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Madsen AV, Mejias-Gomez O, Pedersen LE, Preben Morth J, Kristensen P, Jenkins TP, Goletz S. Structural trends in antibody-antigen binding interfaces: a computational analysis of 1833 experimentally determined 3D structures. Comput Struct Biotechnol J 2024; 23:199-211. [PMID: 38161735 PMCID: PMC10755492 DOI: 10.1016/j.csbj.2023.11.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Antibodies are attractive therapeutic candidates due to their ability to bind cognate antigens with high affinity and specificity. Still, the underlying molecular rules governing the antibody-antigen interface remain poorly understood, making in silico antibody design inherently difficult and keeping the discovery and design of novel antibodies a costly and laborious process. This study investigates the characteristics of antibody-antigen binding interfaces through a computational analysis of more than 850,000 atom-atom contacts from the largest reported set of antibody-antigen complexes with 1833 nonredundant, experimentally determined structures. The analysis compares binding characteristics of conventional antibodies and single-domain antibodies (sdAbs) targeting both protein- and peptide antigens. We find clear patterns in the number antibody-antigen contacts and amino acid frequencies in the paratope. The direct comparison of sdAbs and conventional antibodies helps elucidate the mechanisms employed by sdAbs to compensate for their smaller size and the fact that they harbor only half the number of complementarity-determining regions compared to conventional antibodies. Furthermore, we pinpoint antibody interface hotspot residues that are often found at the binding interface and the amino acid frequencies at these positions. These findings have direct potential applications in antibody engineering and the design of improved antibody libraries.
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Affiliation(s)
- Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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2
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Sørensen CV, Fernández J, Adams AC, Wildenauer HHK, Schoffelen S, Ledsgaard L, Pucca MB, Fiebig M, Cerni FA, Tulika T, Voldborg BG, Karatt-Vellatt A, Morth JP, Ljungars A, Grav LM, Lomonte B, Laustsen AH. Antibody-dependent enhancement of toxicity of myotoxin II from Bothrops asper. Nat Commun 2024; 15:173. [PMID: 38228619 PMCID: PMC10791742 DOI: 10.1038/s41467-023-42624-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/17/2023] [Indexed: 01/18/2024] Open
Abstract
Improved therapies are needed against snakebite envenoming, which kills and permanently disables thousands of people each year. Recently developed neutralizing monoclonal antibodies against several snake toxins have shown promise in preclinical rodent models. Here, we use phage display technology to discover a human monoclonal antibody and show that this antibody causes antibody-dependent enhancement of toxicity (ADET) of myotoxin II from the venomous pit viper, Bothrops asper, in a mouse model of envenoming that mimics a snakebite. While clinical ADET related to snake venom has not yet been reported in humans, this report of ADET of a toxin from the animal kingdom highlights the necessity of assessing even well-known antibody formats in representative preclinical models to evaluate their therapeutic utility against toxins or venoms. This is essential to avoid potential deleterious effects as exemplified in the present study.
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Affiliation(s)
- Christoffer V Sørensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Julián Fernández
- Instituto Clodomiro Picado, Facultad de Microbiologia, Universidad de Costa Rica, San Jose, Costa Rica
| | - Anna Christina Adams
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Helen H K Wildenauer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Sanne Schoffelen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Line Ledsgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Manuela B Pucca
- Medical School, Federal University of Roraima, Boa Vista, BR-69310-000, Brazil
| | - Michael Fiebig
- Absolute Antibody Ltd, Wilton Centre, Redcar, Cleveland, TS10 4RF, UK
| | - Felipe A Cerni
- Postgraduate Program in Tropical Medicine, University of the State of Amazonas, Manaus, BR-69040-000, Brazil
| | - Tulika Tulika
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Bjørn G Voldborg
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | | | - J Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Anne Ljungars
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Lise M Grav
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiologia, Universidad de Costa Rica, San Jose, Costa Rica.
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark.
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3
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Weikum J, van Dyck JF, Subramani S, Klebl DP, Storflor M, Muench SP, Abel S, Sobott F, Morth JP. The bacterial magnesium transporter MgtA reveals highly selective interaction with specific cardiolipin species. Biochim Biophys Acta Mol Cell Res 2024; 1871:119614. [PMID: 37879515 DOI: 10.1016/j.bbamcr.2023.119614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 09/13/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
The bacterial magnesium transporter A (MgtA) is a specialized P-type ATPase important for Mg2+ import into the cytoplasm; disrupted magnesium homeostasis is linked to intrinsic ribosome instability and antibacterial resistance in Salmonella strains. Here, we show that MgtA has functional specificity for cardiolipin 18:1. Still, it reaches maximum activity only in combination with cardiolipin 16:0, equivalent to the major components of native cardiolipin found in E. coli membranes. Native mass spectrometry indicates the presence of two binding sites for cardiolipin, agreeing with the kinetic studies revealing that a cooperative relationship likely exists between the two cardiolipin variants. This is the first experimental evidence of cooperative effects between lipids of the same class, with only minor variations in their acyl chain composition, acting on a membrane protein. In summary, our results reveal that MgtA exhibits a highly complex interaction with one cardiolipin 18:1 and one cardiolipin 16:0, affecting protein activity and stability, contributing to our understanding of the particular interactions between lipid environment and membrane proteins. Further, a better understanding of Mg2+ homeostasis in bacteria, due to its role as a virulence regulator, will provide further insights into the regulation and mechanism of bacterial infections.
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Affiliation(s)
- Julia Weikum
- Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318 Oslo, Norway; Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| | - Jeroen F van Dyck
- Department of Chemistry, University of Antwerp, Campus Groenenborger, Groenenborgerlaan 171, G.V. 418, 2020 Antwerpen, Belgium
| | - Saranya Subramani
- Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318 Oslo, Norway
| | - David P Klebl
- School of Biomedical Sciences & The Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Merete Storflor
- Infections Biology Lab, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Stephen P Muench
- School of Biomedical Sciences & The Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Sören Abel
- Infections Biology Lab, Department of Pharmacy, UiT-The Arctic University of Norway, 9037 Tromsø, Norway
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Campus Groenenborger, Groenenborgerlaan 171, G.V. 418, 2020 Antwerpen, Belgium; School of Molecular and Cellular Biology & The Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom.
| | - J Preben Morth
- Membrane Transport Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, P.O. Box 1137, Blindern, 0318 Oslo, Norway; Enzyme and Protein Chemistry, Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs. Lyngby, Denmark; Institute for Experimental Medical Research (IEMR), Oslo University Hospital, Ullevål PB 4956 Nydalen, NO-0424 Oslo, Norway.
