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Alfonso C, Sobrinos-Sanguino M, Luque-Ortega JR, Zorrilla S, Monterroso B, Nuero OM, Rivas G. Studying Macromolecular Interactions of Cellular Machines by the Combined Use of Analytical Ultracentrifugation, Light Scattering, and Fluorescence Spectroscopy Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:89-107. [PMID: 38507202 DOI: 10.1007/978-3-031-52193-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Cellular machines formed by the interaction and assembly of macromolecules are essential in many processes of the living cell. These assemblies involve homo- and hetero-associations, including protein-protein, protein-DNA, protein-RNA, and protein-polysaccharide associations, most of which are reversible. This chapter describes the use of analytical ultracentrifugation, light scattering, and fluorescence-based methods, well-established biophysical techniques, to characterize interactions leading to the formation of macromolecular complexes and their modulation in response to specific or unspecific factors. We also illustrate, with several examples taken from studies on bacterial processes, the advantages of the combined use of subsets of these techniques as orthogonal analytical methods to analyze protein oligomerization and polymerization, interactions with ligands, hetero-associations involving membrane proteins, and protein-nucleic acid complexes.
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Affiliation(s)
- Carlos Alfonso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Marta Sobrinos-Sanguino
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Silvia Zorrilla
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Begoña Monterroso
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Oscar M Nuero
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Germán Rivas
- Structural and Chemical Biology Department, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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2
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Baca CF, Yu Y, Rostøl JT, Majumder P, Patel DJ, Marraffini LA. The CRISPR effector Cam1 mediates membrane depolarization for phage defence. Nature 2024; 625:797-804. [PMID: 38200316 PMCID: PMC10808066 DOI: 10.1038/s41586-023-06902-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/27/2023] [Indexed: 01/12/2024]
Abstract
Prokaryotic type III CRISPR-Cas systems provide immunity against viruses and plasmids using CRISPR-associated Rossman fold (CARF) protein effectors1-5. Recognition of transcripts of these invaders with sequences that are complementary to CRISPR RNA guides leads to the production of cyclic oligoadenylate second messengers, which bind CARF domains and trigger the activity of an effector domain6,7. Whereas most effectors degrade host and invader nucleic acids, some are predicted to contain transmembrane helices without an enzymatic function. Whether and how these CARF-transmembrane helix fusion proteins facilitate the type III CRISPR-Cas immune response remains unknown. Here we investigate the role of cyclic oligoadenylate-activated membrane protein 1 (Cam1) during type III CRISPR immunity. Structural and biochemical analyses reveal that the CARF domains of a Cam1 dimer bind cyclic tetra-adenylate second messengers. In vivo, Cam1 localizes to the membrane, is predicted to form a tetrameric transmembrane pore, and provides defence against viral infection through the induction of membrane depolarization and growth arrest. These results reveal that CRISPR immunity does not always operate through the degradation of nucleic acids, but is instead mediated via a wider range of cellular responses.
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Affiliation(s)
- Christian F Baca
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University and Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - You Yu
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jakob T Rostøl
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Puja Majumder
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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3
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Mégret-Cavalier M, Pozza A, Cece Q, Bonneté F, Broutin I, Phan G. Starting with an Integral Membrane Protein Project for Structural Biology: Production, Purification, Detergent Quantification, and Buffer Optimization-Case Study of the Exporter CntI from Pseudomonas aeruginosa. Methods Mol Biol 2024; 2715:415-430. [PMID: 37930543 DOI: 10.1007/978-1-0716-3445-5_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Production, extraction, purification, and stabilization of integral membrane proteins are key steps for successful structural biology studies, in particular for X-ray crystallography or single particle microscopy. Here, we present the purification protocol of CntI from Pseudomonas aeruginosa, a new metallophore exporter of the Drug Metabolite Transporter (DMT) family involved in pseudopaline secretion. Subsequent to CntI purification, we optimized the buffer pH, salts, and additives by differential scanning fluorimetry (DSF), also known as Thermofluor Assay (TFA) or fluorescent thermal stability assay (FTSA), with the use of dye 1-AnilinoNaphthalene-8-Sulfonic acid (ANS), a fluorescent molecule compatible with detergents. After the buffer optimization, the purified CntI was analyzed by Size Exclusion Chromatography coupled with Multi-Angle Laser Light Scattering (SEC-MALLS), UV absorbance, and Refractive Index detectors, in order to determine the absolute molar mass of the protein-detergent complex, the detergent amount bound to the protein and the amount of protein-free detergent micelles. Altogether, these biophysical techniques give preliminary and mandatory information about the suitability of the purified membrane protein for further biophysical or structural investigations.
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Affiliation(s)
- Maxime Mégret-Cavalier
- Université Paris Cité, CNRS, UMR 8038, Laboratoire CiTCoM (Cibles Thérapeutiques et Conception de Médicaments), Faculté de Pharmacie de Paris, Paris, France
| | - Alexandre Pozza
- Université Paris Cité, CNRS, UMR 7099, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Quentin Cece
- Université Paris Cité, CNRS, UMR 8038, Laboratoire CiTCoM (Cibles Thérapeutiques et Conception de Médicaments), Faculté de Pharmacie de Paris, Paris, France
| | - Françoise Bonneté
- Université Paris Cité, CNRS, UMR 7099, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, Paris, France
| | - Isabelle Broutin
- Université Paris Cité, CNRS, UMR 8038, Laboratoire CiTCoM (Cibles Thérapeutiques et Conception de Médicaments), Faculté de Pharmacie de Paris, Paris, France.
| | - Gilles Phan
- Université Paris Cité, CNRS, UMR 8038, Laboratoire CiTCoM (Cibles Thérapeutiques et Conception de Médicaments), Faculté de Pharmacie de Paris, Paris, France.
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Yeow J, Luo M, Chng SS. Molecular mechanism of phospholipid transport at the bacterial outer membrane interface. Nat Commun 2023; 14:8285. [PMID: 38092770 PMCID: PMC10719372 DOI: 10.1038/s41467-023-44144-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria is an asymmetric lipid bilayer with outer leaflet lipopolysaccharides and inner leaflet phospholipids (PLs). This unique lipid asymmetry renders the OM impermeable to external insults, including antibiotics and bile salts. To maintain this barrier, the OmpC-Mla system removes mislocalized PLs from the OM outer leaflet, and transports them to the inner membrane (IM); in the first step, the OmpC-MlaA complex transfers PLs to the periplasmic chaperone MlaC, but mechanistic details are lacking. Here, we biochemically and structurally characterize the MlaA-MlaC transient complex. We map the interaction surfaces between MlaA and MlaC in Escherichia coli, and show that electrostatic interactions are important for MlaC recruitment to the OM. We further demonstrate that interactions with MlaC modulate conformational states in MlaA. Finally, we solve a 2.9-Å cryo-EM structure of a disulfide-trapped OmpC-MlaA-MlaC complex in nanodiscs, reinforcing the mechanism of MlaC recruitment, and highlighting membrane thinning as a plausible strategy for directing lipids for transport. Our work offers critical insights into retrograde PL transport by the OmpC-Mla system in maintaining OM lipid asymmetry.
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Affiliation(s)
- Jiang Yeow
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Min Luo
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117558, Singapore
- Center for Bioimaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, 117557, Singapore
| | - Shu-Sin Chng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore (SCELSE-NUS), Singapore, 117456, Singapore.
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Kristensen SS, Lukassen MV, Siebenhaar S, Diep DB, Morth JP, Mathiesen G. Lactiplantibacillus plantarum as a novel platform for production and purification of integral membrane proteins using RseP as the benchmark. Sci Rep 2023; 13:14361. [PMID: 37658186 PMCID: PMC10474122 DOI: 10.1038/s41598-023-41559-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023] Open
Abstract
The present study describes a detailed procedure for expressing and purifying the integral membrane protein RseP using the pSIP system and Lactiplantibacillus plantarum as an expression host. RseP is a membrane-bound site-2-protease and a known antibacterial target in multiple human pathogens. In the present study, we screened five RseP orthologs from Gram-positive bacteria and found RseP from Enterococcus faecium (EfmRseP) to yield the highest protein levels. The production conditions were optimized and EfmRseP was purified by immobilized metal ion affinity chromatography followed by size-exclusion chromatography. The purification resulted in an overall yield of approximately 1 mg of pure protein per 3 g of wet-weight cell pellet. The structural integrity of the purified protein was confirmed using circular dichroism. We further assessed the expression and purification of RseP from E. faecium in the Gram-negative Escherichia coli. Detection of soluble protein failed in two of the three E. coli strains tested. Purification of EfmRseP expressed in E. coli C43(DE3) resulted in a protein with lower purity compared to EfmRseP expressed in L. plantarum. To our knowledge, this is the first time L. plantarum and the pSIP expression system have been applied for the production of membrane proteins.
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Affiliation(s)
- Sofie S Kristensen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
| | - Marie V Lukassen
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Suzana Siebenhaar
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), Kongens Lyngby, Denmark
| | - Dzung B Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - J Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), Kongens Lyngby, Denmark.
| | - Geir Mathiesen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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Tavoulari S, Sichrovsky M, Kunji ERS. Fifty years of the mitochondrial pyruvate carrier: New insights into its structure, function, and inhibition. Acta Physiol (Oxf) 2023; 238:e14016. [PMID: 37366179 PMCID: PMC10909473 DOI: 10.1111/apha.14016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
The mitochondrial pyruvate carrier (MPC) resides in the mitochondrial inner membrane, where it links cytosolic and mitochondrial metabolism by transporting pyruvate produced in glycolysis into the mitochondrial matrix. Due to its central metabolic role, it has been proposed as a potential drug target for diabetes, non-alcoholic fatty liver disease, neurodegeneration, and cancers relying on mitochondrial metabolism. Little is known about the structure and mechanism of MPC, as the proteins involved were only identified a decade ago and technical difficulties concerning their purification and stability have hindered progress in functional and structural analyses. The functional unit of MPC is a hetero-dimer comprising two small homologous membrane proteins, MPC1/MPC2 in humans, with the alternative complex MPC1L/MPC2 forming in the testis, but MPC proteins are found throughout the tree of life. The predicted topology of each protomer consists of an amphipathic helix followed by three transmembrane helices. An increasing number of inhibitors are being identified, expanding MPC pharmacology and providing insights into the inhibitory mechanism. Here, we provide critical insights on the composition, structure, and function of the complex and we summarize the different classes of small molecule inhibitors and their potential in therapeutics.
