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Li W, Lückstädt W, Wöhner B, Bub S, Schulz A, Socher E, Arnold P. Structural and functional properties of meprin β metalloproteinase with regard to cell signaling. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119136. [PMID: 34626678 DOI: 10.1016/j.bbamcr.2021.119136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/05/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
The metalloproteinase meprin β plays an important role during collagen I deposition in the skin, mucus detachment in the small intestine and also regulates the abundance of different cell surface proteins such as the interleukin-6 receptor (IL-6R), the triggering receptor expressed on myeloid cells 2 (TREM2), the cluster of differentiation 99 (CD99), the amyloid precursor protein (APP) and the cluster of differentiation 109 (CD109). With that, regulatory mechanisms that control meprin β activity and regulate its release from the cell surface to enable access to distant substrates are increasingly important. Here, we will summarize factors that alternate meprin β activity and thereby regulate its proteolytic activity on the cell surface or in the supernatant. We will also discuss cleavage of the IL-6R and TREM2 on the cell surface and compare it to CD109. CD109, as a substrate of meprin β, is cleaved within the protein core, thereby releasing defined fragments from the cell surface. At last, we will also summarize the role of proteases in general and meprin β in particular in substrate release on extracellular vesicles.
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Affiliation(s)
- Wenjia Li
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Wiebke Lückstädt
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel (CAU), Kiel, Germany
| | - Birte Wöhner
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel (CAU), Kiel, Germany
| | - Simon Bub
- Department of Molecular-Neurology, University Hospital Erlangen, Erlangen, Germany
| | - Antonia Schulz
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel (CAU), Kiel, Germany
| | - Eileen Socher
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Philipp Arnold
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany.
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Kato Y, Hin N, Maita N, Thomas AG, Kurosawa S, Rojas C, Yorita K, Slusher BS, Fukui K, Tsukamoto T. Structural basis for potent inhibition of d-amino acid oxidase by thiophene carboxylic acids. Eur J Med Chem 2018; 159:23-34. [PMID: 30265959 PMCID: PMC6193832 DOI: 10.1016/j.ejmech.2018.09.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/10/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022]
Abstract
A series of thiophene-2-carboxylic acids and thiophene-3-carboxylic acids were identified as a new class of DAO inhibitors. Structure-activity relationship (SAR) studies revealed that small substituents are well-tolerated on the thiophene ring of both the 2-carboxylic acid and 3-carboxylic acid scaffolds. Crystal structures of human DAO in complex with potent thiophene carboxylic acids revealed that Tyr224 was tightly stacked with the thiophene ring of the inhibitors, resulting in the disappearance of the secondary pocket observed with other DAO inhibitors. Molecular dynamics simulations of the complex revealed that Tyr224 preferred the stacked conformation irrespective of whether Tyr224 was stacked or not in the initial state of the simulations. MM/GBSA indicated a substantial hydrophobic interaction between Tyr244 and the thiophene-based inhibitor. In addition, the active site was tightly closed with an extensive network of hydrogen bonds including those from Tyr224 in the stacked conformation. The introduction of a large branched side chain to the thiophene ring markedly decreased potency. These results are in marked contrast to other DAO inhibitors that can gain potency with a branched side chain extending to the secondary pocket due to Tyr224 repositioning. These insights should be of particular importance in future efforts to optimize DAO inhibitors with novel scaffolds.
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Affiliation(s)
- Yusuke Kato
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Niyada Hin
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Nobuo Maita
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Ajit G Thomas
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Sumire Kurosawa
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Camilo Rojas
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Kazuko Yorita
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan
| | - Barbara S Slusher
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Kiyoshi Fukui
- Institute for Enzyme Research, Tokushima University, Tokushima, 770-8503, Japan.