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Merklinger L, Morth JP. Phospholipid Preparations to Characterize Protein-Lipid Interactions In Vitro. Bio Protoc 2023; 22:e4887. [PMID: 38026763 PMCID: PMC10665634 DOI: 10.21769/bioprotoc.4887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 12/01/2023] Open
Abstract
The lipid bilayers of the cell are composed of various lipid classes and species. These engage in cell signaling and regulation by recruiting cytosolic proteins to the membrane and interacting with membrane-embedded proteins to alternate their activity and stability. Like lipids, membrane proteins are amphipathic and are stabilized by the hydrophobic forces of the lipid bilayer. Membrane protein-lipid interactions are difficult to investigate since membrane proteins need to be reconstituted in a lipid-mimicking environment. A common and well-established approach is the detergent-based solubilization of the membrane proteins in detergent micelles. Nowadays, nanodiscs and liposomes are used to mimic the lipid bilayer and enable the work with membrane proteins in a more natural environment. However, these protocols need optimization and are labor intensive. The present protocol describes straightforward instructions on how the preparation of lipids is performed and how the lipid detergent mixture is integrated with the membrane protein MARCH5. The lipidation protocol was performed prior to an activity assay specific to membrane-bound E3 ubiquitin ligases and a stability assay that could be used for any membrane protein of choice.
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Affiliation(s)
- Lisa Merklinger
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Perdreau-Dahl H, Lipsett DB, Frisk M, Kermani F, Carlson CR, Brech A, Shen X, Bergan-Dahl A, Hou Y, Tuomainen T, Tavi P, Jones PP, Lunde M, Wasserstrom JA, Laporte J, Ullrich ND, Christensen G, Morth JP, Louch WE. BIN1, Myotubularin, and Dynamin-2 Coordinate T-Tubule Growth in Cardiomyocytes. Circ Res 2023; 132:e188-e205. [PMID: 37139790 DOI: 10.1161/circresaha.122.321732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND Transverse tubules (t-tubules) form gradually in the developing heart, critically enabling maturation of cardiomyocyte Ca2+ homeostasis. The membrane bending and scaffolding protein BIN1 (amphiphysin-2) has been implicated in this process. However, it is unclear which of the various reported BIN1 isoforms are involved, and whether BIN1 function is regulated by its putative binding partners MTM1 (myotubularin), a phosphoinositide 3'-phosphatase, and DNM2 (dynamin-2), a GTPase believed to mediate membrane fission. METHODS We investigated the roles of BIN1, MTM1, and DNM2 in t-tubule formation in developing mouse cardiomyocytes, and in gene-modified HL-1 and human-induced pluripotent stem cell-derived cardiomyocytes. T-tubules and proteins of interest were imaged by confocal and Airyscan microscopy, and expression patterns were examined by RT-qPCR and Western blotting. Ca2+ release was recorded using Fluo-4. RESULTS We observed that in the postnatal mouse heart, BIN1 localizes along Z-lines from early developmental stages, consistent with roles in initial budding and scaffolding of t-tubules. T-tubule proliferation and organization were linked to a progressive and parallel increase in 4 detected BIN1 isoforms. All isoforms were observed to induce tubulation in cardiomyocytes but produced t-tubules with differing geometries. BIN1-induced tubulations contained the L-type Ca2+ channel, were colocalized with caveolin-3 and the ryanodine receptor, and effectively triggered Ca2+ release. BIN1 upregulation during development was paralleled by increasing expression of MTM1. Despite no direct binding between MTM1 and murine cardiac BIN1 isoforms, which lack exon 11, high MTM1 levels were necessary for BIN1-induced tubulation, indicating a central role of phosphoinositide homeostasis. In contrast, the developing heart exhibited declining levels of DNM2. Indeed, we observed that high levels of DNM2 are inhibitory for t-tubule formation, although this protein colocalizes with BIN1 along Z-lines, and binds all 4 isoforms. CONCLUSIONS These findings indicate that BIN1, MTM1, and DNM2 have balanced and collaborative roles in controlling t-tubule growth in cardiomyocytes.
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Affiliation(s)
- Harmonie Perdreau-Dahl
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- KG Jebsen Center for Cardiac Research, University of Oslo, Norway (H.P.-D., D.B.L., M.F., X.S., A.B.-D., Y.H., M.L., G.C., W.E.L.)
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership University of Oslo, Norway (H.P.-D., J.P.M.)
- Institut MitoVasc, CNRS UMR 6015, INSERM U1083, Université d'Angers, France (H.P.-D.)
| | - David B Lipsett
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- KG Jebsen Center for Cardiac Research, University of Oslo, Norway (H.P.-D., D.B.L., M.F., X.S., A.B.-D., Y.H., M.L., G.C., W.E.L.)
| | - Michael Frisk
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- KG Jebsen Center for Cardiac Research, University of Oslo, Norway (H.P.-D., D.B.L., M.F., X.S., A.B.-D., Y.H., M.L., G.C., W.E.L.)
| | - Fatemeh Kermani
- Division of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Germany (F.K., N.D.U.)
| | - Cathrine R Carlson
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
| | - Andreas Brech
- Department of Molecular Cell Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Montebello, Norway (A.B.)
| | - Xin Shen
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- KG Jebsen Center for Cardiac Research, University of Oslo, Norway (H.P.-D., D.B.L., M.F., X.S., A.B.-D., Y.H., M.L., G.C., W.E.L.)
| | - Anna Bergan-Dahl
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- KG Jebsen Center for Cardiac Research, University of Oslo, Norway (H.P.-D., D.B.L., M.F., X.S., A.B.-D., Y.H., M.L., G.C., W.E.L.)
| | - Yufeng Hou
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- KG Jebsen Center for Cardiac Research, University of Oslo, Norway (H.P.-D., D.B.L., M.F., X.S., A.B.-D., Y.H., M.L., G.C., W.E.L.)
| | - Tomi Tuomainen
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland (T.T., P.T.)
| | - Pasi Tavi
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland (T.T., P.T.)
| | - Peter P Jones
- Department of Physiology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand (P.P.J.)
| | - Marianne Lunde
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- KG Jebsen Center for Cardiac Research, University of Oslo, Norway (H.P.-D., D.B.L., M.F., X.S., A.B.-D., Y.H., M.L., G.C., W.E.L.)
| | | | - Jocelyn Laporte
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR7104, Strasbourg University, Illkirch, France (J.L.)
| | - Nina D Ullrich
- Division of Cardiovascular Physiology, Institute of Physiology and Pathophysiology, Heidelberg University, Germany (F.K., N.D.U.)
- German Center for Cardiovascular Research (DZHK), Partner Site Heidelberg/Mannheim, Germany (N.D.U.)
| | - Geir Christensen
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- KG Jebsen Center for Cardiac Research, University of Oslo, Norway (H.P.-D., D.B.L., M.F., X.S., A.B.-D., Y.H., M.L., G.C., W.E.L.)
| | - J Preben Morth
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership University of Oslo, Norway (H.P.-D., J.P.M.)
