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Frey L, Zhou J, Cereghetti G, Weber ME, Rhyner D, Pokharna A, Wenchel L, Kadavath H, Cao Y, Meier BH, Peter M, Greenwald J, Riek R, Mezzenga R. A structural rationale for reversible vs irreversible amyloid fibril formation from a single protein. Nat Commun 2024; 15:8448. [PMID: 39349464 PMCID: PMC11442456 DOI: 10.1038/s41467-024-52681-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 09/18/2024] [Indexed: 10/02/2024] Open
Abstract
Reversible and irreversible amyloids are two diverging cases of protein (mis)folding associated with the cross-β motif in the protein folding and aggregation energy landscape. Yet, the molecular origins responsible for the formation of reversible vs irreversible amyloids have remained unknown. Here we provide evidence at the atomic level of distinct folding motifs for irreversible and reversible amyloids derived from a single protein sequence: human lysozyme. We compare the 2.8 Å structure of irreversible amyloid fibrils determined by cryo-electron microscopy helical reconstructions with molecular insights gained by solid-state NMR spectroscopy on reversible amyloids. We observe a canonical cross-β-sheet structure in irreversible amyloids, whereas in reversible amyloids, there is a less-ordered coexistence of β-sheet and helical secondary structures that originate from a partially unfolded lysozyme, thus carrying a "memory" of the original folded protein precursor. We also report the structure of hen egg-white lysozyme irreversible amyloids at 3.2 Å resolution, revealing another canonical amyloid fold, and reaffirming that irreversible amyloids undergo a complete conversion of the native protein into the cross-β structure. By combining atomic force microscopy, cryo-electron microscopy and solid-state NMR, we show that a full unfolding of the native protein precursor is a requirement for establishing irreversible amyloid fibrils.
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Affiliation(s)
- Lukas Frey
- Institute of Molecular Physical Science, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, Switzerland
| | - Jiangtao Zhou
- ETH Zurich, Department of Health Sciences and Technology, Zurich, Switzerland.
| | - Gea Cereghetti
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, United Kingdom
| | - Marco E Weber
- Institute of Molecular Physical Science, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, Switzerland
| | - David Rhyner
- Institute of Molecular Physical Science, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, Switzerland
| | - Aditya Pokharna
- Institute of Molecular Physical Science, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, Switzerland
| | - Luca Wenchel
- Institute of Molecular Physical Science, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, Switzerland
| | - Harindranath Kadavath
- Institute of Molecular Physical Science, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, Switzerland
| | - Yiping Cao
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Beat H Meier
- Institute of Molecular Physical Science, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jason Greenwald
- Institute of Molecular Physical Science, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, Switzerland
| | - Roland Riek
- Institute of Molecular Physical Science, ETH Zürich, Vladimir-Prelog-Weg 2, Zürich, Switzerland.
| | - Raffaele Mezzenga
- ETH Zurich, Department of Health Sciences and Technology, Zurich, Switzerland.
- ETH Zurich, Department of Materials, Zurich, Switzerland.
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2
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Schofield LC, Dialpuri JS, Murshudov GN, Agirre J. Post-translational modifications in the Protein Data Bank. Acta Crystallogr D Struct Biol 2024; 80:647-660. [PMID: 39207896 PMCID: PMC11394121 DOI: 10.1107/s2059798324007794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024] Open
Abstract
Proteins frequently undergo covalent modification at the post-translational level, which involves the covalent attachment of chemical groups onto amino acids. This can entail the singular or multiple addition of small groups, such as phosphorylation; long-chain modifications, such as glycosylation; small proteins, such as ubiquitination; as well as the interconversion of chemical groups, such as the formation of pyroglutamic acid. These post-translational modifications (PTMs) are essential for the normal functioning of cells, as they can alter the physicochemical properties of amino acids and therefore influence enzymatic activity, protein localization, protein-protein interactions and protein stability. Despite their inherent importance, accurately depicting PTMs in experimental studies of protein structures often poses a challenge. This review highlights the role of PTMs in protein structures, as well as the prevalence of PTMs in the Protein Data Bank, directing the reader to accurately built examples suitable for use as a modelling reference.