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Affiliation(s)
- Sotiria Tavoulari
- Medical Research Council Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Maximilian Sichrovsky
- Medical Research Council Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Edmund R. S. Kunji
- Medical Research Council Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
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7
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Bayrak M, Mata J, Conn C, Floury J, Logan A. Application of small angle scattering (SAS) in structural characterisation of casein and casein-based products during digestion. Food Res Int 2023; 169:112810. [PMID: 37254386 DOI: 10.1016/j.foodres.2023.112810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/01/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
In recent years, small and ultra-small angle scattering techniques, collectively known as small angle scattering (SAS) have been used to study various food structures during the digestion process. These techniques play an important role in structural characterisation due to the non-destructive nature (especially when using neutrons), various in situ capabilities and a large length scale (of 1 nm to ∼20 μm) they cover. The application of these techniques in the structural characterisation of dairy products has expanded significantly in recent years. Casein, a major dairy protein, forms the basis of a wide range of gel structures at different length scales. These gel structures have been extensively researched utilising scattering techniques to obtain structural information at the nano and micron scale that complements electron and confocal microscopy. Especially, neutrons have provided opportunity to study these gels in their natural environment by using various in situ options. One such example is understanding changes in casein gel structures during digestion in the gastrointestinal tract, which is essential for designing personalised food structures for a wide range of food-related diseases and improve health outcomes. In this review, we present an overview of casein gels investigated using small angle and ultra-small angle scattering techniques. We also reviewed their digestion using newly built setups recently employed in various research. To gain a greater understanding of micro and nano-scale structural changes during digestion, such as the effect of digestive juices and mechanical breakdown on structure, new setups for semi-solid food materials are needed to be optimised.
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Affiliation(s)
- Meltem Bayrak
- CSIRO Agriculture and Food, 671 Sneydes Road, Werribee, Victoria 3030, Australia; School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia.
| | - Jitendra Mata
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia.
| | - Charlotte Conn
- School of Science, College of Science, Engineering and Health, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia.
| | | | - Amy Logan
- CSIRO Agriculture and Food, 671 Sneydes Road, Werribee, Victoria 3030, Australia.
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VanderWal AR, Park JU, Polevoda B, Nicosia JK, Vargas AMM, Kellogg EH, O’Connell MR. Csx28 is a membrane pore that enhances CRISPR-Cas13b-dependent antiphage defense. Science 2023; 380:410-415. [PMID: 37104586 PMCID: PMC10228660 DOI: 10.1126/science.abm1184] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/27/2023] [Indexed: 04/29/2023]
Abstract
Type VI CRISPR-Cas systems use RNA-guided ribonuclease (RNase) Cas13 to defend bacteria against viruses, and some of these systems encode putative membrane proteins that have unclear roles in Cas13-mediated defense. We show that Csx28, of type VI-B2 systems, is a transmembrane protein that assists to slow cellular metabolism upon viral infection, increasing antiviral defense. High-resolution cryo-electron microscopy reveals that Csx28 forms an octameric pore-like structure. These Csx28 pores localize to the inner membrane in vivo. Csx28's antiviral activity in vivo requires sequence-specific cleavage of viral messenger RNAs by Cas13b, which subsequently results in membrane depolarization, slowed metabolism, and inhibition of sustained viral infection. Our work suggests a mechanism by which Csx28 acts as a downstream, Cas13b-dependent effector protein that uses membrane perturbation as an antiviral defense strategy.
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Affiliation(s)
- Arica R. VanderWal
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | - Jung-Un Park
- Department of Molecular Biology and Genetics, Cornell University; Ithaca, USA
| | - Bogdan Polevoda
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | - Julia K. Nicosia
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | - Adrian M. Molina Vargas
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
| | | | - Mitchell R. O’Connell
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester; Rochester, USA
- Center for RNA Biology, University of Rochester; Rochester, USA
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Wang Z, Ding W, Ruan M, Liu Y, Yang J, Zhang H, Shen B, Wang J, Li Y. NMR and Patch-Clamp Characterization of Yeast Mitochondrial Pyruvate Carrier Complexes. Biomolecules 2023; 13:biom13050719. [PMID: 37238591 DOI: 10.3390/biom13050719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/07/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
The mitochondrial pyruvate carrier (Mpc) plays an indispensable role in the transport of pyruvates across the mitochondrial inner membrane. Despite the two distinct homologous proteins, Mpc1 and Mpc2, were identified in 2012, there are still controversies on the basic functional units and oligomeric state of Mpc complexes. In this study, yeast Mpc1 and Mpc2 proteins were expressed in a prokaryotic heterologous system. Both homo- and hetero-dimers were successfully reconstituted in mixed detergents. Interactions among Mpc monomers were recorded utilizing paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) methods. By single-channel patch-clamp assays, we discovered that both the Mpc1-Mpc2 hetero-dimer and Mpc1 homo-dimer are able to transport K+ ions. Furthermore, the Mpc1-Mpc2 hetero-dimer demonstrated the ability to transport pyruvates, at a rate significantly higher than that of the Mpc1 homo-dimer, indicating that it could be the basic functional unit of Mpc complexes. Our findings provide valuable insights for further structural determination and the study of the transport mechanism of Mpc complexes.
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Affiliation(s)
- Zhen Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Hefei Institutes of Physical Science (Branch of Graduate School), University of Science and Technology of China, Hefei 230026, China
| | - Wen Ding
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Maosen Ruan
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yong Liu
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Hefei Institutes of Physical Science (Branch of Graduate School), University of Science and Technology of China, Hefei 230026, China
| | - Jing Yang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Huiqin Zhang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Bing Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei 230032, China
| | - Junfeng Wang
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Hefei Institutes of Physical Science (Branch of Graduate School), University of Science and Technology of China, Hefei 230026, China
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Yunyan Li
- High Magnetic Field Laboratory, CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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Dhandapani G, Wachtel E, Patchornik G. Conjugated surfactant micelles: A non‐denaturing purification platform for concentrated human immunoglobulin G. NANO SELECT 2023. [DOI: 10.1002/nano.202200251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
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11
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Mathieu‐Gaedke M, Böker A, Glebe U. How to Characterize the Protein Structure and Polymer Conformation in Protein‐Polymer Conjugates – a Perspective. MACROMOL CHEM PHYS 2023. [DOI: 10.1002/macp.202200353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Maria Mathieu‐Gaedke
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Alexander Böker
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
| | - Ulrich Glebe
- Chair of Polymer Materials and Polymer Technologies Institute of Chemistry University of Potsdam Karl‐Liebknecht‐Str. 24–25 14476 Potsdam‐Golm Germany
- Fraunhofer Institute for Applied Polymer Research IAP Geiselbergstr. 69 14476 Potsdam‐Golm Germany
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12
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A MademoiseLLE domain binding platform links the key RNA transporter to endosomes. PLoS Genet 2022; 18:e1010269. [PMID: 35727840 PMCID: PMC9249222 DOI: 10.1371/journal.pgen.1010269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/01/2022] [Accepted: 05/20/2022] [Indexed: 11/19/2022] Open
Abstract
Spatiotemporal expression can be achieved by transport and translation of mRNAs at defined subcellular sites. An emerging mechanism mediating mRNA trafficking is microtubule-dependent co-transport on shuttling endosomes. Although progress has been made in identifying various components of the endosomal mRNA transport machinery, a mechanistic understanding of how these RNA-binding proteins are connected to endosomes is still lacking. Here, we demonstrate that a flexible MademoiseLLE (MLLE) domain platform within RNA-binding protein Rrm4 of Ustilago maydis is crucial for endosomal attachment. Our structure/function analysis uncovered three MLLE domains at the C-terminus of Rrm4 with a functionally defined hierarchy. MLLE3 recognises two PAM2-like sequences of the adaptor protein Upa1 and is essential for endosomal shuttling of Rrm4. MLLE1 and MLLE2 are most likely accessory domains exhibiting a variable binding mode for interaction with currently unknown partners. Thus, endosomal attachment of the mRNA transporter is orchestrated by a sophisticated MLLE domain binding platform. Eukaryotic cells rely on sophisticated intracellular logistics. Macromolecules like mRNA must be transported to defined subcellular destinations for local translation. This is mediated by active transport along the cytoskeleton. Endosomes are carrier vehicles that shuttle along microtubules by the action of molecular motors. It is currently unclear how mRNAs are attached mechanistically to these membranous units during transport. We study the model microorganism Ustilago maydis where numerous components of endosomal mRNA transport have already been identified. Previously, we found that the key RNA-binding protein Rrm4 interacts with the endosomal adaptor protein Upa1. Here, we perform a structure/function analysis and discovered that Rrm4 contains not one but three different versions of a protein-protein interaction domain, called the MademoiseLLE domain, to facilitate the attachment with transport endosomes. Importantly, they function with a strict hierarchy with one essential domain and the others play accessory roles. This is currently, the most detailed mechanistic description of how an RNA-binding protein and its bound cargo mRNAs are attached to endosomes. The usage of three similar protein-protein interaction domains forming a complex binding platform with a defined hierarchy might be operational also in other unknown protein-protein interactions.