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark (J.P.M.)
| | - William E Louch
- Institute for Experimental Medical Research (IEMR), Oslo University Hospital and University of Oslo, Norway (H.P.-D., D.B.L., M.F., C.R.C., X.S., A.B.-D., Y.H., M.L., G.C., J.P.M., W.E.L.)
- KG Jebsen Center for Cardiac Research, University of Oslo, Norway (H.P.-D., D.B.L., M.F., X.S., A.B.-D., Y.H., M.L., G.C., W.E.L.)
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7
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Mejias-Gomez O, Madsen AV, Skovgaard K, Pedersen LE, Morth JP, Jenkins TP, Kristensen P, Goletz S. A window into the human immune system: comprehensive characterization of the complexity of antibody complementary-determining regions in functional antibodies. MAbs 2023; 15:2268255. [PMID: 37876265 PMCID: PMC10601506 DOI: 10.1080/19420862.2023.2268255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
The human immune system uses antibodies to neutralize foreign antigens. They are composed of heavy and light chains, both with constant and variable regions. The variable region has six hypervariable loops, also known as complementary-determining regions (CDRs) that determine antibody diversity and antigen specificity. Knowledge of their significance, and certain residues present in these areas, is vital for antibody therapeutics development. This study includes an analysis of more than 11,000 human antibody sequences from the International Immunogenetics information system (IMGT). The analysis included parameters such as length distribution, overall amino acid diversity, amino acid frequency per CDR and residue position within antibody chains. Overall, our findings confirm existing knowledge, such as CDRH3's high length diversity and amino acid variability, increased aromatic residue usage, particularly tyrosine, charged and polar residues like aspartic acid, serine, and the flexible residue glycine. Specific residue positions within each CDR influence these occurrences, implying a unique amino acid type distribution pattern. We compared amino acid type usage in CDRs and non-CDR regions, both in globular and transmembrane proteins, which revealed distinguishing features, such as increased frequency of tyrosine, serine, aspartic acid, and arginine. These findings should prove useful for future optimization, improvement of affinity, synthetic antibody library design, or the creation of antibodies de-novo in silico.
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Affiliation(s)
- Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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8
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Merklinger L, Bauer J, Pedersen PA, Damgaard RB, Morth JP. Phospholipids alter activity and stability of mitochondrial membrane-bound ubiquitin ligase MARCH5. Life Sci Alliance 2022; 5:5/8/e202101309. [PMID: 35459736 PMCID: PMC9034062 DOI: 10.26508/lsa.202101309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/24/2022] Open
Abstract
This study shows that lipids can act as regulators for the ubiquitination process and can control the stability and activity of a membrane-embedded E3 ubiquitin ligase. Mitochondrial homeostasis is tightly controlled by ubiquitination. The mitochondrial integral membrane ubiquitin ligase MARCH5 is a crucial regulator of mitochondrial membrane fission, fusion, and disposal through mitophagy. In addition, the lipid composition of mitochondrial membranes can determine mitochondrial dynamics and organelle turnover. However, how lipids influence the ubiquitination processes that control mitochondrial homeostasis remains unknown. Here, we show that lipids common to the mitochondrial membranes interact with MARCH5 and affect its activity and stability depending on the lipid composition in vitro. As the only one of the tested lipids, cardiolipin binding to purified MARCH5 induces a significant decrease in thermal stability, whereas stabilisation increases the strongest in the presence of phosphatidic acid. Furthermore, we observe that the addition of lipids to purified MARCH5 alters the ubiquitination pattern. Specifically, cardiolipin enhances auto-ubiquitination of MARCH5. Our work shows that lipids can directly affect the activity of ubiquitin ligases and suggests that the lipid composition in mitochondrial membranes could control ubiquitination-dependent mechanisms that regulate the dynamics and turnover of mitochondria.
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Affiliation(s)
- Lisa Merklinger
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Johannes Bauer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership University of Oslo, Oslo, Norway
| | - Per A Pedersen
- Department of Biology, University Copenhagen, August Krogh Bygningen, Copenhagen, Denmark
| | - Rune Busk Damgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - J Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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9
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Røjel N, Kari J, Sørensen TH, Badino SF, Morth JP, Schaller K, Cavaleiro AM, Borch K, Westh P. Substrate binding in the processive cellulase Cel7A: Transition state of complexation and roles of conserved tryptophan residues. J Biol Chem 2020; 295:1454-1463. [PMID: 31848226 PMCID: PMC7008363 DOI: 10.1074/jbc.ra119.011420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/17/2019] [Indexed: 11/06/2022] Open
Abstract
Cellobiohydrolases effectively degrade cellulose and are of biotechnological interest because they can convert lignocellulosic biomass to fermentable sugars. Here, we implemented a fluorescence-based method for real-time measurements of complexation and decomplexation of the processive cellulase Cel7A and its insoluble substrate, cellulose. The method enabled detailed kinetic and thermodynamic analyses of ligand binding in a heterogeneous system. We studied WT Cel7A and several variants in which one or two of four highly conserved Trp residues in the binding tunnel had been replaced with Ala. WT Cel7A had on/off-rate constants of 1 × 105 m-1 s-1 and 5 × 10-3 s-1, respectively, reflecting the slow dynamics of a solid, polymeric ligand. Especially the off-rate constant was many orders of magnitude lower than typical values for small, soluble ligands. Binding rate and strength both were typically lower for the Trp variants, but effects of the substitutions were moderate and sometimes negligible. Hence, we propose that lowering the activation barrier for complexation is not a major driving force for the high conservation of the Trp residues. Using so-called Φ-factor analysis, we analyzed the kinetic and thermodynamic results for the variants. The results of this analysis suggested a transition state for complexation and decomplexation in which the reducing end of the ligand is close to the tunnel entrance (near Trp-40), whereas the rest of the binding tunnel is empty. We propose that this structure defines the highest free-energy barrier of the overall catalytic cycle and hence governs the turnover rate of this industrially important enzyme.
