz GJ. Dopamine transporter forms stable dimers in the live cell plasma membrane in a phosphatidylinositol 4,5-bisphosphate-independent manner. J Biol Chem 2019; 294:5632-5642. [PMID: 30705091 PMCID: PMC6462504 DOI: 10.1074/jbc.ra118.006178] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/28/2019] [Indexed: 01/01/2023] Open
Abstract
The human dopamine transporter (hDAT) regulates the level of the neurotransmitter dopamine (DA) in the synaptic cleft and recycles DA for storage in the presynaptic vesicular pool. Many neurotransmitter transporters exist as oligomers, but the physiological role of oligomerization remains unclear; for example, it has been speculated to be a prerequisite for amphetamine-induced release and protein trafficking. Previous studies point to an oligomeric quaternary structure of hDAT; however, the exact stoichiometry and the fraction of co-existing oligomeric states are not known. Here, we used single-molecule brightness analysis to quantify the degree of oligomerization of heterologously expressed hDAT fused to monomeric GFP (mGFP–hDAT) in Chinese hamster ovary (CHO) cells. We observed that monomers and dimers of mGFP–hDAT co-exist and that higher-order molecular complexes of mGFP–hDAT are absent at the plasma membrane. The mGFP–hDAT dimers were stable over several minutes, and the fraction of dimers was independent of the mGFP–hDAT surface density. Furthermore, neither oxidation nor depletion of cholesterol had any effect on the fraction of dimers. Unlike for the human serotonin transporter (hSERT), in which direct binding of phosphatidylinositol 4,5-bisphosphate (PIP2) stabilized the oligomers, the stability of mGFP–hDAT dimers was PIP2 independent.
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Affiliation(s)
- Anand Kant Das
- From the Institute of Applied Physics, TU Wien, Getreidemarkt 9, A-1060, Vienna and
| | - Oliver Kudlacek
- the Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University Vienna, Waehringerstrasse 13a, A-1090 Vienna, Austria
| | - Florian Baumgart
- From the Institute of Applied Physics, TU Wien, Getreidemarkt 9, A-1060, Vienna and
| | - Kathrin Jaentsch
- the Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University Vienna, Waehringerstrasse 13a, A-1090 Vienna, Austria
| | - Thomas Stockner
- the Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University Vienna, Waehringerstrasse 13a, A-1090 Vienna, Austria
| | - Harald H Sitte
- the Center for Physiology and Pharmacology, Institute of Pharmacology, Medical University Vienna, Waehringerstrasse 13a, A-1090 Vienna, Austria
| | - Gerhard J Schütz
- From the Institute of Applied Physics, TU Wien, Getreidemarkt 9, A-1060, Vienna and
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70
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Xu H, Clairfeuille T, Jao CC, Ho H, Sweeney Z, Payandeh J, Koth CM. A Flexible and Scalable High-Throughput Platform for Recombinant Membrane Protein Production. Methods Mol Biol 2019; 2025:389-402. [PMID: 31267463 DOI: 10.1007/978-1-4939-9624-7_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Integral membrane proteins (MP) are implicated in many disease processes and are the primary targets of numerous marketed drugs. Despite recent advances in the areas of MP solubilization, stabilization, and reconstitution, it remains a time-consuming task to identify the combination of constructs and purification conditions that will enable MP structure-function studies outside of the lipid bilayer. In this chapter, we describe a strategy for rapidly identifying and optimizing the solubilization and purification conditions for nearly any recombinant MP, based on the use of a noninvasive fluorescent probe (His-Glow) that specifically binds to the common hexahistidine affinity tag of expressed targets. This His-Glow approach permits fluorescent size-exclusion chromatography (FSEC) without the need for green fluorescent protein (GFP) fusion. A two-stage detergent screening strategy is employed at the solubilization stage, whereby appropriate detergent families are identified first, followed by optimization within these families. Screening up to 96 unique combinations of solubilization conditions and constructs can be achieved in less than 24 h. At the outset of each new project, we screen six different detergents for each construct and the subsequent implementation of a simple thermostability challenge further aids in the identification of constructs and conditions suitable for large-scale production. Our strategy streamlines the parallel optimization of appropriate production conditions for multiple MP targets to rapidly enable downstream biochemical, immunization, or structural studies.
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Affiliation(s)
- Hui Xu
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Thomas Clairfeuille
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Christine C Jao
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Hoangdung Ho
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Zachary Sweeney
- Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA, USA
- Denali Therapeutics, South San Francisco, CA, USA
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA.
| | - Christopher M Koth
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA.
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71
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Chornenkyy Y, Wang W, Wei A, Nelson PT. Alzheimer's disease and type 2 diabetes mellitus are distinct diseases with potential overlapping metabolic dysfunction upstream of observed cognitive decline. Brain Pathol 2019; 29:3-17. [PMID: 30106209 PMCID: PMC6427919 DOI: 10.1111/bpa.12655] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/09/2018] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) and type 2 diabetes mellitus (T2DM) are highly prevalent aging-related diseases associated with significant morbidity and mortality. Some findings in human and animal models have linked T2DM to AD-type dementia. Despite epidemiological associations between the T2DM and cognitive impairment, the interrelational mechanisms are unclear. The preponderance of evidence in longitudinal studies with autopsy confirmation have indicated that vascular mechanisms, rather than classic AD-type pathologies, underlie the cognitive decline often seen in self-reported T2DM. T2DM is associated with cardiovascular and cerebrovascular disease (CVD), and is associated with increased risk of infarcts and small vessel disease in the brain and other organs. Neuropathological examinations of post-mortem brains demonstrated evidence of cerebrovascular disease and little to no correlation between T2DM and β-amyloid deposits or neurofibrillary tangles. Nevertheless, the mechanisms upstream of early AD-specific pathology remain obscure. In this regard, there may indeed be overlap between the pathologic mechanisms of T2DM/"metabolic syndrome," and AD. More specifically, cerebral insulin processing, glucose metabolism, mitochondrial function, and/or lipid metabolism could be altered in patients in early AD and directly influence symptomatology and/or neuropathology.