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Tavoulari S, Schirris TJJ, Mavridou V, Thangaratnarajah C, King MS, Jones DTD, Ding S, Fearnley IM, Kunji ERS. Key features of inhibitor binding to the human mitochondrial pyruvate carrier hetero-dimer. Mol Metab 2022; 60:101469. [PMID: 35278701 PMCID: PMC8968063 DOI: 10.1016/j.molmet.2022.101469] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE The mitochondrial pyruvate carrier (MPC) has emerged as a promising drug target for metabolic disorders, including non-alcoholic steatohepatitis and diabetes, metabolically dependent cancers and neurodegenerative diseases. A range of structurally diverse small molecule inhibitors have been proposed, but the nature of their interaction with MPC is not understood, and the composition of the functional human MPC is still debated. The goal of this study was to characterise the human MPC protein in vitro, to understand the chemical features that determine binding of structurally diverse inhibitors and to develop novel higher affinity ones. METHODS We recombinantly expressed and purified human MPC hetero-complexes and studied their composition, transport and inhibitor binding properties by establishing in vitro transport assays, high throughput thermostability shift assays and pharmacophore modeling. RESULTS We determined that the functional unit of human MPC is a hetero-dimer. We compared all different classes of MPC inhibitors to find that three closely arranged hydrogen bond acceptors followed by an aromatic ring are shared characteristics of all inhibitors and represent the minimal requirement for high potency. We also demonstrated that high affinity binding is not attributed to covalent bond formation with MPC cysteines, as previously proposed. Following the basic pharmacophore properties, we identified 14 new inhibitors of MPC, one outperforming compound UK5099 by tenfold. Two are the commonly prescribed drugs entacapone and nitrofurantoin, suggesting an off-target mechanism associated with their adverse effects. CONCLUSIONS This work defines the composition of human MPC and the essential MPC inhibitor characteristics. In combination with the functional assays we describe, this new understanding will accelerate the development of clinically relevant MPC modulators.
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Affiliation(s)
- Sotiria Tavoulari
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
| | - Tom J J Schirris
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Vasiliki Mavridou
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Chancievan Thangaratnarajah
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Daniel T D Jones
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Shujing Ding
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Ian M Fearnley
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
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14
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Weiler AJ, Spitz O, Gudzuhn M, Schott-Verdugo SN, Kamel M, Thiele B, Streit WR, Kedrov A, Schmitt L, Gohlke H, Kovacic F. A phospholipase B from Pseudomonas aeruginosa with activity towards endogenous phospholipids affects biofilm assembly. Biochim Biophys Acta Mol Cell Biol Lipids 2022; 1867:159101. [DOI: 10.1016/j.bbalip.2021.159101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/29/2022]
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15
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Rashid I, Tsai MS, Sverzhinsky A, Hlaing AS, Shih B, Thwin AC, Lin JG, Maw SS, Pascal JM, Tomkinson AE. Purification and Characterization of Human DNA Ligase IIIα Complexes After Expression in Insect Cells. Methods Mol Biol 2022; 2444:243-269. [PMID: 35290642 PMCID: PMC9278544 DOI: 10.1007/978-1-0716-2063-2_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
With improvements in biophysical approaches, there is growing interest in characterizing large, flexible multi-protein complexes. The use of recombinant baculoviruses to express heterologous genes in cultured insect cells has advantages for the expression of human protein complexes because of the ease of co-expressing multiple proteins in insect cells and the presence of a conserved post-translational machinery that introduces many of the same modifications found in human cells. Here we describe the preparation of recombinant baculoviruses expressing DNA ligase IIIα, XRCC1, and TDP1, their subsequent co-expression in cultured insect cells, the purification of complexes containing DNA ligase IIIα from insect cell lysates, and their characterization by multi-angle light scattering linked to size exclusion chromatography and negative stain electron microscopy.
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Affiliation(s)
- Ishtiaque Rashid
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Miaw-Sheue Tsai
- Biological Systems and Engineering Division, Department of BioEngineering & BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Aye Su Hlaing
- Biological Systems and Engineering Division, Department of BioEngineering & BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brian Shih
- Biological Systems and Engineering Division, Department of BioEngineering & BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aye C Thwin
- Biological Systems and Engineering Division, Department of BioEngineering & BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Judy G Lin
- Biological Systems and Engineering Division, Department of BioEngineering & BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Su S Maw
- Biological Systems and Engineering Division, Department of BioEngineering & BioMedical Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA.
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16
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Hwang J, Park K, Lee GY, Yoon BY, Kim H, Roh SH, Lee BC, Kim K, Lim HH. Transmembrane topology and oligomeric nature of an astrocytic membrane protein, MLC1. Open Biol 2021; 11:210103. [PMID: 34847774 PMCID: PMC8633789 DOI: 10.1098/rsob.210103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
MLC1 is a membrane protein mainly expressed in astrocytes, and genetic mutations lead to the development of a leukodystrophy, megalencephalic leukoencephalopathy with subcortical cysts disease. Currently, the biochemical properties of the MLC1 protein are largely unknown. In this study, we aimed to characterize the transmembrane (TM) topology and oligomeric nature of the MLC1 protein. Systematic immunofluorescence staining data revealed that the MLC1 protein has eight TM domains and that both the N- and C-terminus face the cytoplasm. We found that MLC1 can be purified as an oligomer and could form a trimeric complex in both detergent micelles and reconstituted proteoliposomes. Additionally, a single-molecule photobleaching experiment showed that MLC1 protein complexes could consist of three MLC1 monomers in the reconstituted proteoliposomes. These results can provide a basis for both the high-resolution structural determination and functional characterization of the MLC1 protein.
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Affiliation(s)
- Junmo Hwang
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), 61 Cheomdan-ro, Dong-gu, Daegu 41068, Republic of Korea
| | - Kunwoong Park
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), 61 Cheomdan-ro, Dong-gu, Daegu 41068, Republic of Korea
| | - Ga-Young Lee
- Brain Research Core Facility, Korea Brain Research Institute (KBRI), Daegu, Republic of Korea
| | - Bo Young Yoon
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), 61 Cheomdan-ro, Dong-gu, Daegu 41068, Republic of Korea
| | - Hyunmin Kim
- School of Biological Science, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Sung Hoon Roh
- School of Biological Science, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Byoung-Cheol Lee
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), 61 Cheomdan-ro, Dong-gu, Daegu 41068, Republic of Korea
| | - Kipom Kim
- Brain Research Core Facility, Korea Brain Research Institute (KBRI), Daegu, Republic of Korea
| | - Hyun-Ho Lim
- Neurovascular Unit Research Group, Korea Brain Research Institute (KBRI), 61 Cheomdan-ro, Dong-gu, Daegu 41068, Republic of Korea,Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
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17
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Biophysical and functional characterization of the human TAS1R2 sweet taste receptor overexpressed in a HEK293S inducible cell line. Sci Rep 2021; 11:22238. [PMID: 34782704 PMCID: PMC8593021 DOI: 10.1038/s41598-021-01731-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/01/2021] [Indexed: 01/02/2023] Open
Abstract
Sweet taste perception is mediated by a heterodimeric receptor formed by the assembly of the TAS1R2 and TAS1R3 subunits. TAS1R2 and TAS1R3 are class C G-protein-coupled receptors whose members share a common topology, including a large extracellular N-terminal domain (NTD) linked to a seven transmembrane domain (TMD) by a cysteine-rich domain. TAS1R2-NTD contains the primary binding site for sweet compounds, including natural sugars and high-potency sweeteners, whereas the TAS1R2-TMD has been shown to bind a limited number of sweet tasting compounds. To understand the molecular mechanisms governing receptor–ligand interactions, we overexpressed the human TAS1R2 (hTAS1R2) in a stable tetracycline-inducible HEK293S cell line and purified the detergent-solubilized receptor. Circular dichroism spectroscopic studies revealed that hTAS1R2 was properly folded with evidence of secondary structures. Using size exclusion chromatography coupled to light scattering, we found that the hTAS1R2 subunit is a dimer. Ligand binding properties were quantified by intrinsic tryptophan fluorescence. Due to technical limitations, natural sugars have not been tested. However, we showed that hTAS1R2 is capable of binding high potency sweeteners with Kd values that are in agreement with physiological detection. This study offers a new experimental strategy to identify new sweeteners or taste modulators that act on the hTAS1R2 and is a prerequisite for structural query and biophysical studies.
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18
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Neves AT, Stenner R, Race PR, Curnow P. Expression, purification and preliminary characterisation of the choline transporter LicB from opportunistic bacterial pathogens. Protein Expr Purif 2021; 190:106011. [PMID: 34737041 DOI: 10.1016/j.pep.2021.106011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/31/2021] [Indexed: 11/28/2022]
Abstract
Many opportunistic bacteria that infect the upper respiratory tract decorate their cell surface with phosphorylcholine to support colonisation and outgrowth. These surface modifications require the active import of choline from the host environment, a process thought to be mediated by a family of dedicated integral membrane proteins that act as choline permeases. Here, we present the expression and purification of the archetype of these choline transporters, LicB from Haemophilus influenzae. We show that LicB can be recombinantly produced in Escherichia coli and purified to homogeneity in a stable, folded state using the detergent n-dodecyl-β-d-maltopyranoside. Equilibrium binding studies with the fluorescent ligand dansylcholine suggest that LicB is selective towards choline, with reduced affinity for acetylcholine and no apparent activity towards other small molecules including glycine, carnitine and betaine. We also identify a conserved sequence motif within the LicB family and show that mutations within this motif compromise protein structure and function. Our results are consistent with previous observations that LicB is a specific high-affinity choline transporter, and provide an experimental platform for further studies of this permease family.
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Affiliation(s)
| | | | - Paul R Race
- School of Biochemistry, University of Bristol, UK
| | - Paul Curnow
- School of Biochemistry, University of Bristol, UK.
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19
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Ferens FG, Summers WAT, Bharaj A, Stetefeld J, Court DA. A C-Terminally Truncated Variant of Neurospora crassa VDAC Assembles Into a Partially Functional Form in the Mitochondrial Outer Membrane and Forms Multimers in vitro. Front Physiol 2021; 12:739001. [PMID: 34603088 PMCID: PMC8485043 DOI: 10.3389/fphys.2021.739001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/11/2021] [Indexed: 11/23/2022] Open
Abstract
The voltage-dependent anion-selective channel (VDAC) is a porin in the mitochondrial outer membrane (MOM). Unlike bacterial porins, several mitochondrial β-barrels comprise an odd number of β-strands, as is the case for the 19-β-stranded VDAC. Previously, a variant of a VDAC from Neurospora crassa, VDAC-ΔC, lacking the predicted 19th β-strand, was found to form gated, anion-selective channels in artificial membranes. In vivo, the two C-terminal β-strands (β18 and β19) in VDAC form a β-hairpin necessary for import from the cytoplasm into mitochondria and the β-signal required for assembly in the mitochondrial outer membrane resides in β19. The current study demonstrated that the putative 18-stranded β-barrel formed by VDAC-ΔC can be imported and assembled in the MOM in vivo and can also partially rescue the phenotype associated with the deletion of VDAC from a strain of N. crassa. Furthermore, when expressed and purified from Escherichia coli, VDAC-ΔC can be folded into a β-strand-rich form in decyl-maltoside. Size exclusion chromatography (SEC) alone or combined with multi-angle light scattering (SEC-MALS) and analytical ultracentrifugation revealed that, unlike full-length VDACs, VDAC-ΔC can self-organize into dimers and higher order oligomers in the absence of sterol.