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Affiliation(s)
- Lucy C Schofield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Jordan S Dialpuri
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Garib N Murshudov
- MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
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3
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Rodrigues AV, Moriarty NW, Kakumanu R, DeGiovanni A, Pereira JH, Gin JW, Chen Y, Baidoo EEK, Petzold CJ, Adams PD. Characterization of lignin degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid (PDC). J Biol Chem 2024:107736. [PMID: 39222681 DOI: 10.1016/j.jbc.2024.107736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/22/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is CHMS dehydrogenase, which acts on the substrate 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS). We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.
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Affiliation(s)
- Andria V Rodrigues
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States.
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Ramu Kakumanu
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Andy DeGiovanni
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Jose Henrique Pereira
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Jennifer W Gin
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States; Department of Energy Agile BioFoundry, Emeryville, California United States
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States; Department of Energy Agile BioFoundry, Emeryville, California United States
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States; Department of Energy Agile BioFoundry, Emeryville, California United States
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, California, 94608, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States; Department of Bioengineering, University of California Berkeley, Berkeley California 94720, United States.
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4
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Frey L, Ghosh D, Qureshi BM, Rhyner D, Guerrero-Ferreira R, Pokharna A, Kwiatkowski W, Serdiuk T, Picotti P, Riek R, Greenwald J. On the pH-dependence of α-synuclein amyloid polymorphism and the role of secondary nucleation in seed-based amyloid propagation. eLife 2024; 12:RP93562. [PMID: 39196271 DOI: 10.7554/elife.93562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2024] Open
Abstract
The aggregation of the protein α-synuclein is closely associated with several neurodegenerative disorders and as such the structures of the amyloid fibril aggregates have high scientific and medical significance. However, there are dozens of unique atomic-resolution structures of these aggregates, and such a highly polymorphic nature of the α-synuclein fibrils hampers efforts in disease-relevant in vitro studies on α-synuclein amyloid aggregation. In order to better understand the factors that affect polymorph selection, we studied the structures of α-synuclein fibrils in vitro as a function of pH and buffer using cryo-EM helical reconstruction. We find that in the physiological range of pH 5.8-7.4, a pH-dependent selection between Type 1, 2, and 3 polymorphs occurs. Our results indicate that even in the presence of seeds, the polymorph selection during aggregation is highly dependent on the buffer conditions, attributed to the non-polymorph-specific nature of secondary nucleation. We also uncovered two new polymorphs that occur at pH 7.0 in phosphate-buffered saline. The first is a monofilament Type 1 fibril that highly resembles the structure of the juvenile-onset synucleinopathy polymorph found in patient-derived material. The second is a new Type 5 polymorph that resembles a polymorph that has been recently reported in a study that used diseased tissues to seed aggregation. Taken together, our results highlight the shallow amyloid energy hypersurface that can be altered by subtle changes in the environment, including the pH which is shown to play a major role in polymorph selection and in many cases appears to be the determining factor in seeded aggregation. The results also suggest the possibility of producing disease-relevant structure in vitro.