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Affiliation(s)
| | - Wang‐Xia Wang
- University of Kentucky College of MedicineLexingtonKY
- Sanders‐Brown Center on Aging, Department of PathologyUniversity of KentuckyLexingtonKY
| | - Angela Wei
- Department of BiologyUniversity of KentuckyLexingtonKY
| | - Peter T. Nelson
- University of Kentucky College of MedicineLexingtonKY
- Sanders‐Brown Center on Aging, Department of PathologyUniversity of KentuckyLexingtonKY
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72
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Jeckelmann JM, Erni B. Carbohydrate Transport by Group Translocation: The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System. Subcell Biochem 2019; 92:223-274. [PMID: 31214989 DOI: 10.1007/978-3-030-18768-2_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The Bacterial Phosphoenolpyruvate (PEP) : Sugar Phosphotransferase System (PTS) mediates the uptake and phosphorylation of carbohydrates, and controls the carbon- and nitrogen metabolism in response to the availability of sugars. PTS occur in eubacteria and in a few archaebacteria but not in animals and plants. All PTS comprise two cytoplasmic phosphotransferase proteins (EI and HPr) and a species-dependent, variable number of sugar-specific enzyme II complexes (IIA, IIB, IIC, IID). EI and HPr transfer phosphorylgroups from PEP to the IIA units. Cytoplasmic IIA and IIB units sequentially transfer phosphates to the sugar, which is transported by the IIC and IICIID integral membrane protein complexes. Phosphorylation by IIB and translocation by IIC(IID) are tightly coupled. The IIC(IID) sugar transporters of the PTS are in the focus of this review. There are four structurally different PTS transporter superfamilies (glucose, glucitol, ascorbate, mannose) . Crystal structures are available for transporters of two superfamilies: bcIICmal (MalT, 5IWS, 6BVG) and bcIICchb (ChbC, 3QNQ) of B. subtilis from the glucose family, and IICasc (UlaA, 4RP9, 5ZOV) of E. coli from the ascorbate superfamily . They are homodimers and each protomer has an independent transport pathway which functions by an elevator-type alternating-access mechanism. bcIICmal and bcIICchb have the same fold, IICasc has a completely different fold. Biochemical and biophysical data accumulated in the past with the transporters for mannitol (IICBAmtl) and glucose (IICBglc) are reviewed and discussed in the context of the bcIICmal crystal structures. The transporters of the mannose superfamily are dimers of protomers consisting of a IIC and a IID protein chain. The crystal structure is not known and the topology difficult to predict. Biochemical data indicate that the IICIID complex employs a different transport mechanism . Species specific IICIID serve as a gateway for the penetration of bacteriophage lambda DNA across, and insertion of class IIa bacteriocins into the inner membrane. PTS transporters are inserted into the membrane by SecYEG translocon and have specific lipid requirements. Immunoelectron- and fluorescence microscopy indicate a non-random distribution and supramolecular complexes of PTS proteins.
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Affiliation(s)
- Jean-Marc Jeckelmann
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
| | - Bernhard Erni
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
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73
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Aguayo-Ortiz R, Straub JE, Dominguez L. Influence of membrane lipid composition on the structure and activity of γ-secretase. Phys Chem Chem Phys 2018; 20:27294-27304. [PMID: 30357233 PMCID: PMC11260083 DOI: 10.1039/c8cp04138e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
γ-Secretase (GS) is a multi-subunit membrane-embedded aspartyl protease that cleaves more than 80 integral membrane proteins, including the amyloid precursor protein (APP) to produce the amyloid-β (Aβ) peptide. Oligomerization and aggregation of the 42-amino acid length Aβ isoform in the brain has been associated with the development and progression of Alzheimer's disease (AD). Based on recent experimental structural studies and using multiscale computational modeling approaches, the conformational states and protein-membrane interactions of the GS complex embedded in six homogeneous and six heterogeneous lipid bilayers were characterized. In order to identify potential lipid and cholesterol binding sites, GS regions with high lipid/cholesterol occupancy values were analyzed using atomistic and coarse-grained simulations. Long lipid residence times were observed to be correlated with a large number of hydrogen bonds between the charged headgroups and key GS amino acids. This observation provides a plausible explanation for the inhibition of GS by charged lipids observed in previous experimental studies. Computed lateral pressure profiles suggest that higher transmembrane pressures favor active state conformations of the catalytic subunit. A probable mechanism for the regulation of the local stress response in cholesterol-rich multicomponent lipid bilayers is identified. Finally, it is demonstrated that interactions between the nicastrin extracellular domain and lipid headgroups leads to a compact structural conformation of the GS complex. Overall, this study provides valuable insight into the effect of bilayer lipid composition on the GS structural ensemble and its function.
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Affiliation(s)
- Rodrigo Aguayo-Ortiz
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City, 04510, Mexico.
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74
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Ahmed D, Roy D, Cassol E. Examining Relationships between Metabolism and Persistent Inflammation in HIV Patients on Antiretroviral Therapy. Mediators Inflamm 2018; 2018:6238978. [PMID: 30363715 PMCID: PMC6181007 DOI: 10.1155/2018/6238978] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 09/06/2018] [Indexed: 12/30/2022] Open
Abstract
With the advent of antiretroviral therapy (ART), HIV-infected individuals are now living longer and healthier lives. However, ART does not completely restore health and treated individuals are experiencing increased rates of noncommunicable diseases such as dyslipidemia, insulin resistance, type 2 diabetes, cardiovascular disease, and nonalcoholic fatty liver disease. While it is well known that persistent immune activation and inflammation contribute to the development of these comorbid diseases, the mechanisms underlying this chronic activation remain incompletely understood. In this review, we will discuss emerging evidence that suggests that alterations in cellular metabolism may play a central role in driving this immune dysfunction in HIV patients on ART.
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Affiliation(s)
- Duale Ahmed
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - David Roy
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada
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75
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Xia W, Ma L, Chen X, Li X, Zhang Y. Physicochemical and structural properties of composite gels prepared with myofibrillar protein and lecithin at various ionic strengths. Food Hydrocoll 2018. [DOI: 10.1016/j.foodhyd.2018.03.044] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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76
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Dudek J, Hartmann M, Rehling P. The role of mitochondrial cardiolipin in heart function and its implication in cardiac disease. Biochim Biophys Acta Mol Basis Dis 2018; 1865:810-821. [PMID: 30837070 DOI: 10.1016/j.bbadis.2018.08.025] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/14/2018] [Accepted: 08/17/2018] [Indexed: 01/21/2023]
Abstract
Mitochondria play an essential role in the energy metabolism of the heart. Many of the essential functions are associated with mitochondrial membranes and oxidative phosphorylation driven by the respiratory chain. Mitochondrial membranes are unique in the cell as they contain the phospholipid cardiolipin. The important role of cardiolipin in cardiovascular health is highlighted by several cardiac diseases, in which cardiolipin plays a fundamental role. Barth syndrome, Sengers syndrome, and Dilated cardiomyopathy with ataxia (DCMA) are genetic disorders, which affect cardiolipin biosynthesis. Other cardiovascular diseases including ischemia/reperfusion injury and heart failure are also associated with changes in the cardiolipin pool. Here, we summarize molecular functions of cardiolipin in mitochondrial biogenesis and morphology. We highlight the role of cardiolipin for the respiratory chain, metabolite carriers, and mitochondrial metabolism and describe links to apoptosis and mitochondria specific autophagy (mitophagy) with possible implications in cardiac disease.