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Affiliation(s)
- Fraser G Ferens
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | | | - Ameet Bharaj
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
| | - Deborah A Court
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
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20
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Majeed S, Ahmad AB, Sehar U, Georgieva ER. Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins. MEMBRANES 2021; 11:685. [PMID: 34564502 PMCID: PMC8470526 DOI: 10.3390/membranes11090685] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.
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Affiliation(s)
- Saman Majeed
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Akram Bani Ahmad
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Ujala Sehar
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Elka R Georgieva
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Science Center, Lubbock, TX 79409, USA
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21
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Amaya C, Cameron CJF, Devarkar SC, Seager SJH, Gerstein MB, Xiong Y, Schlieker C. Nodal modulator (NOMO) is required to sustain endoplasmic reticulum morphology. J Biol Chem 2021; 297:100937. [PMID: 34224731 PMCID: PMC8327139 DOI: 10.1016/j.jbc.2021.100937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 06/24/2021] [Accepted: 07/01/2021] [Indexed: 12/03/2022] Open
Abstract
The endoplasmic reticulum (ER) is a membrane-bound organelle responsible for protein folding, lipid synthesis, and calcium homeostasis. Maintenance of ER structural integrity is crucial for proper function, but much remains to be learned about the molecular players involved. To identify proteins that support the structure of the ER, we performed a proteomic screen and identified nodal modulator (NOMO), a widely conserved type I transmembrane protein of unknown function, with three nearly identical orthologs specified in the human genome. We found that overexpression of NOMO1 imposes a sheet morphology on the ER, whereas depletion of NOMO1 and its orthologs causes a collapse of ER morphology concomitant with the formation of membrane-delineated holes in the ER network positive for the lysosomal marker lysosomal-associated protein 1. In addition, the levels of key players of autophagy including microtubule-associated protein light chain 3 and autophagy cargo receptor p62/sequestosome 1 strongly increase upon NOMO depletion. In vitro reconstitution of NOMO1 revealed a "beads on a string" structure likely representing consecutive immunoglobulin-like domains. Extending NOMO1 by insertion of additional immunoglobulin folds results in a correlative increase in the ER intermembrane distance. Based on these observations and a genetic epistasis analysis including the known ER-shaping proteins Atlastin2 and Climp63, we propose a role for NOMO1 in the functional network of ER-shaping proteins.
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Affiliation(s)
- Catherine Amaya
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Christopher J F Cameron
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Swapnil C Devarkar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Sebastian J H Seager
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Mark B Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA; Department of Computer Science, Yale University, New Haven, Connecticut, USA; Department of Statistics and Data Science, Yale University, New Haven, Connecticut, USA
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA
| | - Christian Schlieker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA; Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA.
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22
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The mitochondrial ADP/ATP carrier exists and functions as a monomer. Biochem Soc Trans 2021; 48:1419-1432. [PMID: 32725219 PMCID: PMC7458400 DOI: 10.1042/bst20190933] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
For more than 40 years, the oligomeric state of members of the mitochondrial carrier family (SLC25) has been the subject of debate. Initially, the consensus was that they were dimeric, based on the application of a large number of different techniques. However, the structures of the mitochondrial ADP/ATP carrier, a member of the family, clearly demonstrated that its structural fold is monomeric, lacking a conserved dimerisation interface. A re-evaluation of previously published data, with the advantage of hindsight, concluded that technical errors were at the basis of the earlier dimer claims. Here, we revisit this topic, as new claims for the existence of dimers of the bovine ADP/ATP carrier have emerged using native mass spectrometry of mitochondrial membrane vesicles. However, the measured mass does not agree with previously published values, and a large number of post-translational modifications are proposed to account for the difference. Contrarily, these modifications are not observed in electron density maps of the bovine carrier. If they were present, they would interfere with the structure and function of the carrier, including inhibitor and substrate binding. Furthermore, the reported mass does not account for three tightly bound cardiolipin molecules, which are consistently observed in other studies and are important stabilising factors for the transport mechanism. The monomeric carrier has all of the required properties for a functional transporter and undergoes large conformational changes that are incompatible with a stable dimerisation interface. Thus, our view that the native mitochondrial ADP/ATP carrier exists and functions as a monomer remains unaltered.
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23
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Missel JW, Salustros N, Becares ER, Steffen JH, Laursen AG, Garcia AS, Garcia-Alai MM, Kolar Č, Gourdon P, Gotfryd K. Cyclohexyl-α maltoside as a highly efficient tool for membrane protein studies. Curr Res Struct Biol 2021; 3:85-94. [PMID: 34235488 PMCID: PMC8244287 DOI: 10.1016/j.crstbi.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/09/2021] [Accepted: 03/05/2021] [Indexed: 01/06/2023] Open
Abstract
Membrane proteins (MPs) constitute a large fraction of the proteome, but exhibit physicochemical characteristics that impose challenges for successful sample production crucial for subsequent biophysical studies. In particular, MPs have to be extracted from the membranes in a stable form. Reconstitution into detergent micelles represents the most common procedure in recovering MPs for subsequent analysis. n-dodecyl-β-D-maltoside (DDM) remains one of the most popular conventional detergents used in production of MPs. Here we characterize the novel DDM analogue 4-trans-(4-trans-propylcyclohexyl)-cyclohexyl α-maltoside (t-PCCαM), possessing a substantially lower critical micelle concentration (CMC) than the parental compound that represents an attractive feature when handling MPs. Using three different types of MPs of human and prokaryotic origin, i.e., a channel, a primary and a secondary active transporter, expressed in yeast and bacterial host systems, respectively, we investigate the performance of t-PCCαM in solubilization and affinity purification together with its capacity to preserve native fold and activity. Strikingly, t-PCCαM displays favorable behavior in extracting and stabilizing the three selected targets. Importantly, t-PCCαM promoted extraction of properly folded protein, enhanced thermostability and provided negatively-stained electron microscopy samples of promising quality. All-in-all, t-PCCαM emerges as competitive surfactant applicable to a broad portfolio of challenging MPs for downstream structure-function analysis.
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Affiliation(s)
- Julie Winkel Missel
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Nina Salustros
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Eva Ramos Becares
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Jonas Hyld Steffen
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Amalie Gerdt Laursen
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Maria M Garcia-Alai
- European Molecular Biology Laboratory Hamburg, Notkestrasse 85, D-22607, Hamburg, Germany.,Centre for Structural Systems Biology, Notkestrasse 85, D-22607, Hamburg, Germany
| | - Čeněk Kolar
- Glycon Biochemicals GmbH, Im Biotechnologie Park TGZ 1, D-14943, Luckenwalde, Germany
| | - Pontus Gourdon
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark.,Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84, Lund, Sweden
| | - Kamil Gotfryd
- Department of Biomedical Sciences, Copenhagen University, Maersk Tower 7-9, Nørre Allé 14, DK-2200, Copenhagen N, Denmark
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24
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Errasti-Murugarren E, Bartoccioni P, Palacín M. Membrane Protein Stabilization Strategies for Structural and Functional Studies. MEMBRANES 2021; 11:membranes11020155. [PMID: 33671740 PMCID: PMC7926488 DOI: 10.3390/membranes11020155] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Accounting for nearly two-thirds of known druggable targets, membrane proteins are highly relevant for cell physiology and pharmacology. In this regard, the structural determination of pharmacologically relevant targets would facilitate the intelligent design of new drugs. The structural biology of membrane proteins is a field experiencing significant growth as a result of the development of new strategies for structure determination. However, membrane protein preparation for structural studies continues to be a limiting step in many cases due to the inherent instability of these molecules in non-native membrane environments. This review describes the approaches that have been developed to improve membrane protein stability. Membrane protein mutagenesis, detergent selection, lipid membrane mimics, antibodies, and ligands are described in this review as approaches to facilitate the production of purified and stable membrane proteins of interest for structural and functional studies.
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Affiliation(s)
- Ekaitz Errasti-Murugarren
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
| | - Paola Bartoccioni
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
| | - Manuel Palacín
- Laboratory of Amino acid Transporters and Disease, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac 10, 08028 Barcelona, Spain;
- CIBERER (Centro Español en Red de Biomedicina de Enfermedades Raras), 28029 Barcelona, Spain
- Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, 08028 Barcelona, Spain
- Correspondence: (E.E.-M.); (M.P.)
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25
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Sauer DB, Song J, Wang B, Hilton JK, Karpowich NK, Mindell JA, Rice WJ, Wang DN. Structure and inhibition mechanism of the human citrate transporter NaCT. Nature 2021; 591:157-161. [PMID: 33597751 PMCID: PMC7933130 DOI: 10.1038/s41586-021-03230-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022]
Abstract
Citrate is most well-known as an intermediate in the TCA cycle of the cell. In addition to this essential role in energy metabolism, the tricarboxylate anion also acts as both a precursor and a regulator of fatty acid synthesis 1–3. Thus, the rate of fatty acid synthesis correlates directly with the cytosolic citrate concentration 4,5. Liver cells import citrate via the sodium-dependent citrate transporter NaCT (SLC13A5), and as a consequence this protein is a potential target for anti-obesity drugs. To understand the structural basis of its inhibition mechanism, we have determined cryo-electron microscopy structures of human NaCT in complex with citrate and with a small molecule inhibitor. These structures reveal how the inhibitor, bound at the same site as citrate, arrests the protein’s transport cycle. The NaCT-inhibitor structure also explains why the compound selectively inhibits NaCT over two homologous human dicarboxylate transporters, and suggests ways to further improve the affinity and selectivity. Finally, the NaCT structures provide a framework for understanding how various mutations abolish NaCT’s transport activity in the brain and thereby cause SLC13A5-Epilepsy in newborns 6–8.