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery, Johns Hopkins University, Baltimore, MD, 21205, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD, 21205, USA
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Harborne SPD, Ruprecht JJ, Kunji ERS. Calcium-induced conformational changes in the regulatory domain of the human mitochondrial ATP-Mg/Pi carrier. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1847:1245-53. [PMID: 26164100 PMCID: PMC4562336 DOI: 10.1016/j.bbabio.2015.07.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/15/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022]
Abstract
The mitochondrial ATP-Mg/Pi carrier imports adenine nucleotides from the cytosol into the mitochondrial matrix and exports phosphate. The carrier is regulated by the concentration of cytosolic calcium, altering the size of the adenine nucleotide pool in the mitochondrial matrix in response to energetic demands. The protein consists of three domains; (i) the N-terminal regulatory domain, which is formed of two pairs of fused calcium-binding EF-hands, (ii) the C-terminal mitochondrial carrier domain, which is involved in transport, and (iii) a linker region with an amphipathic α-helix of unknown function. The mechanism by which calcium binding to the regulatory domain modulates substrate transport in the carrier domain has not been resolved. Here, we present two new crystal structures of the regulatory domain of the human isoform 1. Careful analysis by SEC confirmed that although the regulatory domain crystallised as dimers, full-length ATP-Mg/Pi carrier is monomeric. Therefore, the ATP-Mg/Pi carrier must have a different mechanism of calcium regulation than the architecturally related aspartate/glutamate carrier, which is dimeric. The structure showed that an amphipathic α-helix is bound to the regulatory domain in a hydrophobic cleft of EF-hand 3/4. Detailed bioinformatics analyses of different EF-hand states indicate that upon release of calcium, EF-hands close, meaning that the regulatory domain would release the amphipathic α-helix. We propose a mechanism for ATP-Mg/Pi carriers in which the amphipathic α-helix becomes mobile upon release of calcium and could block the transport of substrates across the mitochondrial inner membrane.
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Affiliation(s)
- Steven P D Harborne
- The Medical Research Council, Mitochondrial Biology Unit, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Jonathan J Ruprecht
- The Medical Research Council, Mitochondrial Biology Unit, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK
| | - Edmund R S Kunji
- The Medical Research Council, Mitochondrial Biology Unit, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.
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Arnold P, Schmidt F, Prox J, Zunke F, Pietrzik C, Lucius R, Becker-Pauly C. Calcium negatively regulates meprin β activity and attenuates substrate cleavage. FASEB J 2015; 29:3549-57. [DOI: 10.1096/fj.15-272310] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/27/2015] [Indexed: 12/31/2022]
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Allen MD, Qamar S, Vadivelu MK, Sandford RN, Bycroft M. A high-resolution structure of the EF-hand domain of human polycystin-2. Protein Sci 2014; 23:1301-8. [PMID: 24990821 PMCID: PMC4244000 DOI: 10.1002/pro.2513] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/25/2014] [Accepted: 06/29/2014] [Indexed: 01/11/2023]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) affects over 1:1000 of the worldwide population and is caused by mutations in two genes, PKD1 and PKD2. PKD2 encodes a 968-amino acid membrane spanning protein, Polycystin-2 (PC-2), which is a member of the TRP ion channel family. The C-terminal cytoplasmic tail contains an EF-hand motif followed by a short coiled-coil domain. We have determined the structure of the EF-hand region of PC-2 using NMR spectroscopy. The use of different boundaries, compared with those used in previous studies, have enabled us to determine a high resolution structure and show that the EF hand motif forms a standard calcium-binding pocket. The affinity of this pocket for calcium has been measured and mutants that both decrease and increase its affinity for the metal ion have been created.
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Affiliation(s)
- Mark D Allen
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, United Kingdom
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Ca2+-binding properties and regulatory roles of lobster troponin C sites II and IV. FEBS Lett 2013; 587:2612-6. [DOI: 10.1016/j.febslet.2013.06.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 06/14/2013] [Accepted: 06/21/2013] [Indexed: 11/18/2022]
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Nara M, Morii H, Tanokura M. Coordination to divalent cations by calcium-binding proteins studied by FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012. [PMID: 23201542 DOI: 10.1016/j.bbamem.2012.11.025] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We review the Fourier-transform infrared (FTIR) spectroscopy of side-chain COO(-) groups of Ca(2+)-binding proteins: parvalbumins, bovine calmodulin, akazara scallop troponin C and related calcium binding proteins and peptide analogues. The COO(-) stretching vibration modes can be used to identify the coordination modes of COO(-) groups of Ca(2+)-binding proteins to metal ions: bidentate, unidentate, and pseudo-bridging. FTIR spectroscopy demonstrates that the coordination structure of Mg(2+) is distinctly different from that of Ca(2+) in the Ca(2+)-binding site in solution. The interpretation of COO(-) stretches is ensured on the basis of the spectra of calcium-binding peptide analogues. The implication of COO(-) stretches is discussed for Ca(2+)-binding proteins. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Masayuki Nara
- Laboratory of Chemistry, College of Liberal Arts and Sciences, Tokyo Medical and Dental University, Chiba 272-0827, Japan.
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