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Affiliation(s)
- Jan Dudek
- Institute of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Magnus Hartmann
- Institute of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany
| | - Peter Rehling
- Institute of Cellular Biochemistry, University Medical Center Göttingen, D-37073 Göttingen, Germany; Max Planck Institute for Biophysical Chemistry, D-37077 Göttingen, Germany.
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77
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Garcia ES, van Leeuwen JJA, Safi C, Sijtsma L, van den Broek LAM, Eppink MHM, Wijffels RH, van den Berg C. Techno-Functional Properties of Crude Extracts from the Green Microalga Tetraselmis suecica. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:7831-7838. [PMID: 29976070 PMCID: PMC6150664 DOI: 10.1021/acs.jafc.8b01884] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/13/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
A mild fractionation process to extract functional biomolecules from green microalgae was implemented. The process includes bead milling, centrifugation, and filtration with several membrane cut-offs. For each fraction, the corresponding composition was measured, and the surface activity and gelation behavior were determined. A maximum protein yield of 12% was obtained in the supernatant after bead milling and between 3.2 and 11.7% after filtration. Compared to whey protein isolate, most of the algae fractions exhibited comparable or enhanced functionality. Surface activity for air-water and oil-water interfaces and gelation activities were notably superior for the retentate fractions compared to the permeates. It is proposed that such functionality in the retentates is due to the presence of hydrophobic compounds and molecular complexes exhibiting a similar behavior as Pickering particles. We demonstrated that excellent functionality can be obtained with crude fractions, requiring minimum processing and, thus, constituting an interesting option for commercial applications.
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Affiliation(s)
- E. Suarez Garcia
- Bioprocess
Engineering, AlgaePARC, Wageningen University
and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - J. J. A. van Leeuwen
- Wageningen
Food & Biobased Research, Wageningen
University and Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - C. Safi
- Wageningen
Food & Biobased Research, Wageningen
University and Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - L. Sijtsma
- Wageningen
Food & Biobased Research, Wageningen
University and Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - L. A. M. van den Broek
- Wageningen
Food & Biobased Research, Wageningen
University and Research, P.O. Box 17, 6700 AA Wageningen, The Netherlands
| | - M. H. M. Eppink
- Bioprocess
Engineering, AlgaePARC, Wageningen University
and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
| | - R. H. Wijffels
- Bioprocess
Engineering, AlgaePARC, Wageningen University
and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
- Nord
University, Faculty of Biosciences and Aquaculture, N-8049 Bodø, Norway
| | - C. van den Berg
- Bioprocess
Engineering, AlgaePARC, Wageningen University
and Research, P.O. Box 16, 6700 AA Wageningen, The Netherlands
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78
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Specific cardiolipin-SecY interactions are required for proton-motive force stimulation of protein secretion. Proc Natl Acad Sci U S A 2018; 115:7967-7972. [PMID: 30012626 DOI: 10.1073/pnas.1721536115] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The transport of proteins across or into membranes is a vital biological process, achieved in every cell by the conserved Sec machinery. In bacteria, SecYEG combines with the SecA motor protein for secretion of preproteins across the plasma membrane, powered by ATP hydrolysis and the transmembrane proton-motive force (PMF). The activities of SecYEG and SecA are modulated by membrane lipids, particularly cardiolipin (CL), a specialized phospholipid known to associate with a range of energy-transducing machines. Here, we identify two specific CL binding sites on the Thermotoga maritima SecA-SecYEG complex, through application of coarse-grained molecular dynamics simulations. We validate the computational data and demonstrate the conserved nature of the binding sites using in vitro mutagenesis, native mass spectrometry, biochemical analysis, and fluorescence spectroscopy of Escherichia coli SecYEG. The results show that the two sites account for the preponderance of functional CL binding to SecYEG, and mediate its roles in ATPase and protein transport activity. In addition, we demonstrate an important role for CL in the conferral of PMF stimulation of protein transport. The apparent transient nature of the CL interaction might facilitate proton exchange with the Sec machinery, and thereby stimulate protein transport, by a hitherto unexplored mechanism. This study demonstrates the power of coupling the high predictive ability of coarse-grained simulation with experimental analyses, toward investigation of both the nature and functional implications of protein-lipid interactions.
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79
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Abstract
Outer-membrane porins are often considered as passive conduits of small molecules across lipid bilayers. Using native mass spectrometry experiments we identify a pH-sensitive lipid-binding mechanism of outer membrane porin F, which enables increased threading of a colicin-derived peptide through open channels. Supported by molecular dynamics simulations and channel recording experiments, we posit that this mechanism attenuates channel opening in response to changes in environmental conditions, specifically pH. These findings have important consequences for mass spectrometry experiments, wherein the role of charge is often overlooked, and they also could help provide understanding of antibiotics that gain access to Gram-negative bacteria through porin-mediated pathways. Strong interactions between lipids and proteins occur primarily through association of charged headgroups and amino acid side chains, rendering the protonation status of both partners important. Here we use native mass spectrometry to explore lipid binding as a function of charge of the outer membrane porin F (OmpF). We find that binding of anionic phosphatidylglycerol (POPG) or zwitterionic phosphatidylcholine (POPC) to OmpF is sensitive to electrospray polarity while the effects of charge are less pronounced for other proteins in outer or mitochondrial membranes: the ferripyoverdine receptor (FpvA) or the voltage-dependent anion channel (VDAC). Only marginal charge-induced differences were observed for inner membrane proteins: the ammonia channel (AmtB) or the mechanosensitive channel. To understand these different sensitivities, we performed an extensive bioinformatics analysis of membrane protein structures and found that OmpF, and to a lesser extent FpvA and VDAC, have atypically high local densities of basic and acidic residues in their lipid headgroup-binding regions. Coarse-grained molecular dynamics simulations, in mixed lipid bilayers, further implicate changes in charge by demonstrating preferential binding of anionic POPG over zwitterionic POPC to protonated OmpF, an effect not observed to the same extent for AmtB. Moreover, electrophysiology and mass-spectrometry–based ligand-binding experiments, at low pH, show that POPG can maintain OmpF channels in open conformations for extended time periods. Since the outer membrane is composed almost entirely of anionic lipopolysaccharide, with similar headgroup properties to POPG, such anionic lipid binding could prevent closure of OmpF channels, thereby increasing access of antibiotics that use porin-mediated pathways.