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Affiliation(s)
- David B Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA
| | - Jacob K Hilton
- Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Nathan K Karpowich
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.,Department of Cell Biology, New York University School of Medicine, New York, NY, USA.,Janssen Pharmaceuticals, Spring House, PA, USA
| | - Joseph A Mindell
- Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - William J Rice
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA. .,Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY, USA.
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA. .,Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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26
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Functional Characterization of the γ-Aminobutyric Acid Transporter from Mycobacterium smegmatis MC 2 155 Reveals Sodium-Driven GABA Transport. J Bacteriol 2021; 203:JB.00642-20. [PMID: 33288625 PMCID: PMC7847548 DOI: 10.1128/jb.00642-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 12/01/2022] Open
Abstract
The spread of multidrug-resistant tuberculosis increases its global health impact in humans. As there is transmission both to and from animals, the spread of the disease also increases its effects in a broad range of animal species. Characterizing the mycobacterial transporters involved in the uptake and/or catabolism of host-derived nutrients required by mycobacteria may identify novel drug targets against tuberculosis. Here, we identify and characterize a member of the amino acid-polyamine-organocation superfamily, a potential γ-aminobutyric acid (GABA) transport protein, GabP, from Mycobacterium smegmatis. The protein was expressed to a level allowing its purification to homogeneity, and size exclusion chromatography coupled with multiangle laser light scattering (SEC-MALLS) analysis of the purified protein showed that it was dimeric. We showed that GabP transported γ-aminobutyric acid both in vitro and when overexpressed in E. coli. Additionally, transport was greatly reduced in the presence of β-alanine, suggesting it could be either a substrate or inhibitor of GabP. Using GabP reconstituted into proteoliposomes, we demonstrated that γ-aminobutyric acid uptake is driven by the sodium gradient and is stimulated by membrane potential. Molecular docking showed that γ-aminobutyric acid binds MsGabP, another Mycobacterium smegmatis putative GabP, and the Mycobacterium tuberculosis homologue in the same manner. This study represents the first expression, purification, and characterization of an active γ-aminobutyric acid transport protein from mycobacteria. IMPORTANCE The spread of multidrug-resistant tuberculosis increases its global health impact in humans. As there is transmission both to and from animals, the spread of the disease also increases its effects in a broad range of animal species. Identifying new mycobacterial transporters will enhance our understanding of mycobacterial physiology and, furthermore, provides new drug targets. Our target protein is the gene product of msmeg_6196, annotated as GABA permease, from Mycobacterium smegmatis strain MC2 155. Our current study demonstrates it is a sodium-dependent GABA transporter that may also transport β-alanine. As GABA may well be an essential nutrient for mycobacterial metabolism inside the host, this could be an attractive target for the development of new drugs against tuberculosis.
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27
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Carvalho V, Prabudiansyah I, Kovacik L, Chami M, Kieffer R, van der Valk R, de Lange N, Engel A, Aubin-Tam ME. The cytoplasmic domain of the AAA+ protease FtsH is tilted with respect to the membrane to facilitate substrate entry. J Biol Chem 2021; 296:100029. [PMID: 33154162 PMCID: PMC7949044 DOI: 10.1074/jbc.ra120.014739] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/28/2020] [Accepted: 11/05/2020] [Indexed: 11/06/2022] Open
Abstract
AAA+ proteases are degradation machines that use ATP hydrolysis to unfold protein substrates and translocate them through a central pore toward a degradation chamber. FtsH, a bacterial membrane-anchored AAA+ protease, plays a vital role in membrane protein quality control. How substrates reach the FtsH central pore is an open key question that is not resolved by the available atomic structures of cytoplasmic and periplasmic domains. In this work, we used both negative stain TEM and cryo-EM to determine 3D maps of the full-length Aquifex aeolicus FtsH protease. Unexpectedly, we observed that detergent solubilization induces the formation of fully active FtsH dodecamers, which consist of two FtsH hexamers in a single detergent micelle. The striking tilted conformation of the cytosolic domain in the FtsH dodecamer visualized by negative stain TEM suggests a lateral substrate entrance between the membrane and cytosolic domain. Such a substrate path was then resolved in the cryo-EM structure of the FtsH hexamer. By mapping the available structural information and structure predictions for the transmembrane helices to the amino acid sequence we identified a linker of ∼20 residues between the second transmembrane helix and the cytosolic domain. This unique polypeptide appears to be highly flexible and turned out to be essential for proper functioning of FtsH as its deletion fully eliminated the proteolytic activity of FtsH.
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Affiliation(s)
- Vanessa Carvalho
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Irfan Prabudiansyah
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Lubomir Kovacik
- BioEM Lab, C-CINA, Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland
| | - Mohamed Chami
- BioEM Lab, C-CINA, Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland
| | - Roland Kieffer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Ramon van der Valk
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Nick de Lange
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Andreas Engel
- BioEM Lab, C-CINA, Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Basel, Switzerland.
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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28
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Pols T, Singh S, Deelman‐Driessen C, Gaastra BF, Poolman B. Enzymology of the pathway for ATP production by arginine breakdown. FEBS J 2021; 288:293-309. [PMID: 32306469 PMCID: PMC7818446 DOI: 10.1111/febs.15337] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 01/02/2023]
Abstract
In cells, the breakdown of arginine to ornithine and ammonium ion plus carbon dioxide is coupled to the generation of metabolic energy in the form of ATP. The arginine breakdown pathway is minimally composed of arginine deiminase, ornithine transcarbamoylase, carbamate kinase, and an arginine/ornithine antiporter; ammonia and carbon dioxide most likely diffuse passively across the membrane. The genes for the enzymes and transporter have been cloned and expressed, and the proteins have been purified from Lactococcus lactis IL1403 and incorporated into lipid vesicles for sustained production of ATP. Here, we study the kinetic parameters and biochemical properties of the individual enzymes and the antiporter, and we determine how the physicochemical conditions, effector composition, and effector concentration affect the enzymes. We report the KM and VMAX values for catalysis and the native oligomeric state of all proteins, and we measured the effect of pathway intermediates, pH, temperature, freeze-thaw cycles, and salts on the activity of the cytosolic enzymes. We also present data on the protein-to-lipid ratio and lipid composition dependence of the antiporter.
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Affiliation(s)
- Tjeerd Pols
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
| | - Shubham Singh
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
| | - Cecile Deelman‐Driessen
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
| | - Bauke F. Gaastra
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
| | - Bert Poolman
- Department of BiochemistryGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced MaterialsUniversity of GroningenThe Netherlands
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29
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Prabudiansyah I, van der Valk R, Aubin-Tam ME. Reconstitution and functional characterization of the FtsH protease in lipid nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183526. [PMID: 33278347 DOI: 10.1016/j.bbamem.2020.183526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/19/2020] [Accepted: 11/24/2020] [Indexed: 01/09/2023]
Abstract
FtsH is a membrane-bound protease that plays a crucial role in proteolytic regulation of many cellular functions. It is universally conserved in bacteria and responsible for the degradation of misfolded or misassembled proteins. A recent study has determined the structure of bacterial FtsH in detergent micelles. To properly study the function of FtsH in a native-like environment, we reconstituted the FtsH complex into lipid nanodiscs. We found that FtsH in membrane scaffold protein (MSP) nanodiscs maintains its native hexameric conformation and is functionally active. We further investigated the effect of the lipid bilayer composition (acyl chain length, saturation, head group charge and size) on FtsH proteolytic activity. We found that the lipid acyl chain length influences AaFtsH activity in nanodiscs, with the greatest activity in a bilayer of di-C18:1 PC. We conclude that MSP nanodiscs are suitable model membranes for further in vitro studies of the FtsH protease complex.
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Affiliation(s)
- Irfan Prabudiansyah
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, the Netherlands
| | - Ramon van der Valk
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, the Netherlands
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, Delft, 2629 HZ, the Netherlands.
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30
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Abel S, Marchi M, Solier J, Finet S, Brillet K, Bonneté F. Structural insights into the membrane receptor ShuA in DDM micelles and in a model of gram-negative bacteria outer membrane as seen by SAXS and MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183504. [PMID: 33157097 DOI: 10.1016/j.bbamem.2020.183504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/20/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022]
Abstract
Successful crystallization of membrane proteins in detergent micelles depends on key factors such as conformational stability of the protein in micellar assemblies, the protein-detergent complex (PDC) monodispersity and favorable protein crystal contacts by suitable shielding of the protein hydrophobic surface by the detergent belt. With the aim of studying the influence of amphiphilic environment on membrane protein structure, stability and crystallizability, we combine molecular dynamics (MD) simulations with SEC-MALLS and SEC-SAXS (Size Exclusion Chromatography in line with Multi Angle Laser Light Scattering or Small Angle X-ray Scattering) experiments to describe the protein-detergent interactions that could help to rationalize PDC crystallization. In this context, we compare the protein-detergent interactions of ShuA from Shigella dysenteriae in n-Dodecyl-β-D-Maltopyranoside (DDM) with ShuA inserted in a realistic model of gram-negative bacteria outer membrane (OM) containing a mixture of bacterial lipopolysaccharide and phospholipids. To evaluate the quality of the PDC models, we compute the corresponding SAXS curves from the MD trajectories and compare with the experimental ones. We show that computed SAXS curves obtained from the MD trajectories reproduce better the SAXS obtained from the SEC-SAXS experiments for ShuA surrounded by 268 DDM molecules. The MD results show that the DDM molecules form around ShuA a closed belt whose the hydrophobic thickness appears slightly smaller (~22 Å) than the hydrophobic transmembrane domain of the protein (24.6 Å) suggested by Orientations of Proteins in Membranes (OPM) database. The simulations also show that ShuA transmembrane domain is remarkably stable in all the systems except for the extracellular and periplasmic loops that exhibit larger movements due to specific molecular interactions with lipopolysaccharides (LPS). We finally point out that this detergent behavior may lead to the occlusion of the periplasmic hydrophilic surface and poor crystal contacts leading to difficulties in crystallization of ShuA in DDM.