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Affiliation(s)
- Lukas Frey
- Institute of Molecular Physical Science, Zürich, Switzerland
| | - Dhiman Ghosh
- Institute of Molecular Physical Science, Zürich, Switzerland
| | - Bilal M Qureshi
- Scientific Center for Optical and Electron Microscopy, Zürich, Switzerland
| | - David Rhyner
- Institute of Molecular Physical Science, Zürich, Switzerland
| | | | - Aditya Pokharna
- Institute of Molecular Physical Science, Zürich, Switzerland
| | | | - Tetiana Serdiuk
- Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Paola Picotti
- Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | - Roland Riek
- Institute of Molecular Physical Science, Zürich, Switzerland
| | - Jason Greenwald
- Institute of Molecular Physical Science, Zürich, Switzerland
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5
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Ahmad MS, Kalam N, Akbar Z, Shah N, Rasheed S, Choudhary MI. Structural basis for the binding of famotidine, cimetidine, guanidine, and pimagedine with serine protease. Biochem Biophys Res Commun 2024; 733:150603. [PMID: 39216203 DOI: 10.1016/j.bbrc.2024.150603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2024] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
Serine proteases are among the important groups of enzymes having significant roles in cell biology. Trypsin is a representative member of the serine superfamily of enzymes, produced by acinar cells of pancreas. It is a validated drug target for various ailments including pancreatitis and colorectal cancer. Premature activation of trypsin is involved in the lysis of pancreatic tissues, which causes pancreatitis. It is also reported to be involved in colorectal carcinoma by activating other proteases, such as matrix metalloproteinase (MMPs). The development of novel trypsin inhibitors with good pharmacokinetic properties could play important roles in pharmaceutical sciences. This study reports the crystal structures of bovine pancreatic trypsin with four molecules; cimetidine, famotidine, pimagedine, and guanidine. These compounds possess binding affinity towards the active site (S1) of trypsin. The structures of all four complexes provided insight of the binding of four different ligands, as well as the dynamics of the active site towards the bind with different size ligands. This study might be helpful in designing of new potent inhibitors of trypsin and trypsin like serine proteases.
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Affiliation(s)
- Malik Shoaib Ahmad
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
| | - Noor Kalam
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Zeeshan Akbar
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Nayab Shah
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - Saima Rasheed
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - M Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
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6
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Guneri D, Alexandrou E, El Omari K, Dvořáková Z, Chikhale RV, Pike DTS, Waudby CA, Morris CJ, Haider S, Parkinson GN, Waller ZAE. Structural insights into i-motif DNA structures in sequences from the insulin-linked polymorphic region. Nat Commun 2024; 15:7119. [PMID: 39164244 PMCID: PMC11336075 DOI: 10.1038/s41467-024-50553-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/12/2024] [Indexed: 08/22/2024] Open
Abstract
The insulin-linked polymorphic region is a variable number of tandem repeats region of DNA in the promoter of the insulin gene that regulates transcription of insulin. This region is known to form the alternative DNA structures, i-motifs and G-quadruplexes. Individuals have different sequence variants of tandem repeats and although previous work investigated the effects of some variants on G-quadruplex formation, there is not a clear picture of the relationship between the sequence diversity, the DNA structures formed, and the functional effects on insulin gene expression. Here we show that different sequence variants of the insulin linked polymorphic region form different DNA structures in vitro. Additionally, reporter genes in cellulo indicate that insulin expression may change depending on which DNA structures form. We report the crystal structure and dynamics of an intramolecular i-motif, which reveal sequences within the loop regions forming additional stabilising interactions that are critical to formation of stable i-motif structures. The outcomes of this work reveal the detail in formation of stable i-motif DNA structures, with potential for rational based drug design for compounds to target i-motif DNA.