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80
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Agwa AJ, Peigneur S, Chow CY, Lawrence N, Craik DJ, Tytgat J, King GF, Henriques ST, Schroeder CI. Gating modifier toxins isolated from spider venom: Modulation of voltage-gated sodium channels and the role of lipid membranes. J Biol Chem 2018; 293:9041-9052. [PMID: 29703751 DOI: 10.1074/jbc.ra118.002553] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 04/25/2018] [Indexed: 11/06/2022] Open
Abstract
Gating modifier toxins (GMTs) are venom-derived peptides isolated from spiders and other venomous creatures and modulate activity of disease-relevant voltage-gated ion channels and are therefore being pursued as therapeutic leads. The amphipathic surface profile of GMTs has prompted the proposal that some GMTs simultaneously bind to the cell membrane and voltage-gated ion channels in a trimolecular complex. Here, we examined whether there is a relationship among spider GMT amphipathicity, membrane binding, and potency or selectivity for voltage-gated sodium (NaV) channels. We used NMR spectroscopy and in silico calculations to examine the structures and physicochemical properties of a panel of nine GMTs and deployed surface plasmon resonance to measure GMT affinity for lipids putatively found in proximity to NaV channels. Electrophysiology was used to quantify GMT activity on NaV1.7, an ion channel linked to chronic pain. Selectivity of the peptides was further examined against a panel of NaV channel subtypes. We show that GMTs adsorb to the outer leaflet of anionic lipid bilayers through electrostatic interactions. We did not observe a direct correlation between GMT amphipathicity and affinity for lipid bilayers. Furthermore, GMT-lipid bilayer interactions did not correlate with potency or selectivity for NaVs. We therefore propose that increased membrane binding is unlikely to improve subtype selectivity and that the conserved amphipathic GMT surface profile is an adaptation that facilitates simultaneous modulation of multiple NaVs.
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Affiliation(s)
- Akello J Agwa
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Steve Peigneur
- Laboratory of Toxicology and Pharmacology, University of Leuven (KU Leuven), 3000 Leuven, Belgium
| | - Chun Yuen Chow
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Nicole Lawrence
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - David J Craik
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Jan Tytgat
- Laboratory of Toxicology and Pharmacology, University of Leuven (KU Leuven), 3000 Leuven, Belgium
| | - Glenn F King
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Sónia Troeira Henriques
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
| | - Christina I Schroeder
- From the Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia and
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81
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Flatt JF, Bruce LJ. The Molecular Basis for Altered Cation Permeability in Hereditary Stomatocytic Human Red Blood Cells. Front Physiol 2018; 9:367. [PMID: 29713289 PMCID: PMC5911802 DOI: 10.3389/fphys.2018.00367] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/27/2018] [Indexed: 11/20/2022] Open
Abstract
Normal human RBCs have a very low basal permeability (leak) to cations, which is continuously corrected by the Na,K-ATPase. The leak is temperature-dependent, and this temperature dependence has been evaluated in the presence of inhibitors to exclude the activity of the Na,K-ATPase and NaK2Cl transporter. The severity of the RBC cation leak is altered in various conditions, most notably the hereditary stomatocytosis group of conditions. Pedigrees within this group have been classified into distinct phenotypes according to various factors, including the severity and temperature-dependence of the cation leak. As recent breakthroughs have provided more information regarding the molecular basis of hereditary stomatocytosis, it has become clear that these phenotypes elegantly segregate with distinct genetic backgrounds. The cryohydrocytosis phenotype, including South-east Asian Ovalocytosis, results from mutations in SLC4A1, and the very rare condition, stomatin-deficient cryohydrocytosis, is caused by mutations in SLC2A1. Mutations in RHAG cause the very leaky condition over-hydrated stomatocytosis, and mutations in ABCB6 result in familial pseudohyperkalemia. All of the above are large multi-spanning membrane proteins and the mutations may either modify the structure of these proteins, resulting in formation of a cation pore, or otherwise disrupt the membrane to allow unregulated cation movement across the membrane. More recently mutations have been found in two RBC cation channels, PIEZO1 and KCNN4, which result in dehydrated stomatocytosis. These mutations alter the activation and deactivation kinetics of these channels, leading to increased opening and allowing greater cation fluxes than in wild type.
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Affiliation(s)
- Joanna F Flatt
- Bristol Institute for Transfusion Sciences, NHS Blood and Transplant, Bristol, United Kingdom
| | - Lesley J Bruce
- Bristol Institute for Transfusion Sciences, NHS Blood and Transplant, Bristol, United Kingdom
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82
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Chen E, Kiebish MA, McDaniel J, Niedzwiecka K, Kucharczyk R, Ravasz D, Gao F, Narain NR, Sarangarajan R, Seyfried TN, Adam-Vizi V, Chinopoulos C. Perturbation of the yeast mitochondrial lipidome and associated membrane proteins following heterologous expression of Artemia-ANT. Sci Rep 2018; 8:5915. [PMID: 29651047 PMCID: PMC5897331 DOI: 10.1038/s41598-018-24305-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 03/29/2018] [Indexed: 12/22/2022] Open
Abstract
Heterologous expression is a landmark technique for studying a protein itself or its effect on the expression host, in which membrane-embedded proteins are a common choice. Yet, the impact of inserting a foreign protein to the lipid environment of host membranes, has never been addressed. Here we demonstrated that heterologous expression of the Artemia franciscana adenine nucleotide translocase (ANT) in yeasts altered lipidomic composition of their inner mitochondrial membranes. Along with this, activities of complex II, IV and ATP synthase, all membrane-embedded components, were significantly decreased while their expression levels remained unaffected. Although the results represent an individual case of expressing a crustacean protein in yeast inner mitochondrial membranes, it cannot be excluded that host lipidome alterations is a more widespread epiphenomenon, potentially biasing heterologous expression experiments. Finally, our results raise the possibility that not only lipids modulate protein function, but also membrane-embedded proteins modulate lipid composition, thus revealing a reciprocal mode of regulation for these two biomolecular entities.
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Affiliation(s)
| | | | | | - Katarzyna Niedzwiecka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Roza Kucharczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
| | - Dora Ravasz
- Department of Medical Biochemistry, Semmelweis University, Budapest, 1094, Hungary.,MTA-SE Lendület Neurobiochemistry Research Group, Budapest, 1094, Hungary
| | - Fei Gao
- BERG LLC, Framingham, MA, 01701, USA
| | | | | | - Thomas N Seyfried
- Biology Department, Boston College, Chestnut Hill, Boston, MA, 02467, USA
| | - Vera Adam-Vizi
- Department of Medical Biochemistry, Semmelweis University, Budapest, 1094, Hungary.,MTA-SE Laboratory for Neurobiochemistry, Budapest, 1094, Hungary
| | - Christos Chinopoulos
- Department of Medical Biochemistry, Semmelweis University, Budapest, 1094, Hungary. .,MTA-SE Lendület Neurobiochemistry Research Group, Budapest, 1094, Hungary.