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Affiliation(s)
- Stéphane Abel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Massimo Marchi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Justine Solier
- Laboratoire d'Electrochimie et de Physico-chimie des Matériaux et des Interfaces, UMR 5279 CNRS Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, INP, F38000 Grenoble, France
| | - Stéphanie Finet
- Institut de Minéralogie, de Physique de Matériaux et de Cosmochimie, UMR 7590 CNRS-Sorbonne université, Bioinformatique et Biophysique, 4 Place Jussieu, F75005 Paris, France
| | - Karl Brillet
- Institut de Biologie Moléculaire et Cellulaire UPR 9002 CNRS, Architecture et Réactivité de l'ARN, 2 allée Konrad Roentgen, F67000 Strasbourg, France
| | - Françoise Bonneté
- Institut de Biologie Physico-Chimique (IBPC) UMR 7099 CNRS Université de Paris, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, 13 rue Pierre et Marie Curie, F75005 Paris, France.
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31
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Small-residue packing motifs modulate the structure and function of a minimal de novo membrane protein. Sci Rep 2020; 10:15203. [PMID: 32938984 PMCID: PMC7495484 DOI: 10.1038/s41598-020-71585-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/26/2020] [Indexed: 11/08/2022] Open
Abstract
Alpha-helical integral membrane proteins contain conserved sequence motifs that are known to be important in helix packing. These motifs are a promising starting point for the construction of artificial proteins, but their potential has not yet been fully explored. Here, we study the impact of introducing a common natural helix packing motif to the transmembrane domain of a genetically-encoded and structurally dynamic de novo membrane protein. The resulting construct is an artificial four-helix bundle with lipophilic regions that are defined only by the amino acids L, G, S, A and W. This minimal proto-protein could be recombinantly expressed by diverse prokaryotic and eukaryotic hosts and was found to co-sediment with cellular membranes. The protein could be extracted and purified in surfactant micelles and was monodisperse and stable in vitro, with sufficient structural definition to support the rapid binding of a heme cofactor. The reduction in conformational diversity imposed by this design also enhances the nascent peroxidase activity of the protein-heme complex. Unexpectedly, strains of Escherichia coli expressing this artificial protein specifically accumulated zinc protoporphyrin IX, a rare cofactor that is not used by natural metalloenzymes. Our results demonstrate that simple sequence motifs can rigidify elementary membrane proteins, and that orthogonal artificial membrane proteins can influence the cofactor repertoire of a living cell. These findings have implications for rational protein design and synthetic biology.
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32
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Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN. Structural basis for the reaction cycle of DASS dicarboxylate transporters. eLife 2020; 9:e61350. [PMID: 32869741 PMCID: PMC7553777 DOI: 10.7554/elife.61350] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/31/2020] [Indexed: 01/09/2023] Open
Abstract
Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release.
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Affiliation(s)
- David B Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Noah Trebesch
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Jennifer J Marden
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Nicolette Cocco
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Akiko Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
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33
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Structural and Functional Characterization of NadR from Lactococcus lactis. Molecules 2020; 25:molecules25081940. [PMID: 32331317 PMCID: PMC7221760 DOI: 10.3390/molecules25081940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/02/2022] Open
Abstract
NadR is a bifunctional enzyme that converts nicotinamide riboside (NR) into nicotinamide mononucleotide (NMN), which is then converted into nicotinamide adenine dinucleotide (NAD). Although a crystal structure of the enzyme from the Gram-negative bacterium Haemophilus influenzae is known, structural understanding of its catalytic mechanism remains unclear. Here, we purified the NadR enzyme from Lactococcus lactis and established an assay to determine the combined activity of this bifunctional enzyme. The conversion of NR into NAD showed hyperbolic dependence on the NR concentration, but sigmoidal dependence on the ATP concentration. The apparent cooperativity for ATP may be explained because both reactions catalyzed by the bifunctional enzyme (phosphorylation of NR and adenylation of NMN) require ATP. The conversion of NMN into NAD followed simple Michaelis-Menten kinetics for NMN, but again with the sigmoidal dependence on the ATP concentration. In this case, the apparent cooperativity is unexpected since only a single ATP is used in the NMN adenylyltransferase catalyzed reaction. To determine the possible structural determinants of such cooperativity, we solved the crystal structure of NadR from L. lactis (NadRLl). Co-crystallization with NAD, NR, NMN, ATP, and AMP-PNP revealed a ‘sink’ for adenine nucleotides in a location between two domains. This sink could be a regulatory site, or it may facilitate the channeling of substrates between the two domains.
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34
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Vitt S, Prinz S, Hellwig N, Morgner N, Ermler U, Buckel W. Molecular and Low-Resolution Structural Characterization of the Na +-Translocating Glutaconyl-CoA Decarboxylase From Clostridium symbiosum. Front Microbiol 2020; 11:480. [PMID: 32300335 PMCID: PMC7145394 DOI: 10.3389/fmicb.2020.00480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/05/2020] [Indexed: 11/13/2022] Open
Abstract
Some anaerobic bacteria use biotin-dependent Na+-translocating decarboxylases (Bdc) of β-keto acids or their thioester analogs as key enzymes in their energy metabolism. Glutaconyl-CoA decarboxylase (Gcd), a member of this protein family, drives the endergonic translocation of Na+ across the membrane with the exergonic decarboxylation of glutaconyl-CoA (ΔG0’ ≈−30 kJ/mol) to crotonyl-CoA. Here, we report on the molecular characterization of Gcd from Clostridium symbiosum based on native PAGE, size exclusion chromatography (SEC) and laser-induced liquid bead ion desorption mass spectrometry (LILBID-MS). The obtained molecular mass of ca. 400 kDa fits to the DNA sequence-derived mass of 379 kDa with a subunit composition of 4 GcdA (65 kDa), 2 GcdB (35 kDa), GcdC1 (15 kDa), GcdC2 (14 kDa), and 2 GcdD (10 kDa). Low-resolution structural information was achieved from preliminary electron microscopic (EM) measurements, which resulted in a 3D reconstruction model based on negative-stained particles. The Gcd structure is built up of a membrane-spanning base primarily composed of the GcdB dimer and a solvent-exposed head with the GcdA tetramer as major component. Both globular parts are bridged by a linker presumably built up of segments of GcdC1, GcdC2 and the 2 GcdDs. The structure of the highly mobile Gcd complex represents a template for the global architecture of the Bdc family.
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Affiliation(s)
- Stella Vitt
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.,Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Simone Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Nils Hellwig
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Ulrich Ermler
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Wolfgang Buckel
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
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35
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Yuan Y, Cao C, Wen M, Li M, Dong Y, Wu L, Wu J, Cui T, Li D, Chou JJ, OuYang B. Structural Characterization of the N-Terminal Domain of the Dictyostelium discoideum Mitochondrial Calcium Uniporter. ACS OMEGA 2020; 5:6452-6460. [PMID: 32258880 PMCID: PMC7114133 DOI: 10.1021/acsomega.9b04045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/20/2020] [Indexed: 06/11/2023]
Abstract
The mitochondrial calcium uniporter (MCU) plays a critical role in mitochondrial calcium uptake into the matrix. In metazoans, the uniporter is a tightly regulated multicomponent system, including the pore-forming subunit MCU and several regulators (MICU1, MICU2, and Essential MCU REgulator, EMRE). The calcium-conducting activity of metazoan MCU requires the single-transmembrane protein EMRE. Dictyostelium discoideum (Dd), however, developed a simplified uniporter for which the pore-forming MCU (DdMCU) alone is necessary and sufficient for calcium influx. Here, we report a crystal structure of the N-terminal domain (NTD) of DdMCU at 1.7 Å resolution. The DdMCU-NTD contains four helices and two strands arranged in a fold that is completely different from the known structures of other MCU-NTD homologues. Biochemical and biophysical analyses of DdMCU-NTD in solution indicated that the domain exists as high-order oligomers. Mutagenesis showed that the acidic residues Asp60, Glu72, and Glu74, which appeared to mediate the interface II, as observed in the crystal structure, participated in the self-assembly of DdMCU-NTD. Intriguingly, the oligomeric complex was disrupted in the presence of calcium. We propose that the calcium-triggered dissociation of NTD regulates the channel activity of DdMCU by a yet unknown mechanism.
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Affiliation(s)
- Yuan Yuan
- State Key Laboratory
of Molecular Biology, CAS Center for Excellence in Molecular Cell
Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - Chan Cao
- State Key Laboratory
of Molecular Biology, CAS Center for Excellence in Molecular Cell
Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - Maorong Wen
- State Key Laboratory
of Molecular Biology, CAS Center for Excellence in Molecular Cell
Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - Min Li
- State Key Laboratory
of Molecular Biology, CAS Center for Excellence in Molecular Cell
Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - Ying Dong
- State Key Laboratory
of Molecular Biology, CAS Center for Excellence in Molecular Cell
Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - Lijie Wu
- Shanghai Institute for Advanced Immunochemical
Studies and iHuman Institute, ShanghaiTech
University, Shanghai 201210, China
| | - Jian Wu
- Ninth People’s
Hospital, Shanghai Jiao Tong University
School of Medicine, Shanghai 200125, China
| | - Tanxing Cui
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard
Medical School, Boston, Massachusetts 02115, United States
| | - Dianfan Li
- State Key Laboratory
of Molecular Biology, CAS Center for Excellence in Molecular Cell
Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, 333 Haike Road, Shanghai 201203, China
| | - James J. Chou
- Department of Biological
Chemistry and Molecular Pharmacology, Harvard
Medical School, Boston, Massachusetts 02115, United States
| | - Bo OuYang
- State Key Laboratory
of Molecular Biology, CAS Center for Excellence in Molecular Cell
Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese
Academy of Sciences, University of Chinese
Academy of Sciences, 333 Haike Road, Shanghai 201203, China
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36
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Haffke M, Duckely M, Bergsdorf C, Jaakola VP, Shrestha B. Development of a biochemical and biophysical suite for integral membrane protein targets: A review. Protein Expr Purif 2020; 167:105545. [DOI: 10.1016/j.pep.2019.105545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/18/2019] [Accepted: 11/24/2019] [Indexed: 12/11/2022]
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37
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Rose-Sperling D, Tran MA, Lauth LM, Goretzki B, Hellmich UA. 19F NMR as a versatile tool to study membrane protein structure and dynamics. Biol Chem 2020; 400:1277-1288. [PMID: 31004560 DOI: 10.1515/hsz-2018-0473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/17/2019] [Indexed: 12/25/2022]
Abstract
To elucidate the structures and dynamics of membrane proteins, highly advanced biophysical methods have been developed that often require significant resources, both for sample preparation and experimental analyses. For very complex systems, such as membrane transporters, ion channels or G-protein coupled receptors (GPCRs), the incorporation of a single reporter at a select site can significantly simplify the observables and the measurement/analysis requirements. Here we present examples using 19F nuclear magnetic resonance (NMR) spectroscopy as a powerful, yet relatively straightforward tool to study (membrane) protein structure, dynamics and ligand interactions. We summarize methods to incorporate 19F labels into proteins and discuss the type of information that can be readily obtained for membrane proteins already from relatively simple NMR spectra with a focus on GPCRs as the membrane protein family most extensively studied by this technique. In the future, these approaches may be of particular interest also for many proteins that undergo complex functional dynamics and/or contain unstructured regions and thus are not amenable to X-ray crystallography or cryo electron microscopy (cryoEM) studies.