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Affiliation(s)
- Nanna Røjel
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - Jeppe Kari
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Silke F Badino
- Institut for Naturvidenskab og Miljo, Roskilde University, DK-4000 Roskilde, Denmark
| | - J Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kay Schaller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | | | - Kim Borch
- Novozymes A/S, DK-2800 Kgs. Lyngby Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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10
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Bauer J, Bakke O, Morth JP. Overview of the membrane-associated RING-CH (MARCH) E3 ligase family. N Biotechnol 2017; 38:7-15. [DOI: 10.1016/j.nbt.2016.12.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/05/2016] [Accepted: 12/13/2016] [Indexed: 12/17/2022]
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11
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Leo JC, Oberhettinger P, Yoshimoto S, Udatha DBRKG, Morth JP, Schütz M, Hori K, Linke D. Secretion of the Intimin Passenger Domain Is Driven by Protein Folding. J Biol Chem 2016; 291:20096-112. [PMID: 27466361 DOI: 10.1074/jbc.m116.731497] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/06/2022] Open
Abstract
Intimin is an essential adhesin of attaching and effacing organisms such as entropathogenic Escherichia coli It is also the prototype of type Ve secretion or inverse autotransport, where the extracellular C-terminal region or passenger is exported with the help of an N-terminal transmembrane β-barrel domain. We recently reported a stalled secretion intermediate of intimin, where the passenger is located in the periplasm but the β-barrel is already inserted into the membrane. Stalling of this mutant is due to the insertion of an epitope tag at the very N terminus of the passenger. Here, we examined how this insertion disrupts autotransport and found that it causes misfolding of the N-terminal immunoglobulin (Ig)-like domain D00. We could also stall the secretion by making an internal deletion in D00, and introducing the epitope tag into the second Ig-like domain, D0, also resulted in reduced passenger secretion. In contrast to many classical autotransporters, where a proximal folding core in the passenger is required for secretion, the D00 domain is dispensable, as the passenger of an intimin mutant lacking D00 entirely is efficiently exported. Furthermore, the D00 domain is slightly less stable than the D0 and D1 domains, unfolding at ∼200 piconewtons (pN) compared with ∼250 pN for D0 and D1 domains as measured by atomic force microscopy. Our results support a model where the secretion of the passenger is driven by sequential folding of the extracellular Ig-like domains, leading to vectorial transport of the passenger domain across the outer membrane in an N to C direction.
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Affiliation(s)
- Jack C Leo
- From the Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Philipp Oberhettinger
- Interfaculty Institute for Microbiology and Infection Medicine, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Shogo Yoshimoto
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and
| | - D B R K Gupta Udatha
- From the Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | | | - Monika Schütz
- Interfaculty Institute for Microbiology and Infection Medicine, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Katsutoshi Hori
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and
| | - Dirk Linke
- From the Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway,
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12
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Hong Z, De Meulemeester L, Jacobi A, Pedersen JS, Morth JP, Andreasen PA, Jensen JK. Crystal Structure of a Two-domain Fragment of Hepatocyte Growth Factor Activator Inhibitor-1: FUNCTIONAL INTERACTIONS BETWEEN THE KUNITZ-TYPE INHIBITOR DOMAIN-1 AND THE NEIGHBORING POLYCYSTIC KIDNEY DISEASE-LIKE DOMAIN. J Biol Chem 2016; 291:14340-14355. [PMID: 27189939 DOI: 10.1074/jbc.m115.707240] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/06/2022] Open
Abstract
Hepatocyte growth factor activator inhibitor-1 (HAI-1) is a type I transmembrane protein and inhibitor of several serine proteases, including hepatocyte growth factor activator and matriptase. The protein is essential for development as knock-out mice die in utero due to placental defects caused by misregulated extracellular proteolysis. HAI-1 contains two Kunitz-type inhibitor domains (Kunitz), which are generally thought of as a functionally self-contained protease inhibitor unit. This is not the case for HAI-1, where our results reveal how interdomain interactions have evolved to stimulate the inhibitory activity of an integrated Kunitz. Here we present an x-ray crystal structure of an HAI-1 fragment covering the internal domain and Kunitz-1. The structure reveals not only that the previously uncharacterized internal domain is a member of the polycystic kidney disease domain family but also how the two domains engage in interdomain interactions. Supported by solution small angle x-ray scattering and a combination of site-directed mutagenesis and functional assays, we show that interdomain interactions not only stabilize the fold of the internal domain but also stimulate the inhibitory activity of Kunitz-1. By completing our structural characterization of the previously unknown N-terminal region of HAI-1, we provide new insight into the interplay between tertiary structure and the inhibitory activity of a multidomain protease inhibitor. We propose a previously unseen mechanism by which the association of an auxiliary domain stimulates the inhibitory activity of a Kunitz-type inhibitor (i.e. the first structure of an intramolecular interaction between a Kunitz and another domain).
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Affiliation(s)
- Zebin Hong
- Department of Molecular Biology and Genetics, Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Laura De Meulemeester
- Department of Molecular Biology and Genetics, Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Annemarie Jacobi
- Department of Molecular Biology and Genetics, Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- Department of Chemistry and iNANO Interdisciplinary Nanoscience Center, Aarhus University, 8000 Aarhus C, Denmark
| | - J Preben Morth
- Norwegian Center of Molecular Medicine (NCMM), University of Oslo, NO-0316 Oslo, Norway
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Jan K Jensen
- Department of Molecular Biology and Genetics, Danish-Chinese Centre for Proteases and Cancer, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark,.
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13
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Perdreau-Dahl HJG, Guldsten H, Progida C, Arntzen M, Thiede B, Bakke O, Morth JP. Structural and biochemical characterization of Sjögren syndrome/scleroderma autoantigen 1 (SSSCA1). Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315096138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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14
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Sommer T, Bjerregaard-Andersen K, Simensen SM, Jensen JK, Jochimsen B, Riss PJ, Etzerodt M, Morth JP. Enzymatic detection and quantification assay of isatin, a putative stress biomarker in blood. ACS Chem Neurosci 2015; 6:1353-60. [PMID: 25891478 DOI: 10.1021/cn500346x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Isatin is an endogenous inhibitor of monoamine oxidase B and is found in human blood and tissue. Increased levels of isatin have been linked to stress and anxiety in rodents and humans; however, the metabolism of isatin in humans is largely unknown. We have developed a fluorescence-based enzymatic assay that can quantify isatin in blood samples. A phase extraction of isatin followed by a second phase extraction combined with an enzymatic reaction performed by an isatin hydrolase is used to extract and quantify isatin in whole blood samples. This results in a purity of more than 95% estimated from RP-HPLC. The hydrophobic molecule isatin is in equilibrium between an organic and aqueous phase; however, conversion by isatin hydrolase to the hydrophilic product isatinate traps it in the aqueous phase, making this step highly specific for isatin. The described protocol also offers a novel method for fast and efficient removal of isatin from any type of sample. The isolated isatinate is converted chemically to anthranilate that allows fluorescent detection and quantification. Pig plasma isatin levels are quantified to a mean of 458 nM ± 91 nM. Biophysical characterization of the isatin hydrolase shows enzymatic functionality between pH 6 and 9 and at temperatures up to 50 °C. Isatin hydrolase is highly selective for manganese ions with a dissociation constant determined to be 9.5 μM. We deliver proof-of-concept for the enzymatic quantification of isatin in blood and provide a straightforward method for further investigation of isatin as a biomarker in human health.