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83
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Domicevica L, Koldsø H, Biggin PC. Multiscale molecular dynamics simulations of lipid interactions with P-glycoprotein in a complex membrane. J Mol Graph Model 2018; 80:147-156. [PMID: 29353693 DOI: 10.1016/j.jmgm.2017.12.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
P-glycoprotein (P-gp) can transport a wide range of very different hydrophobic organic molecules across the membrane. Its ability to extrude molecules from the cell creates delivery problems for drugs that target proteins in the central nervous system (CNS) and also causes drug-resistance in many forms of cancer. Whether a drug will be susceptible to export by P-gp is difficult to predict and currently this is usually assessed with empirical and/or animal models. Thus, there is a need to better understand how P-gp works at the molecular level in order to fulfil the 3Rs: Refinement, reduction and replacement of animals in research. As structural information increasingly becomes available, our understanding at the molecular level improves. Proteins like P-gp are however very dynamic entities and thus one of the most appropriate ways to study them is with molecular dynamics simulations, especially as this can capture the influence of the surrounding environment. Recent parameterization developments have meant that it is now possible to simulate lipid bilayers that more closely resemble in vivo membranes in terms of their composition. In this report we construct a complex lipid bilayer that mimics the composition of brain epithelial cells and examine the interactions of it with P-gp. We find that the negatively charged phosphatidylserine lipids in the inner leaflet of the membrane tend to form an annulus around P-gp. We also observed the interaction of cholesterol with three distinct areas of the P-gp. Potential of mean force (PMF) calculations suggest that a crevice between transmembrane helices 10 and 12 has particularly favourable interaction energy for cholesterol.
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Affiliation(s)
- Laura Domicevica
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Heidi Koldsø
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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84
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Salas-Estrada LA, Leioatts N, Romo TD, Grossfield A. Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions. Biophys J 2018; 114:355-367. [PMID: 29401433 PMCID: PMC5984976 DOI: 10.1016/j.bpj.2017.11.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/20/2017] [Accepted: 11/09/2017] [Indexed: 10/18/2022] Open
Abstract
Rhodopsin, a prototypical G protein-coupled receptor, is a membrane protein that can sense dim light. This highly effective photoreceptor is known to be sensitive to the composition of its lipidic environment, but the molecular mechanisms underlying this fine-tuned modulation of the receptor's function and structural stability are not fully understood. There are two competing hypotheses to explain how this occurs: 1) lipid modulation occurs via solvent-like interactions, where lipid composition controls membrane properties like hydrophobic thickness, which in turn modulate the protein's conformational equilibrium; or 2) protein-lipid interactions are ligand-like, with specific hot spots and long-lived binding events. By analyzing an ensemble of all-atom molecular dynamics simulations of five different states of rhodopsin, we show that a local ordering effect takes place in the membrane upon receptor activation. Likewise, docosahexaenoic acid acyl tails and phosphatidylethanolamine headgroups behave like weak ligands, preferentially binding to the receptor in inactive-like conformations and inducing subtle but significant structural changes.
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Affiliation(s)
- Leslie A Salas-Estrada
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Nicholas Leioatts
- Department of Theoretical and Computational Biophysics, Max Plank Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tod D Romo
- Center for Integrated Research Computing, University of Rochester, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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85
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Bai L, Wang T, Zhao G, Kovach A, Li H. The atomic structure of a eukaryotic oligosaccharyltransferase complex. Nature 2018; 555:328-333. [PMID: 29466327 PMCID: PMC6112861 DOI: 10.1038/nature25755] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/16/2018] [Indexed: 11/29/2022]
Abstract
N-glycosylation is a ubiquitous modification of eukaryotic secretory and membrane-bound proteins; about 90% of glycoproteins are N-glycosylated. The reaction is catalyzed by an eight-protein oligosaccharyltransferase complex, OST, embedded in the ER membrane. Our understanding of eukaryotic protein N-glycosylation has been limited due to the lack of high-resolution structures. Here we report a 3.5-Å resolution cryo-EM structure of the Saccharomyces cerevisiae OST, revealing the structures of Ost1–5, Stt3, Wbp1, and Swp1. We found that seven phospholipids mediate many of the inter-subunit interactions, and an Stt3 N-glycan mediates interaction with Wbp1 and Swp1 in the lumen. Ost3 was found to mediate the OST-Sec61 translocon interface, funneling the acceptor peptide towards the OST catalytic site as the nascent peptide emerges from the translocon. The structure provides novel insights into co-translational protein N-glycosylation and may facilitate the development of small-molecule inhibitors targeting this process.
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Affiliation(s)
- Lin Bai
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Tong Wang
- Advanced Science Research Center at the Graduate Center of the City University of New York, New York, New York, USA
| | - Gongpu Zhao
- David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Amanda Kovach
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
| | - Huilin Li
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
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86
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Claridge SA. Standing, lying, and sitting: translating building principles of the cell membrane to synthetic 2D material interfaces. Chem Commun (Camb) 2018; 54:6681-6691. [DOI: 10.1039/c8cc02596g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lessons can be drawn from cell membranes in controlling noncovalent functionalization of 2D materials to optimize interactions with the environment.
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Affiliation(s)
- S. A. Claridge
- Department of Chemistry and Weldon School of Biomedical Engineering
- Purdue University
- West Lafayette
- USA
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87
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Hien Nguyen T, C. Moore C, B. Moore P, Liu Z. Molecular dynamics study of homo-oligomeric ion channels: Structures of the surrounding lipids and dynamics of water movement. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.1.50] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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88
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Hsu PC, Samsudin F, Shearer J, Khalid S. It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli. J Phys Chem Lett 2017; 8:5513-5518. [PMID: 29053278 DOI: 10.1021/acs.jpclett.7b02432] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The cell envelope of Gram-negative bacteria is composed of two membranes separated by a soluble region. Here, we report microsecond time scale coarse-grained molecular dynamics simulations of models of the Escherichia coli cell envelope that incorporate both membranes and various native membrane proteins. Our results predict that both the inner and outer membranes curve in a manner dependent on the size of the embedded proteins. The tightly cross-linked lipopolysaccharide molecules (LPS) of the outer membrane cause a strong coupling between the movement of proteins and lipids. While the flow of phospholipids is more random, their diffusion is nevertheless influenced by nearby proteins. Our results reveal protein-induced lipid sorting, whereby cardiolipin is significantly enriched within the vicinity of the water channel AqpZ and the multidrug efflux pump AcrBZ. In summary, our results provide unprecedented details of the intricate relationship between both membranes of E. coli and the proteins embedded within them.