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Affiliation(s)
- Dania Rose-Sperling
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, D-55128 Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Mai Anh Tran
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, D-55128 Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Luca M Lauth
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, D-55128 Mainz, Germany
| | - Benedikt Goretzki
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, D-55128 Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Ute A Hellmich
- Institute for Pharmacy and Biochemistry, Johannes Gutenberg University, Johann-Joachim-Becher-Weg 30, D-55128 Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
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38
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Determination of the Molecular Mass of Membrane Proteins Using Size-Exclusion Chromatography with Multiangle Laser Light Scattering (SEC-MALLS ). Methods Mol Biol 2020; 2168:263-269. [PMID: 33582996 DOI: 10.1007/978-1-0716-0724-4_12] [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: 01/27/2023]
Abstract
Size-exclusion chromatography coupled to multiangle laser light scattering (SEC-MALLS) is the perfect method to determine the oligomeric state of membrane proteins as this method works in solution and is totally independent from prior assumptions such as detergent-to-protein ratio or the shape of the protein. In a relatively short time (ca. 30 min), the molecular mass and quality of a membrane protein preparation can be determined. Here, I provide a detailed protocol on how to perform a SEC-MALLS run and show exemplary chromatograms and their analysis.
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39
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Enhanced oligomerization of full-length RAGE by synergy of the interaction of its domains. Sci Rep 2019; 9:20332. [PMID: 31889156 PMCID: PMC6937306 DOI: 10.1038/s41598-019-56993-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/11/2019] [Indexed: 01/10/2023] Open
Abstract
The pattern recognition receptor RAGE (receptor for advanced glycation end-products) transmits proinflammatory signals in several inflammation-related pathological states, including vascular diseases, cancer, neurodegeneration and diabetes. Its oligomerization is believed to be important in signal transduction, but RAGE oligomeric structures and stoichiometries remain unclear. Different oligomerization modes have been proposed in studies involving different truncated versions of the extracellular parts of RAGE. Here, we provide basic characterization of the oligomerization patterns of full-length RAGE (including the transmembrane (TM) and cytosolic regions) and compare the results with oligomerization modes of its four truncated fragments. For this purpose, we used native mass spectrometry, analytical ultracentrifugation, and size-exclusion chromatography coupled with multi-angle light scattering. Our results confirm known oligomerization tendencies of separate domains and highlight the enhanced oligomerization properties of full-length RAGE. Mutational analyses within the GxxxG motif of the TM region show sensitivity of oligomeric distributions to the TM sequence. Using hydrogen–deuterium exchange, we mapped regions involved in TM-dependent RAGE oligomerization. Our data provide experimental evidence for the major role of the C2 and TM domains in oligomerization, underscoring synergy among different oligomerization contact regions along the RAGE sequence. These results also explain the variability of obtained oligomerization modes in RAGE fragments.
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40
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Wang C, Sun B, Zhang X, Huang X, Zhang M, Guo H, Chen X, Huang F, Chen T, Mi H, Yu F, Liu LN, Zhang P. Structural mechanism of the active bicarbonate transporter from cyanobacteria. NATURE PLANTS 2019; 5:1184-1193. [PMID: 31712753 DOI: 10.1038/s41477-019-0538-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/27/2019] [Indexed: 05/11/2023]
Abstract
Bicarbonate transporters play essential roles in pH homeostasis in mammals and photosynthesis in aquatic photoautotrophs. A number of bicarbonate transporters have been characterized, among which is BicA-a low-affinity, high-flux SLC26-family bicarbonate transporter involved in cyanobacterial CO2-concentrating mechanisms (CCMs) that accumulate CO2 and improve photosynthetic carbon fixation. Here, we report the three-dimensional structure of BicA from Synechocystis sp. PCC6803. Crystal structures of the transmembrane domain (BicATM) and the cytoplasmic STAS domain (BicASTAS) of BicA were solved. BicATM was captured in an inward-facing HCO3--bound conformation and adopts a '7+7' fold monomer. HCO3- binds to a cytoplasm-facing hydrophilic pocket within the membrane. BicASTAS is assembled as a compact homodimer structure and is required for the dimerization of BicA. The dimeric structure of BicA was further analysed using cryo-electron microscopy and physiological analysis of the full-length BicA, and may represent the physiological unit of SLC26-family transporters. Comparing the BicATM structure with the outward-facing transmembrane domain structures of other bicarbonate transporters suggests an elevator transport mechanism that is applicable to the SLC26/4 family of sodium-dependent bicarbonate transporters. This study advances our knowledge of the structures and functions of cyanobacterial bicarbonate transporters, and will inform strategies for bioengineering functional BicA in heterologous organisms to increase assimilation of CO2.
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Affiliation(s)
- Chengcheng Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Sun
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, China
| | - Xue Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaowei Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Minhua Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hui Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xin Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fang Huang
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Taiyu Chen
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Hualing Mi
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fang Yu
- Shanghai Key Laboratory of Plant Molecualr Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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41
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Pols T, Sikkema HR, Gaastra BF, Frallicciardi J, Śmigiel WM, Singh S, Poolman B. A synthetic metabolic network for physicochemical homeostasis. Nat Commun 2019; 10:4239. [PMID: 31534136 PMCID: PMC6751199 DOI: 10.1038/s41467-019-12287-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/02/2019] [Indexed: 12/21/2022] Open
Abstract
One of the grand challenges in chemistry is the construction of functional out-of-equilibrium networks, which are typical of living cells. Building such a system from molecular components requires control over the formation and degradation of the interacting chemicals and homeostasis of the internal physical-chemical conditions. The provision and consumption of ATP lies at the heart of this challenge. Here we report the in vitro construction of a pathway in vesicles for sustained ATP production that is maintained away from equilibrium by control of energy dissipation. We maintain a constant level of ATP with varying load on the system. The pathway enables us to control the transmembrane fluxes of osmolytes and to demonstrate basic physicochemical homeostasis. Our work demonstrates metabolic energy conservation and cell volume regulatory mechanisms in a cell-like system at a level of complexity minimally needed for life.
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Affiliation(s)
- Tjeerd Pols
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Hendrik R Sikkema
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jacopo Frallicciardi
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Wojciech M Śmigiel
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Shubham Singh
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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42
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Preparation of alkylated chitosan-based polyelectrolyte hydrogels: The effect of monomer charge on polymerization. Eur Polym J 2019. [DOI: 10.1016/j.eurpolymj.2019.06.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Pan B, Akyuz N, Liu XP, Asai Y, Nist-Lund C, Kurima K, Derfler BH, György B, Limapichat W, Walujkar S, Wimalasena LN, Sotomayor M, Corey DP, Holt JR. TMC1 Forms the Pore of Mechanosensory Transduction Channels in Vertebrate Inner Ear Hair Cells. Neuron 2019; 99:736-753.e6. [PMID: 30138589 DOI: 10.1016/j.neuron.2018.07.033] [Citation(s) in RCA: 206] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 06/10/2018] [Accepted: 07/19/2018] [Indexed: 11/28/2022]
Abstract
The proteins that form the permeation pathway of mechanosensory transduction channels in inner-ear hair cells have not been definitively identified. Genetic, anatomical, and physiological evidence support a role for transmembrane channel-like protein (TMC) 1 in hair cell sensory transduction, yet the molecular function of TMC proteins remains unclear. Here, we provide biochemical evidence suggesting TMC1 assembles as a dimer, along with structural and sequence analyses suggesting similarity to dimeric TMEM16 channels. To identify the pore region of TMC1, we used cysteine mutagenesis and expressed mutant TMC1 in hair cells of Tmc1/2-null mice. Cysteine-modification reagents rapidly and irreversibly altered permeation properties of mechanosensory transduction. We propose that TMC1 is structurally similar to TMEM16 channels and includes ten transmembrane domains with four domains, S4-S7, that line the channel pore. The data provide compelling evidence that TMC1 is a pore-forming component of sensory transduction channels in auditory and vestibular hair cells.
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Affiliation(s)
- Bifeng Pan
- Departments of Otolaryngology and Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Nurunisa Akyuz
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Xiao-Ping Liu
- Departments of Otolaryngology and Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yukako Asai
- Departments of Otolaryngology and Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Carl Nist-Lund
- Departments of Otolaryngology and Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kiyoto Kurima
- Molecular Biology and Genetics Section, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Bruce H Derfler
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Bence György
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Walrati Limapichat
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sanket Walujkar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Lahiru N Wimalasena
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - David P Corey
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Jeffrey R Holt
- Departments of Otolaryngology and Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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44
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High-throughput stability screening for detergent-solubilized membrane proteins. Sci Rep 2019; 9:10379. [PMID: 31316088 PMCID: PMC6637136 DOI: 10.1038/s41598-019-46686-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/03/2019] [Indexed: 01/08/2023] Open
Abstract
Protein stability in detergent or membrane-like environments is the bottleneck for structural studies on integral membrane proteins (IMP). Irrespective of the method to study the structure of an IMP, detergent solubilization from the membrane is usually the first step in the workflow. Here, we establish a simple, high-throughput screening method to identify optimal detergent conditions for membrane protein stabilization. We apply differential scanning fluorimetry in combination with scattering upon thermal denaturation to study the unfolding of integral membrane proteins. Nine different prokaryotic and eukaryotic membrane proteins were used as test cases to benchmark our detergent screening method. Our results show that it is possible to measure the stability and solubility of IMPs by diluting them from their initial solubilization condition into different detergents. We were able to identify groups of detergents with characteristic stabilization and destabilization effects for selected targets. We further show that fos-choline and PEG family detergents may lead to membrane protein destabilization and unfolding. Finally, we determined thenmodynamic parameters that are important indicators of IMP stability. The described protocol allows the identification of conditions that are suitable for downstream handling of membrane proteins during purification.