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Affiliation(s)
- Theis Sommer
- Norwegian Center of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349 Oslo, Norway
| | - Kaare Bjerregaard-Andersen
- Norwegian Center of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349 Oslo, Norway
| | - Stine Marie Simensen
- Norwegian Center of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349 Oslo, Norway
| | - Jan K. Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav
Wieds vej 10C, DK8000 Aarhus C, Denmark
| | - Bjarne Jochimsen
- Department of Molecular Biology and Genetics, Aarhus University, Gustav
Wieds vej 10C, DK8000 Aarhus C, Denmark
| | - Patrick J. Riss
- Department of Chemistry, University of Oslo, Sem Sælands vei 26, 0371 Oslo, Norway
| | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University, Gustav
Wieds vej 10C, DK8000 Aarhus C, Denmark
| | - J. Preben Morth
- Norwegian Center of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349 Oslo, Norway
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15
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Bjerregaard-Andersen K, Sommer T, Jensen JK, Jochimsen B, Etzerodt M, Morth JP. A proton wire and water channel revealed in the crystal structure of isatin hydrolase. J Biol Chem 2014; 289:21351-9. [PMID: 24917679 DOI: 10.1074/jbc.m114.568824] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The high resolution crystal structures of isatin hydrolase from Labrenzia aggregata in the apo and the product state are described. These are the first structures of a functionally characterized metal-dependent hydrolase of this fold. Isatin hydrolase converts isatin to isatinate and belongs to a novel family of metalloenzymes that include the bacterial kynurenine formamidase. The product state, mimicked by bound thioisatinate, reveals a water molecule that bridges the thioisatinate to a proton wire in an adjacent water channel and thus allows the proton released by the reaction to escape only when the product is formed. The functional proton wire present in isatin hydrolase isoform b represents a unique catalytic feature common to all hydrolases is here trapped and visualized for the first time. The local molecular environment required to coordinate thioisatinate allows stronger and more confident identification of orthologous genes encoding isatin hydrolases within the prokaryotic kingdom. The isatin hydrolase orthologues found in human gut bacteria raise the question as to whether the indole-3-acetic acid degradation pathway is present in human gut flora.
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Affiliation(s)
- Kaare Bjerregaard-Andersen
- From the Norwegian Center of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349 Oslo, Norway, the Department for Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus, Denmark
| | - Theis Sommer
- From the Norwegian Center of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349 Oslo, Norway
| | - Jan K Jensen
- the Department for Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus, Denmark
| | - Bjarne Jochimsen
- the Department for Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus, Denmark
| | - Michael Etzerodt
- the Department for Molecular Biology and Genetics, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus, Denmark
| | - J Preben Morth
- From the Norwegian Center of Molecular Medicine, Nordic EMBL Partnership University of Oslo, Gaustadalléen 21, 0349 Oslo, Norway, the Institute for Experimental Medical Research, Oslo University Hospital, N-0424 Oslo, Norway, and
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16
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Nagelhus EA, Amiry-Moghaddam M, Bergersen LH, Bjaalie JG, Eriksson J, Gundersen V, Leergaard TB, Morth JP, Storm-Mathisen J, Torp R, Walhovd KB, Tønjum T. The glia doctrine: addressing the role of glial cells in healthy brain ageing. Mech Ageing Dev 2013; 134:449-59. [PMID: 24141107 DOI: 10.1016/j.mad.2013.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/03/2013] [Accepted: 10/04/2013] [Indexed: 01/14/2023]
Abstract
Glial cells in their plurality pervade the human brain and impact on brain structure and function. A principal component of the emerging glial doctrine is the hypothesis that astrocytes, the most abundant type of glial cells, trigger major molecular processes leading to brain ageing. Astrocyte biology has been examined using molecular, biochemical and structural methods, as well as 3D brain imaging in live animals and humans. Exosomes are extracelluar membrane vesicles that facilitate communication between glia, and have significant potential for biomarker discovery and drug delivery. Polymorphisms in DNA repair genes may indirectly influence the structure and function of membrane proteins expressed in glial cells and predispose specific cell subgroups to degeneration. Physical exercise may reduce or retard age-related brain deterioration by a mechanism involving neuro-glial processes. It is most likely that additional information about the distribution, structure and function of glial cells will yield novel insight into human brain ageing. Systematic studies of glia and their functions are expected to eventually lead to earlier detection of ageing-related brain dysfunction and to interventions that could delay, reduce or prevent brain dysfunction.
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Affiliation(s)
- Erlend A Nagelhus
- Department of Physiology, Institute of Basic Medical Sciences, University of Oslo, Norway; Centre for Molecular Medicine Norway (NCMM), The Nordic EMBL Partnership, University of Oslo, Norway; Department of Neurology, Oslo University Hospital, Norway
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17
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Grøftehauge MK, Therkelsen MØ, Taaning R, Skrydstrup T, Morth JP, Nissen P. Identifying ligand-binding hot spots in proteins using brominated fragments. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1060-5. [PMID: 23989163 PMCID: PMC3758163 DOI: 10.1107/s1744309113018551] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/04/2013] [Indexed: 11/10/2022]
Abstract
High-quality crystals of Thermus thermophilus EF-Tu in the GTP-bound conformation at 1.7-2.7 Å resolution were used to test 18 small organic molecules, all brominated for confident identification in the anomalous difference maps. From this relatively small collection, it was possible to identify a small molecule bound in the functionally important tRNA CCA-end binding pocket. The antibiotic GE2270 A is known to interact with the same pocket in EF-Tu and to disrupt the association with tRNA. Bromide could be located from peaks in the anomalous map in data truncated to very low resolution without refining the structure. Considering the speed with which diffraction data can be collected today, it is proposed that it is worthwhile to collect the extra data from fragment screens while crystals are at hand to increase the knowledge of biological function and drug binding in an experimental structural context.
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Affiliation(s)
| | - Martin Ø. Therkelsen
- Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
| | - Rolf Taaning
- Center for Insoluble Protein Structures (inSPIN), Department of Chemistry and the Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Troels Skrydstrup
- Center for Insoluble Protein Structures (inSPIN), Department of Chemistry and the Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - J. Preben Morth
- Centre for Molecular Medicine Norway, University of Oslo, Forskningsparken, 0349 Oslo, Norway
| | - Poul Nissen
- Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark
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18
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Bublitz M, Musgaard M, Poulsen H, Thøgersen L, Olesen C, Schiøtt B, Morth JP, Møller JV, Nissen P. Ion pathways in the sarcoplasmic reticulum Ca2+-ATPase. J Biol Chem 2013; 288:10759-65. [PMID: 23400778 DOI: 10.1074/jbc.r112.436550] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA) is a transmembrane ion transporter belonging to the P(II)-type ATPase family. It performs the vital task of re-sequestering cytoplasmic Ca(2+) to the sarco/endoplasmic reticulum store, thereby also terminating Ca(2+)-induced signaling such as in muscle contraction. This minireview focuses on the transport pathways of Ca(2+) and H(+) ions across the lipid bilayer through SERCA. The ion-binding sites of SERCA are accessible from either the cytoplasm or the sarco/endoplasmic reticulum lumen, and the Ca(2+) entry and exit channels are both formed mainly by rearrangements of four N-terminal transmembrane α-helices. Recent improvements in the resolution of the crystal structures of rabbit SERCA1a have revealed a hydrated pathway in the C-terminal transmembrane region leading from the ion-binding sites to the cytosol. A comparison of different SERCA conformations reveals that this C-terminal pathway is exclusive to Ca(2+)-free E2 states, suggesting that it may play a functional role in proton release from the ion-binding sites. This is in agreement with molecular dynamics simulations and mutational studies and is in striking analogy to a similar pathway recently described for the related sodium pump. We therefore suggest a model for the ion exchange mechanism in P(II)-ATPases including not one, but two cytoplasmic pathways working in concert.