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Affiliation(s)
- Pin-Chia Hsu
- School of Chemistry, University of Southampton , Southampton SO17 1BJ, U.K
| | - Firdaus Samsudin
- School of Chemistry, University of Southampton , Southampton SO17 1BJ, U.K
| | - Jonathan Shearer
- School of Chemistry, University of Southampton , Southampton SO17 1BJ, U.K
| | - Syma Khalid
- School of Chemistry, University of Southampton , Southampton SO17 1BJ, U.K
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89
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Exogenous Polyunsaturated Fatty Acids Impact Membrane Remodeling and Affect Virulence Phenotypes among Pathogenic Vibrio Species. Appl Environ Microbiol 2017; 83:AEM.01415-17. [PMID: 28864654 DOI: 10.1128/aem.01415-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/25/2017] [Indexed: 01/24/2023] Open
Abstract
The pathogenic Vibrio species (V. cholerae, V. parahaemolyticus, and V. vulnificus) represent a constant threat to human health, causing foodborne and skin wound infections as a result of ingestion of or exposure to contaminated water and seafood. Recent studies have highlighted Vibrio's ability to acquire fatty acids from environmental sources and assimilate them into cell membranes. The possession and conservation of such machinery provokes consideration of fatty acids as important factors in the pathogenic lifestyle of Vibrio species. The findings here link exogenous fatty acid exposure to changes in bacterial membrane phospholipid structure, permeability, phenotypes associated with virulence, and consequent stress responses that may impact survival and persistence of pathogenic Vibrio species. Polyunsaturated fatty acids (PUFAs) (ranging in carbon length and unsaturation) supplied in growth medium were assimilated into bacterial phospholipids, as determined by thin-layer chromatography and liquid chromatography-mass spectrometry. The incorporation of fatty acids variably affected membrane permeability, as judged by uptake of the hydrophobic compound crystal violet. For each species, certain fatty acids were identified as affecting resistance to antimicrobial peptide treatment. Significant fluctuations were observed with regard to both motility and biofilm formation following growth in the presence of individual PUFAs. Our results illustrate the important and complex roles of exogenous fatty acids in the membrane physiology and virulence of a bacterial genus that inhabits aquatic and host environments containing an abundance of diverse fatty acids.IMPORTANCE Bacterial responses to fatty acids include, but are not limited to, degradation for metabolic gain, modification of membrane lipids, alteration of protein function, and regulation of gene expression. Vibrio species exhibit significant diversity with regard to the machinery known to participate in the uptake and incorporation of fatty acids into their membranes. Both aquatic and host niches occupied by Vibrio are rife with various free fatty acids and fatty acid-containing lipids. The roles of fatty acids in the environmental survival and pathogenesis of bacteria have begun to emerge and are expected to expand significantly. The current study demonstrates the responsiveness of V. cholerae, V. parahaemolyticus, and V. vulnificus to exogenous PUFAs. In addition to phospholipid remodeling, PUFA assimilation impacts membrane permeability, motility, biofilm formation, and resistance to polymyxin B.
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90
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Domicevica L, Koldsø H, Biggin PC. Multiscale molecular dynamics simulations of lipid interactions with P-glycoprotein in a complex membrane. J Mol Graph Model 2017; 77:250-258. [PMID: 28903085 DOI: 10.1016/j.jmgm.2017.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/29/2017] [Accepted: 09/01/2017] [Indexed: 11/16/2022]
Abstract
P-glycoprotein (P-gp) can transport a wide range of very different hydrophobic organic molecules across the membrane. Its ability to extrude molecules from the cell creates delivery problems for drugs that target proteins in the central nervous system (CNS) and also causes drug-resistance in many forms of cancer. Whether a drug will be susceptible to export by P-gp is difficult to predict and currently this is usually assessed with empirical and/or animal models. Thus, there is a need to better understand how P-gp works at the molecular level in order to fulfil the 3Rs: Refinement, reduction and replacement of animals in research. As structural information increasingly becomes available, our understanding at the molecular level improves. Proteins like P-gp are however very dynamic entities and thus one of the most appropriate ways to study them is with molecular dynamics simulations, especially as this can capture the influence of the surrounding environment. Recent parameterization developments have meant that it is now possible to simulate lipid bilayers that more closely resemble in vivo membranes in terms of their composition. In this report we construct a complex lipid bilayer that mimics the composition of brain epithelial cells and examine the interactions of it with P-gp. We find that the negatively charged phosphatidylserine lipids in the inner leaflet of the membrane tend to form an annulus around P-gp. We also observed the interaction of cholesterol with three distinct areas of the P-gp. Potential of mean force (PMF) calculations suggest that a crevice between transmembrane helices 10 and 12 has particularly favourable interaction energy for cholesterol.
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Affiliation(s)
- Laura Domicevica
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Heidi Koldsø
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
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91
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Ahmed D, Cassol E. Role of cellular metabolism in regulating type I interferon responses: Implications for tumour immunology and treatment. Cancer Lett 2017; 409:20-29. [PMID: 28888999 DOI: 10.1016/j.canlet.2017.08.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/21/2017] [Accepted: 08/25/2017] [Indexed: 12/31/2022]
Abstract
Type I interferons (IFN) are increasingly recognized for their role in regulating anti-tumour immune responses. However, chronic activation of these pathways can result in immunosuppression and has been linked to poor responses to genotoxic and radiotoxic therapies. Emerging evidence suggests energy, lipid and amino acid metabolism play an important role in regulating and fine tuning type I IFN responses. Further, dysregulation of these processes has been implicated in the pathogenesis of chronic viral infections and autoimmune disorders. Systematic evaluation of these interrelationships in cancer models and patients may have important implications for the development of targeted IFN based anti-cancer therapeutics with minimal toxicity and limited off target effects.
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Affiliation(s)
- Duale Ahmed
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Edana Cassol
- Department of Health Sciences, Carleton University, Ottawa, Ontario, Canada.