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45
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Cryo-EM structure of OSCA1.2 from Oryza sativa elucidates the mechanical basis of potential membrane hyperosmolality gating. Proc Natl Acad Sci U S A 2019; 116:14309-14318. [PMID: 31227607 DOI: 10.1073/pnas.1900774116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sensing and responding to environmental water deficiency and osmotic stresses are essential for the growth, development, and survival of plants. Recently, an osmolality-sensing ion channel called OSCA1 was discovered that functions in sensing hyperosmolality in Arabidopsis Here, we report the cryo-electron microscopy (cryo-EM) structure and function of an OSCA1 homolog from rice (Oryza sativa; OsOSCA1.2), leading to a model of how it could mediate hyperosmolality sensing and transport pathway gating. The structure reveals a dimer; the molecular architecture of each subunit consists of 11 transmembrane (TM) helices and a cytosolic soluble domain that has homology to RNA recognition proteins. The TM domain is structurally related to the TMEM16 family of calcium-dependent ion channels and lipid scramblases. The cytosolic soluble domain possesses a distinct structural feature in the form of extended intracellular helical arms that are parallel to the plasma membrane. These helical arms are well positioned to potentially sense lateral tension on the inner leaflet of the lipid bilayer caused by changes in turgor pressure. Computational dynamic analysis suggests how this domain couples to the TM portion of the molecule to open a transport pathway. Hydrogen/deuterium exchange mass spectrometry (HDXMS) experimentally confirms the conformational dynamics of these coupled domains. These studies provide a framework to understand the structural basis of proposed hyperosmolality sensing in a staple crop plant, extend our knowledge of the anoctamin superfamily important for plants and fungi, and provide a structural mechanism for potentially translating membrane stress to transport regulation.
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46
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Jiao H, Yin Y, Liu Z. Structures of the Mitochondrial CDP-DAG Synthase Tam41 Suggest a Potential Lipid Substrate Pathway from Membrane to the Active Site. Structure 2019; 27:1258-1269.e4. [PMID: 31178220 DOI: 10.1016/j.str.2019.04.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 03/14/2019] [Accepted: 04/29/2019] [Indexed: 11/18/2022]
Abstract
In mitochondria, CDP-diacylglycerol (CDP-DAG) is a crucial precursor for cardiolipin biosynthesis. Mitochondrial CDP-DAG is synthesized by the translocator assembly and maintenance protein 41 (Tam41) through an elusive process. Here we show that Tam41 adopts sequential catalytic mechanism, and report crystal structures of the bulk N-terminal region of Tam41 from Schizosaccharomyces pombe in the apo and CTP-bound state. The structure reveals that Tam41 contains a nucleotidyltransferase (NTase) domain and a winged helix domain. CTP binds to an "L"-shaped pocket sandwiched between the two domains. Rearrangement of a loop region near the active site is essential for opening the CTP-binding pocket. Docking of phosphatidic acid/CDP-DAG in the structure suggests a lipid entry/exit pathway connected to the "L"-shaped pocket. The C-terminal region of SpTam41 contains a positively charged amphipathic helix crucial for membrane association and participates in binding phospholipids. These results provide detailed insights into the mechanism of CDP-DAG biosynthesis in mitochondria.
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Affiliation(s)
- Haizhan Jiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, No. 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Yan Yin
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, No. 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China
| | - Zhenfeng Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, No. 15 Datun Road, Beijing 100101, China; University of Chinese Academy of Sciences, No. 19(A) Yuquan Road, Beijing 100049, China.
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47
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Kwan TOC, Reis R, Siligardi G, Hussain R, Cheruvara H, Moraes I. Selection of Biophysical Methods for Characterisation of Membrane Proteins. Int J Mol Sci 2019; 20:E2605. [PMID: 31137900 PMCID: PMC6566885 DOI: 10.3390/ijms20102605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 02/01/2023] Open
Abstract
Over the years, there have been many developments and advances in the field of integral membrane protein research. As important pharmaceutical targets, it is paramount to understand the mechanisms of action that govern their structure-function relationships. However, the study of integral membrane proteins is still incredibly challenging, mostly due to their low expression and instability once extracted from the native biological membrane. Nevertheless, milligrams of pure, stable, and functional protein are always required for biochemical and structural studies. Many modern biophysical tools are available today that provide critical information regarding to the characterisation and behaviour of integral membrane proteins in solution. These biophysical approaches play an important role in both basic research and in early-stage drug discovery processes. In this review, it is not our objective to present a comprehensive list of all existing biophysical methods, but a selection of the most useful and easily applied to basic integral membrane protein research.
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Affiliation(s)
- Tristan O C Kwan
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Rosana Reis
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Harish Cheruvara
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
| | - Isabel Moraes
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK.
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48
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Wagner M, Smits SHJ, Schmitt L. In vitro NTPase activity of highly purified Pdr5, a major yeast ABC multidrug transporter. Sci Rep 2019; 9:7761. [PMID: 31123301 PMCID: PMC6533308 DOI: 10.1038/s41598-019-44327-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
The ABC transporter Pdr5 of S. cerevisiae is a key player of the PDR network that works as a first line of defense against a wide range of xenobiotic compounds. As the first discovered member of the family of asymmetric PDR ABC transporters, extensive studies have been carried out to elucidate the molecular mechanism of drug efflux and the details of the catalytic cycle. Pdr5 turned out to be an excellent model system to study functional and structural characteristics of asymmetric, uncoupled ABC transporters. However, to date studies have been limited to in vivo or plasma membrane systems, as it was not possible to isolate Pdr5 in a functional state. Here, we describe the solubilization and purification of Pdr5 to homogeneity in a functional state as confirmed by in vitro assays. The ATPase deficient Pdr5 E1036Q mutant was used as a control and proves that detergent-purified wild-type Pdr5 is functional resembling in its activity the one in its physiological environment. Finally, we show that the isolated active Pdr5 is monomeric in solution. Taken together, our results described in this study will enable a variety of functional investigations on Pdr5 required to determine molecular mechanism of this asymmetric ABC transporter.
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Affiliation(s)
- Manuel Wagner
- Institute of Biochemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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Majumder P, Khare S, Athreya A, Hussain N, Gulati A, Penmatsa A. Dissection of Protonation Sites for Antibacterial Recognition and Transport in QacA, a Multi-Drug Efflux Transporter. J Mol Biol 2019; 431:2163-2179. [PMID: 30910733 PMCID: PMC7212025 DOI: 10.1016/j.jmb.2019.03.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 03/14/2019] [Accepted: 03/19/2019] [Indexed: 01/05/2023]
Abstract
QacA is a drug:H+ antiporter with 14 transmembrane helices that confers antibacterial resistance to methicillin-resistant Staphylococcus aureus strains, with homologs in other pathogenic organisms. It is a highly promiscuous antiporter, capable of H+-driven efflux of a wide array of cationic antibacterial compounds and dyes. Our study, using a homology model of QacA, reveals a group of six protonatable residues in its vestibule. Systematic mutagenesis resulted in the identification of D34 (TM1), and a cluster of acidic residues in TM13 including E407 and D411 and D323 in TM10, as being crucial for substrate recognition and transport of monovalent and divalent cationic antibacterial compounds. The transport and binding properties of QacA and its mutants were explored using whole cells, inside-out vesicles, substrate-induced H+ release and microscale thermophoresis-based assays. The activity of purified QacA was also observed using proteoliposome-based substrate-induced H+ transport assay. Our results identify two sites, D34 and D411 as vital players in substrate recognition, while E407 facilitates substrate efflux as a protonation site. We also observe that E407 plays an additional role as a substrate recognition site for the transport of dequalinium, a divalent quaternary ammonium compound. These observations rationalize the promiscuity of QacA for diverse substrates. The study unravels the role of acidic residues in QacA with implications for substrate recognition, promiscuity and processive transport in multidrug efflux transporters, related to QacA.
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Affiliation(s)
- Puja Majumder
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Shashank Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Arunabh Athreya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Nazia Hussain
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Ashutosh Gulati
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
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Tavoulari S, Thangaratnarajah C, Mavridou V, Harbour ME, Martinou JC, Kunji ER. The yeast mitochondrial pyruvate carrier is a hetero-dimer in its functional state. EMBO J 2019; 38:e100785. [PMID: 30979775 PMCID: PMC6517818 DOI: 10.15252/embj.2018100785] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/13/2019] [Accepted: 03/20/2019] [Indexed: 02/02/2023] Open
Abstract
The mitochondrial pyruvate carrier (MPC) is critical for cellular homeostasis, as it is required in central metabolism for transporting pyruvate from the cytosol into the mitochondrial matrix. MPC has been implicated in many diseases and is being investigated as a drug target. A few years ago, small membrane proteins, called MPC1 and MPC2 in mammals and Mpc1, Mpc2 and Mpc3 in yeast, were proposed to form large protein complexes responsible for this function. However, the MPC complexes have never been isolated and their composition, oligomeric state and functional properties have not been defined. Here, we identify the functional unit of MPC from Saccharomyces cerevisiae In contrast to earlier hypotheses, we demonstrate that MPC is a hetero-dimer, not a multimeric complex. When not engaged in hetero-dimers, the yeast Mpc proteins can also form homo-dimers that are, however, inactive. We show that the earlier described substrate transport properties and inhibitor profiles are embodied by the hetero-dimer. This work provides a foundation for elucidating the structure of the functional complex and the mechanism of substrate transport and inhibition.
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Affiliation(s)
- Sotiria Tavoulari
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Vasiliki Mavridou
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michael E Harbour
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Edmund Rs Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
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