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Affiliation(s)
- Maike Bublitz
- Centre for Membrane Pumps in Cells and Disease (PUMPkin), Aarhus University, DK-8000 Aarhus C, Denmark
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19
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20
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Affiliation(s)
- Maike Bublitz
- Centre for Membrane Pumps in Cells and Disease – PUMPKIN, Danish National Research Foundation, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark
| | - J. Preben Morth
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, P.O. Box 1125, Blindern, N-0318 Oslo, Norway
- Institute for Experimental Medical Research, Oslo University Hospital Ullevaal, N-0407 Oslo, Norway
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease – PUMPKIN, Danish National Research Foundation, Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
- Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus, Denmark
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21
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Jensen JK, Thompson LC, Bucci JC, Nissen P, Gettins PGW, Peterson CB, Andreasen PA, Morth JP. Crystal structure of plasminogen activator inhibitor-1 in an active conformation with normal thermodynamic stability. J Biol Chem 2011; 286:29709-17. [PMID: 21697084 DOI: 10.1074/jbc.m111.236554] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The serpin plasminogen activator inhibitor-1 (PAI-1) is a crucial regulator in fibrinolysis and tissue remodeling. PAI-1 has been associated with several pathological conditions and is a validated prognostic marker in human cancers. However, structural information about the native inhibitory form of PAI-1 has been elusive because of its inherent conformational instability and rapid conversion to a latent, inactive structure. Here we report the crystal structure of PAI-1 W175F at 2.3 Å resolution as the first model of the metastable native molecule. Structural comparison with a quadruple mutant (14-1B) previously used as representative of the active state uncovered key differences. The most striking differences occur near the region that houses three of the four mutations in the 14-1B PAI-1 structure. Prominent changes are localized within a loop connecting β-strand 3A with the F helix, in which a previously observed 3(10)-helix is absent in the new structure. Notably these structural changes are found near the binding site for the cofactor vitronectin. Because vitronectin is the only known physiological regulator of PAI-1 that slows down the latency conversion, the structure of this region is important. Furthermore, the previously identified chloride-binding site close to the F-helix is absent from the present structure and likely to be artifactual, because of its dependence on the 14-1B mutations. Instead we found a different chlorine-binding site that is likely to be present in wild type PAI-1 and that more satisfactorily accounts for the chlorine stabilizing effect on PAI-1.
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Affiliation(s)
- Jan K Jensen
- Department of Molecular Biology, Aarhus University, Aarhus C, Denmark.
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Morth JP, Pedersen BP, Buch-Pedersen MJ, Andersen JP, Vilsen B, Palmgren MG, Nissen P. A structural overview of the plasma membrane Na+,K+-ATPase and H+-ATPase ion pumps. Nat Rev Mol Cell Biol 2011; 12:60-70. [PMID: 21179061 DOI: 10.1038/nrm3031] [Citation(s) in RCA: 235] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Plasma membrane ATPases are primary active transporters of cations that maintain steep concentration gradients. The ion gradients and membrane potentials derived from them form the basis for a range of essential cellular processes, in particular Na(+)-dependent and proton-dependent secondary transport systems that are responsible for uptake and extrusion of metabolites and other ions. The ion gradients are also both directly and indirectly used to control pH homeostasis and to regulate cell volume. The plasma membrane H(+)-ATPase maintains a proton gradient in plants and fungi and the Na(+),K(+)-ATPase maintains a Na(+) and K(+) gradient in animal cells. Structural information provides insight into the function of these two distinct but related P-type pumps.
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Affiliation(s)
- J Preben Morth
- Danish National Research Foundation, Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Denmark
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23
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Yatime L, Laursen M, Morth JP, Esmann M, Nissen P, Fedosova NU. Structural insights into the high affinity binding of cardiotonic steroids to the Na+,K+-ATPase. J Struct Biol 2010; 174:296-306. [PMID: 21182963 DOI: 10.1016/j.jsb.2010.12.004] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 12/13/2010] [Accepted: 12/15/2010] [Indexed: 02/08/2023]
Abstract
The Na+,K+-ATPase belongs to the P-ATPase family, whose characteristic property is the formation of a phosphorylated intermediate. The enzyme is also a defined target for cardiotonic steroids which inhibit its functional activity and initiate intracellular signaling. Here we describe the 4.6 Å resolution crystal structure of the pig kidney Na+,K+-ATPase in its phosphorylated form stabilized by high affinity binding of the cardiotonic steroid ouabain. The steroid binds to a site formed at transmembrane segments αM1-αM6, plugging the ion pathway from the extracellular side. This structure differs from the previously reported low affinity complex with potassium. Most importantly, the A domain has rotated in response to phosphorylation and αM1-2 move towards the ouabain molecule, providing for high affinity interactions and closing the ion pathway from the extracellular side. The observed re-arrangements of the Na+,K+-ATPase stabilized by cardiotonic steroids may affect protein-protein interactions within the intracellular signal transduction networks.