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92
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Musatov A, Sedlák E. Role of cardiolipin in stability of integral membrane proteins. Biochimie 2017; 142:102-111. [PMID: 28842204 DOI: 10.1016/j.biochi.2017.08.013] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/21/2017] [Indexed: 01/13/2023]
Abstract
Cardiolipin (CL) is a unique phospholipid with a dimeric structure having four acyl chains and two phosphate groups found almost exclusively in certain membranes of bacteria and of mitochondria of eukaryotes. CL interacts with numerous proteins and has been implicated in function and stabilization of several integral membrane proteins (IMPs). While both functional and stabilization roles of CL in IMPs has been generally acknowledged, there are, in fact, only limited number of quantitative analysis that support this function of CL. This is likely caused by relatively complex determination of parameters characterizing stability of IMPs and particularly intricate assessment of role of specific phospholipids such as CL in IMPs stability. This review aims to summarize quantitative findings regarding stabilization role of CL in IMPs reported up to now.
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Affiliation(s)
- Andrej Musatov
- Department of Biophysics, Institute of Experimental Physics Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia.
| | - Erik Sedlák
- Centre for Interdisciplinary Biosciences, P.J. Šafárik University, Jesenná 5, 040 01 Košice, Slovakia.
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93
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Govaerts C. Lipids Can Make Them Stick Together. Trends Biochem Sci 2017; 42:329-330. [DOI: 10.1016/j.tibs.2017.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 03/07/2017] [Indexed: 10/19/2022]
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94
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Vermaas JV, Pogorelov TV, Tajkhorshid E. Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents. J Phys Chem B 2017; 121:3764-3776. [PMID: 28241729 PMCID: PMC5558153 DOI: 10.1021/acs.jpcb.6b11378] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanics of the protein-lipid interactions of transmembrane proteins are difficult to capture with conventional atomic molecular dynamics, due to the slow lateral diffusion of lipids restricting sampling to states near the initial membrane configuration. The highly mobile membrane mimetic (HMMM) model accelerates lipid dynamics by modeling the acyl tails nearest to the membrane center as a fluid organic solvent while maintaining an atomic description of the lipid headgroups and short acyl tails. The HMMM has been applied to many peripheral protein systems; however, the organic solvent used to date caused deformations in transmembrane proteins by intercalating into the protein and disrupting interactions between individual side chains. We ameliorate the effect of the solvent on transmembrane protein structure through the development of two new in silico Lennard-Jones solvents. The parameters for the new solvents were determined through an extensive parameter search in order to match the bulk properties of alkanes in a highly simplified model. Using these new solvents, we substantially improve the insertion free energy profiles of 10 protein side chain analogues across the entire bilayer. In addition, we reduce the intercalation of solvent into transmembrane systems, resulting in native-like transmembrane protein structures from five different topological classes within a HMMM bilayer. The parametrization of the solvents, in addition to their computed physical properties, is discussed. By combining high lipid lateral diffusion with intact transmembrane proteins, we foresee the developed solvents being useful to efficiently identify membrane composition inhomogeneities and lipid binding caused by the presence of membrane proteins.
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Affiliation(s)
- Josh V Vermaas
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Taras V Pogorelov
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Department of Chemistry, School of Chemical Sciences, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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95
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Agwa AJ, Henriques ST, Schroeder CI. Gating modifier toxin interactions with ion channels and lipid bilayers: Is the trimolecular complex real? Neuropharmacology 2017; 127:32-45. [PMID: 28400258 DOI: 10.1016/j.neuropharm.2017.04.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 03/31/2017] [Accepted: 04/05/2017] [Indexed: 11/15/2022]
Abstract
Spider peptide toxins have attracted attention because of their ability to target voltage-gated ion channels, which are involved in several pathologies including chronic pain and some cardiovascular conditions. A class of these peptides acts by modulating the gating mechanism of voltage-gated ion channels and are thus called gating modifier toxins (GMTs). In addition to their interactions with voltage-gated ion channels, some GMTs have affinity for lipid bilayers. This review discusses the potential importance of the cell membrane on the mode of action of GMTs. We propose that peptide-membrane interactions can anchor GMTs at the cell surface, thereby increasing GMT concentration in the vicinity of the channel binding site. We also propose that modulating peptide-membrane interactions might be useful for increasing the therapeutic potential of spider toxins. Furthermore, we explore the advantages and limitations of the methodologies currently used to examine peptide-membrane interactions. Although GMT-lipid membrane binding does not appear to be a requirement for the activity of all GMTs, it is an important feature, and future studies with GMTs should consider the trimolecular peptide-lipid membrane-channel complex. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.'
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Affiliation(s)
- Akello J Agwa
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sónia T Henriques
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Christina I Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
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96
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Cárdenes R, Zhang C, Klementieva O, Werner S, Guttmann P, Pratsch C, Cladera J, Bijnens BH. 3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: A pilot study. PLoS One 2017; 12:e0174324. [PMID: 28376110 PMCID: PMC5380311 DOI: 10.1371/journal.pone.0174324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/07/2017] [Indexed: 12/28/2022] Open
Abstract
Structural analysis of biological membranes is important for understanding cell and sub-cellular organelle function as well as their interaction with the surrounding environment. Imaging of whole cells in three dimension at high spatial resolution remains a significant challenge, particularly for thick cells. Cryo-transmission soft X-ray microscopy (cryo-TXM) has recently gained popularity to image, in 3D, intact thick cells (∼10μm) with details of sub-cellular architecture and organization in near-native state. This paper reports a new tool to segment and quantify structural changes of biological membranes in 3D from cryo-TXM images by tracking an initial 2D contour along the third axis of the microscope, through a multi-scale ridge detection followed by an active contours-based model, with a subsequent refinement along the other two axes. A quantitative metric that assesses the grayscale profiles perpendicular to the membrane surfaces is introduced and shown to be linearly related to the membrane thickness. Our methodology has been validated on synthetic phantoms using realistic microscope properties and structure dimensions, as well as on real cryo-TXM data. Results demonstrate the validity of our algorithms for cryo-TXM data analysis.