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Affiliation(s)
- Laure Yatime
- Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, Denmark
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24
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Hein KL, Kragh-Hansen U, Morth JP, Jeppesen MD, Otzen D, Møller JV, Nissen P. Crystallographic analysis reveals a unique lidocaine binding site on human serum albumin. J Struct Biol 2010; 171:353-60. [DOI: 10.1016/j.jsb.2010.03.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Accepted: 03/23/2010] [Indexed: 10/19/2022]
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25
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Liu XY, Gourdon P, Andersen JL, Bublitz M, Pedersen BP, Yatime L, Nyblom M, Olesen C, Møller JV, Nissen P, Morth JP. A systematic approach to membrane protein crystallization in bilayers. Acta Crystallogr A 2010. [DOI: 10.1107/s010876731009971x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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26
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Poulsen H, Khandelia H, Morth JP, Bublitz M, Mouritsen OG, Egebjerg J, Nissen P. Neurological disease mutations compromise a C-terminal ion pathway in the Na(+)/K(+)-ATPase. Nature 2010; 467:99-102. [PMID: 20720542 DOI: 10.1038/nature09309] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 06/24/2010] [Indexed: 12/14/2022]
Abstract
The Na(+)/K(+)-ATPase pumps three sodium ions out of and two potassium ions into the cell for each ATP molecule that is split, thereby generating the chemical and electrical gradients across the plasma membrane that are essential in, for example, signalling, secondary transport and volume regulation in animal cells. Crystal structures of the potassium-bound form of the pump revealed an intimate docking of the alpha-subunit carboxy terminus at the transmembrane domain. Here we show that this element is a key regulator of a previously unrecognized ion pathway. Current models of P-type ATPases operate with a single ion conduit through the pump, but our data suggest an additional pathway in the Na(+)/K(+)-ATPase between the ion-binding sites and the cytoplasm. The C-terminal pathway allows a cytoplasmic proton to enter and stabilize site III when empty in the potassium-bound state, and when potassium is released the proton will also return to the cytoplasm, thus allowing an overall asymmetric stoichiometry of the transported ions. The C terminus controls the gate to the pathway. Its structure is crucial for pump function, as demonstrated by at least eight mutations in the region that cause severe neurological diseases. This novel model for ion transport by the Na(+)/K(+)-ATPase is established by electrophysiological studies of C-terminal mutations in familial hemiplegic migraine 2 (FHM2) and is further substantiated by molecular dynamics simulations. A similar ion regulation is likely to apply to the H(+)/K(+)-ATPase and the Ca(2+)-ATPase.
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Affiliation(s)
- Hanne Poulsen
- PUMPKIN - Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Department of Molecular Biology, Aarhus University, DK-8000 Aarhus C, Denmark.
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Pedersen BP, Morth JP, Nissen P. Structure determination using poorly diffracting membrane-protein crystals: the H+-ATPase and Na+,K+-ATPase case history. Acta Crystallogr D Biol Crystallogr 2010; 66:309-13. [PMID: 20179343 DOI: 10.1107/s0907444909053244] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 12/10/2009] [Indexed: 11/10/2022]
Abstract
An approach is presented for the structure determination of membrane proteins on the basis of poorly diffracting crystals which exploits molecular replacement for heavy-atom site identification at 6-9 A maximum resolution and improvement of the heavy-atom-derived phases by multi-crystal averaging using quasi-isomorphous data sets. The multi-crystal averaging procedure allows real-space density averaging followed by phase combination between non-isomorphous native data sets to exploit crystal-to-crystal nonisomorphism despite the crystals belonging to the same space group. This approach has been used in the structure determination of H(+)-ATPase and Na(+),K(+)-ATPase using Ca(2+)-ATPase models and its successful application to the Mhp1 symporter using LeuT as a search model is demonstrated.
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Affiliation(s)
- Bjørn P Pedersen
- Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Aarhus University, Department of Molecular Biology, Gustav Wieds Vej 10C, DK 8000 Aarhus, Denmark
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Sorensen TLM, Morth JP, Pedersen BP, Poulsen H, Toustrup-Jensen MS, Pedersen J, Andersen JP, Vilsen B, Nissen P. X-ray crystallographic studies of the pig renal Na +,K +-ATPase. Acta Crystallogr A 2009. [DOI: 10.1107/s0108767309099462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Morth JP, Laursen M, Bublitz M, Moncoq K, Olesen C, Moeller JV, Young HS, Nissen P. The structure of the Ca 2+-ATPase bound to cyclopiazonic acid reveals a complexed divalent ion. Acta Crystallogr A 2009. [DOI: 10.1107/s0108767309096986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Toustrup-Jensen MS, Holm R, Einholm AP, Schack VR, Morth JP, Nissen P, Andersen JP, Vilsen B. The C terminus of Na+,K+-ATPase controls Na+ affinity on both sides of the membrane through Arg935. J Biol Chem 2009; 284:18715-25. [PMID: 19416970 DOI: 10.1074/jbc.m109.015099] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Na(+),K(+)-ATPase C terminus has a unique location between transmembrane segments, appearing to participate in a network of interactions. We have examined the functional consequences of amino acid substitutions in this region and deletions of the C terminus of varying lengths. Assays revealing separately the mutational effects on internally and externally facing Na(+) sites, as well as E(1)-E(2) conformational changes, have been applied. The results pinpoint the two terminal tyrosines, Tyr(1017) and Tyr(1018), as well as putative interaction partners, Arg(935) in the loop between transmembrane segments M8 and M9 and Lys(768) in transmembrane segment M5, as crucial to Na(+) activation of phosphorylation of E(1), a partial reaction reflecting Na(+) interaction on the cytoplasmic side of the membrane. Tyr(1017), Tyr(1018), and Arg(935) are furthermore indispensable to Na(+) interaction on the extracellular side of the membrane, as revealed by inability of high Na(+) concentrations to drive the transition from E(1)P to E(2)P backwards toward E(1)P and inhibit Na(+)-ATPase activity in mutants. Lys(768) is not important for Na(+) binding from the external side of the membrane but is involved in stabilization of the E(2) form. These data demonstrate that the C terminus controls Na(+) affinity on both sides of the membrane and suggest that Arg(935) constitutes an important link between the C terminus and the third Na(+) site, involving an arginine-pi stacking interaction between Arg(935) and the C-terminal tyrosines. Lys(768) may interact preferentially with the C terminus in E(1) and E(1)P forms and with the loop between transmembrane segments M6 and M7 in E(2) and E(2)P forms.
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Affiliation(s)
- Mads S Toustrup-Jensen
- Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, Aarhus University, DK-8000 Aarhus C, Denmark
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Laursen M, Bublitz M, Moncoq K, Olesen C, Møller JV, Young HS, Nissen P, Morth JP. Cyclopiazonic acid is complexed to a divalent metal ion when bound to the sarcoplasmic reticulum Ca2+-ATPase. J Biol Chem 2009; 284:13513-13518. [PMID: 19289472 DOI: 10.1074/jbc.c900031200] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have determined the structure of the sarco(endo)plasmic reticulum Ca(2+)-ATPase (SERCA) in an E2.P(i)-like form stabilized as a complex with MgF(4)(2-), an ATP analog, adenosine 5'-(beta,gamma-methylene)triphosphate (AMPPCP), and cyclopiazonic acid (CPA). The structure determined at 2.5A resolution leads to a significantly revised model of CPA binding when compared with earlier reports. It shows that a divalent metal ion is required for CPA binding through coordination of the tetramic acid moiety at a characteristic kink of the M1 helix found in all P-type ATPase structures, which is expected to be part of the cytoplasmic cation access pathway. Our model is consistent with the biochemical data on CPA function and provides new measures in structure-based drug design targeting Ca(2+)-ATPases, e.g. from pathogens. We also present an extended structural basis of ATP modulation pinpointing key residues at or near the ATP binding site. A structural comparison to the Na(+),K(+)-ATPase reveals that the Phe(93) side chain occupies the equivalent binding pocket of the CPA site in SERCA, suggesting an important role of this residue in stabilization of the potassium-occluded E2 state of Na(+),K(+)-ATPase.