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Affiliation(s)
| | - Chong Zhang
- Physense, Universitat Pompeu Fabra, Barcelona, Spain
| | - Oxana Klementieva
- Institute of Neuropathology, IDIBELL-University Hospital Bellvitge, L’Hospitalet de Llobregat, Spain
- Experimental Dementia Research Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Stephan Werner
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute Soft Matters and Functional Materials, Electron Storage Ring BESSY II, Berlin, Germany
| | - Peter Guttmann
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute Soft Matters and Functional Materials, Electron Storage Ring BESSY II, Berlin, Germany
| | - Christoph Pratsch
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute Soft Matters and Functional Materials, Electron Storage Ring BESSY II, Berlin, Germany
| | - Josep Cladera
- Biophysics Unit & Centre of Studies in Biophysics, Dept. of Biochemistry & Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Bart H. Bijnens
- Physense, Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
- * E-mail:
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97
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Carranza G, Angius F, Ilioaia O, Solgadi A, Miroux B, Arechaga I. Cardiolipin plays an essential role in the formation of intracellular membranes in Escherichia coli. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1124-1132. [PMID: 28284722 DOI: 10.1016/j.bbamem.2017.03.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/22/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
Mitochondria, chloroplasts and photosynthetic bacteria are characterized by the presence of complex and intricate membrane systems. In contrast, non-photosynthetic bacteria lack membrane structures within their cytoplasm. However, large scale over-production of some membrane proteins, such as the fumarate reductase, the mannitol permease MtlA, the glycerol acyl transferase PlsB, the chemotaxis receptor Tsr or the ATP synthase subunit b, can induce the proliferation of intra cellular membranes (ICMs) in the cytoplasm of Escherichia coli. These ICMs are particularly rich in cardiolipin (CL). Here, we have studied the effect of CL in the generation of these membranous structures. We have deleted the three genes (clsA, clsB and clsC) responsible of CL biosynthesis in E. coli and analysed the effect of these mutations by fluorescent and electron microscopy and by lipid mass spectrometry. We have found that CL is essential in the formation of non-lamellar structures in the cytoplasm of E. coli cells. These results could help to understand the structuration of membranes in E. coli and other membrane organelles, such as mitochondria and ER.
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Affiliation(s)
- Gerardo Carranza
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria - CSIC - SODERCAN, Santander, Spain
| | - Federica Angius
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, Paris, France
| | - Oana Ilioaia
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, Paris, France
| | - Audrey Solgadi
- Université Paris-Saclay, Institut Paris Saclay d'Innovation Thérapeutique, INSERM, CNRS, - Plateforme SAMM - CHATENAY-MALABRY, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS, Univ Paris Diderot, Sorbonne Paris Cité, PSL Research University, Paris, France.
| | - Ignacio Arechaga
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria - CSIC - SODERCAN, Santander, Spain.
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98
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Taylor KC, Sanders CR. Regulation of KCNQ/Kv7 family voltage-gated K + channels by lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:586-597. [PMID: 27818172 DOI: 10.1016/j.bbamem.2016.10.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 10/24/2016] [Accepted: 10/31/2016] [Indexed: 12/19/2022]
Abstract
Many years of studies have established that lipids can impact membrane protein structure and function through bulk membrane effects, by direct but transient annular interactions with the bilayer-exposed surface of protein transmembrane domains, and by specific binding to protein sites. Here, we focus on how phosphatidylinositol 4,5-bisphosphate (PIP2) and polyunsaturated fatty acids (PUFAs) impact ion channel function and how the structural details of the interactions of these lipids with ion channels are beginning to emerge. We focus on the Kv7 (KCNQ) subfamily of voltage-gated K+ channels, which are regulated by both PIP2 and PUFAs and play a variety of important roles in human health and disease. This article is part of a Special Issue entitled: Lipid order/lipid defects and lipid-control of protein activity edited by Dirk Schneider.
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Affiliation(s)
- Keenan C Taylor
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
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99
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Revin VV, Gromova NV, Revina ES, Martynova MI, Seikina AI, Revina NV, Imarova OG, Solomadin IN, Tychkov AY, Zhelev N. Role of Membrane Lipids in the Regulation of Erythrocytic Oxygen-Transport Function in Cardiovascular Diseases. BIOMED RESEARCH INTERNATIONAL 2016; 2016:3429604. [PMID: 27872848 PMCID: PMC5107249 DOI: 10.1155/2016/3429604] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/05/2016] [Accepted: 10/04/2016] [Indexed: 01/11/2023]
Abstract
The composition and condition of membrane lipids, the morphology of erythrocytes, and hemoglobin distribution were explored with the help of laser interference microscopy (LIM) and Raman spectroscopy. It is shown that patients with cardiovascular diseases (CVD) have significant changes in the composition of their phospholipids and the fatty acids of membrane lipids. Furthermore, the microviscosity of the membranes and morphology of the erythrocytes are altered causing disordered oxygen transport by hemoglobin. Basic therapy carried out with the use of antiaggregants, statins, antianginals, beta-blockers, and calcium antagonists does not help to recover the morphofunctional properties of erythrocytes. Based on the results the authors assume that, for the relief of the ischemic crisis and further therapeutic treatment, it is necessary to include, in addition to cardiovascular disease medicines, medication that increases the ability of erythrocytes' hemoglobin to transport oxygen to the tissues. We assume that the use of LIM and Raman spectroscopy is advisable for early diagnosis of changes in the structure and functional state of erythrocytes when cardiovascular diseases develop.
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Affiliation(s)
- Victor V. Revin
- Federal State-Financed Academic Institution of Higher Education “National Research Ogarev Mordovia State University”, Saransk 430005, Russia
| | - Natalia V. Gromova
- Federal State-Financed Academic Institution of Higher Education “National Research Ogarev Mordovia State University”, Saransk 430005, Russia
| | - Elvira S. Revina
- Federal State-Financed Academic Institution of Higher Education “National Research Ogarev Mordovia State University”, Saransk 430005, Russia
| | - Maria I. Martynova
- Federal State-Financed Academic Institution of Higher Education “National Research Ogarev Mordovia State University”, Saransk 430005, Russia
| | - Angelina I. Seikina
- Federal State-Financed Academic Institution of Higher Education “National Research Ogarev Mordovia State University”, Saransk 430005, Russia
| | - Nadezhda V. Revina
- Federal State-Financed Academic Institution of Higher Education “National Research Ogarev Mordovia State University”, Saransk 430005, Russia
| | - Oksana G. Imarova
- GBUZ RM “National Hospital for War Veterans”, Saransk 430005, Russia
| | - Ilia N. Solomadin
- Federal State-Financed Academic Institution of Higher Education “National Research Ogarev Mordovia State University”, Saransk 430005, Russia
| | - Alexander Yu. Tychkov
- Federal State-Financed Academic Institution of Higher Education “National Research Ogarev Mordovia State University”, Saransk 430005, Russia
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100
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Gew LT, Misran M. Energetic mixing of anti-SNAP25 on lipid monolayers: degree of saturation of C18 fatty acids. SURF INTERFACE ANAL 2016. [DOI: 10.1002/sia.6144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lai Ti Gew
- Department of Biological Sciences, Faculty of Science and Technology; Sunway University; No. 5, Jalan Universiti, Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Department of Chemistry, Faculty of Science; University of Malaya; Kuala Lumpur 50603 Malaysia
| | - Misni Misran
- Department of Chemistry, Faculty of Science; University of Malaya; Kuala Lumpur 50603 Malaysia
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