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Affiliation(s)
- Mette Laursen
- Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark; Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Maike Bublitz
- Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark; Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - Karine Moncoq
- Department of Biochemistry and National Institute for Nanotechnology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Claus Olesen
- Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark; Department of Physiology and Biophysics, Aarhus University, Ole Worms Allé, Bldg. 1160, DK-8000 Aarhus C, Denmark
| | - Jesper Vuust Møller
- Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark; Department of Physiology and Biophysics, Aarhus University, Ole Worms Allé, Bldg. 1160, DK-8000 Aarhus C, Denmark
| | - Howard S Young
- Department of Biochemistry and National Institute for Nanotechnology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Poul Nissen
- Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark; Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
| | - J Preben Morth
- Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark; Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark.
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Morth JP, Poulsen H, Toustrup-Jensen MS, Schack VR, Egebjerg J, Andersen JP, Vilsen B, Nissen P. The structure of the Na+,K+-ATPase and mapping of isoform differences and disease-related mutations. Philos Trans R Soc Lond B Biol Sci 2009; 364:217-27. [PMID: 18957371 DOI: 10.1098/rstb.2008.0201] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Na+,K+-ATPase transforms the energy of ATP to the maintenance of steep electrochemical gradients for sodium and potassium across the plasma membrane. This activity is tissue specific, in particular due to variations in the expressions of the alpha subunit isoforms one through four. Several mutations in alpha2 and 3 have been identified that link the specific function of the Na+,K+-ATPase to the pathophysiology of neurological diseases such as rapid-onset dystonia parkinsonism and familial hemiplegic migraine type 2. We show a mapping of the isoform differences and the disease-related mutations on the recently determined crystal structure of the pig renal Na+,K+-ATPase and a structural comparison to Ca2+-ATPase. Furthermore, we present new experimental data that address the role of a stretch of three conserved arginines near the C-terminus of the alpha subunit (Arg1003-Arg1005).
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Affiliation(s)
- J Preben Morth
- Centre for Membrane Pumps in Cells and Disease-PUMPKIN, Danish National Research Foundation, University of Aarhus, Gustav Wieds Vej 10C, Aarhus C, Denmark
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Khandelia H, Poulsen H, Morth JP, Nissen P, Mouritsen O. Molecular Insights Into The Modulation Of Sodium Binding Affinity And Voltage Sensitivity Of The Sodium-Potassium Pump From Molecular Dynamics Simulations, Electrophysiology And Structure. Biophys J 2009. [DOI: 10.1016/j.bpj.2008.12.1864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Morth JP, Sørensen TLM, Nissen P. Membrane's Eleven: heavy-atom derivatives of membrane-protein crystals. Acta Crystallogr D Biol Crystallogr 2006; 62:877-82. [PMID: 16855303 DOI: 10.1107/s0907444906023547] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 06/20/2006] [Indexed: 11/10/2022]
Abstract
A database has been assembled of heavy-atom derivatives used in the structure determination of membrane proteins. The database can serve as a guide to the design of experiments in the search for heavy-atom derivatives of new membrane-protein crystals. The database pinpoints organomercurials, platinum(II) and trimethyllead compounds as being particularly useful. On the other hand, lanthanide and uranyl compounds are poorly represented, which may be a consequence of these compounds having aggressive effects in crystal-soaking procedures. Furthermore, the database highlights the variety of methods applied in the preparation of heavy-atom-derivatized crystals and in phasing. Cocrystallization can be further exploited. Phases have predominantly been obtained by SIRAS/MIRAS methods rather than SAD/MAD in recent structure determinations.
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Affiliation(s)
- J Preben Morth
- Center for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
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Nowak E, Panjikar S, Morth JP, Jordanova R, Svergun DI, Tucker PA. Structural and functional aspects of the sensor histidine kinase PrrB from Mycobacterium tuberculosis. Structure 2006; 14:275-85. [PMID: 16472747 DOI: 10.1016/j.str.2005.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Revised: 10/16/2005] [Accepted: 10/18/2005] [Indexed: 10/25/2022]
Abstract
We describe the solution structures of two- and three-domain constructs of the sensor histidine kinase PrrB from Mycobacterium tuberculosis, which allow us to locate the HAMP linker relative to the ATP binding and dimerization domains. We show that the three-domain construct is active both for autophosphorylation and for phosphotransfer to the cognate response regulator, PrrA. We also describe the high-resolution crystal structure of the catalytic domain alone, and we show that, in solution, it binds ATP. The conformational flexibility of this domain is discussed and related to other structural information.
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Affiliation(s)
- Elzbieta Nowak
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22 603 Hamburg, Germany
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Abstract
We report the identification of a novel two-component system in Mycobacterium tuberculosis. We show that the putative histidine kinase with the genomic locus tag Rv3220c is able to self-phosphorylate in the presence of Mg2+/ATP and subsequently transfer the phosphoryl group to a novel response regulator PdtaR. This creates a biochemical link between the two proteins and establishes a newly identified two component system, which acts at the level of transcriptional antitermination. We also suggest that this system has potential for the development of lead compounds for inhibition of phosphotransfer.
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Affiliation(s)
- J Preben Morth
- European Molecular Biology Laboratory (EMBL) Hamburg, Notkestrasse 85, 22603 Hamburg, Germany
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Morth JP, Feng V, Perry LJ, Svergun DI, Tucker PA. The crystal and solution structure of a putative transcriptional antiterminator from Mycobacterium tuberculosis. Structure 2005; 12:1595-605. [PMID: 15341725 DOI: 10.1016/j.str.2004.06.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2004] [Revised: 06/22/2004] [Accepted: 06/24/2004] [Indexed: 10/26/2022]
Abstract
We describe the crystal structure of Rv1626 from Mycobacterium tuberculosis at 1.48 A resolution and the corresponding solution structure determined from small angle X-ray scattering. The N-terminal domain shows structural homology to the receiver domains found in bacterial two-component systems. The C-terminal domain has high structural homology to a recently discovered RNA binding domain involved in transcriptional antitermination. The molecule in solution was found to be monomeric as it is in the crystal, but in solution it undergoes a conformational change that is triggered by changes in ionic strength. This is the first structure that links the phosphorylation cascade of the two-component systems with the antitermination event in the transcriptional machinery. Rv1626 belongs to a family of proteins, which we propose calling phosphorylation-dependent transcriptional antitermination regulators, so far only found in bacteria, and includes NasT, a protein from the assimilatory nitrate/nitrite reductase operon of Azetobacter vinelandii.
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Affiliation(s)
- J Preben Morth
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, Germany
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