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Affiliation(s)
- Dilek Guneri
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Effrosyni Alexandrou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Kamel El Omari
- Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, OX11 0DE, UK
| | - Zuzana Dvořáková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00, Brno, Czech Republic
| | - Rupesh V Chikhale
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Daniel T S Pike
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Christopher A Waudby
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Christopher J Morris
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | - Shozeb Haider
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
- UCL Centre for Advanced Research Computing, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Gary N Parkinson
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | - Zoë A E Waller
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
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7
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Francesconi V, Rizzo M, Pozzi C, Tagliazucchi L, Konchie Simo CU, Saporito G, Landi G, Mangani S, Carbone A, Schenone S, Santarém N, Tavares J, Cordeiro-da-Silva A, Costi MP, Tonelli M. Identification of Innovative Folate Inhibitors Leveraging the Amino Dihydrotriazine Motif from Cycloguanil for Their Potential as Anti- Trypanosoma brucei Agents. ACS Infect Dis 2024; 10:2755-2774. [PMID: 38953453 DOI: 10.1021/acsinfecdis.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Folate enzymes, namely, dihydrofolate reductase (DHFR) and pteridine reductase (PTR1) are acknowledged targets for the development of antiparasitic agents against Trypanosomiasis and Leishmaniasis. Based on the amino dihydrotriazine motif of the drug Cycloguanil (Cyc), a known inhibitor of both folate enzymes, we have identified two novel series of inhibitors, the 2-amino triazino benzimidazoles (1) and 2-guanidino benzimidazoles (2), as their open ring analogues. Enzymatic screening was carried out against PTR1, DHFR, and thymidylate synthase (TS). The crystal structures of TbDHFR and TbPTR1 in complex with selected compounds experienced in both cases a substrate-like binding mode and allowed the rationalization of the main chemical features supporting the inhibitor ability to target folate enzymes. Biological evaluation of both series was performed against T. brucei and L. infantum and the toxicity against THP-1 human macrophages. Notably, the 5,6-dimethyl-2-guanidinobenzimidazole 2g resulted to be the most potent (Ki = 9 nM) and highly selective TbDHFR inhibitor, 6000-fold over TbPTR1 and 394-fold over hDHFR. The 5,6-dimethyl tricyclic analogue 1g, despite showing a lower potency and selectivity profile than 2g, shared a comparable antiparasitic activity against T. brucei in the low micromolar domain. The dichloro-substituted 2-guanidino benzimidazoles 2c and 2d revealed their potent and broad-spectrum antitrypanosomatid activity affecting the growth of T. brucei and L. infantum parasites. Therefore, both chemotypes could represent promising templates that could be valorized for further drug development.
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Affiliation(s)
- Valeria Francesconi
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
| | - Marco Rizzo
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena 53100, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIMMP), Via Luigi Sacconi 6, Sesto Fiorentino (FI) 50019, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
- Doctorate School in Clinical and Experimental Medicine (CEM), University of Modena and Reggio Emilia, Via Campi 287, Modena 41125, Italy
| | - Claude U Konchie Simo
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Giulia Saporito
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | - Anna Carbone
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
| | - Silvia Schenone
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
| | - Nuno Santarém
- i3S - Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen, 208, Porto 4200-135, Portugal
| | - Joana Tavares
- i3S - Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen, 208, Porto 4200-135, Portugal
| | - Anabela Cordeiro-da-Silva
- i3S - Institute for Research and Innovation in Health, University of Porto, Rua Alfredo Allen, 208, Porto 4200-135, Portugal
- Department of Life Science, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal
| | - Maria Paola Costi
- Department of Life Science, University of Modena and Reggio Emilia, via Campi 103, Modena 41125, Italy
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy
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8
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Dalwani S, Metz A, Huschmann FU, Weiss MS, Wierenga RK, Venkatesan R. Crystallographic fragment-binding studies of the Mycobacterium tuberculosis trifunctional enzyme suggest binding pockets for the tails of the acyl-CoA substrates at its active sites and a potential substrate-channeling path between them. Acta Crystallogr D Struct Biol 2024; 80:605-619. [PMID: 39012716 DOI: 10.1107/s2059798324006557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an α2β2 tetrameric enzyme in which the α-chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) active sites, and the β-chain provides the 3-ketoacyl-CoA thiolase (KAT) active site. Linear, medium-chain and long-chain 2E-enoyl-CoA molecules are the preferred substrates of MtTFE. Previous crystallographic binding and modeling studies identified binding sites for the acyl-CoA substrates at the three active sites, as well as the NAD binding pocket at the HAD active site. These studies also identified three additional CoA binding sites on the surface of MtTFE that are different from the active sites. It has been proposed that one of these additional sites could be of functional relevance for the substrate channeling (by surface crawling) of reaction intermediates between the three active sites. Here, 226 fragments were screened in a crystallographic fragment-binding study of MtTFE crystals, resulting in the structures of 16 MtTFE-fragment complexes. Analysis of the 121 fragment-binding events shows that the ECH active site is the `binding hotspot' for the tested fragments, with 41 binding events. The mode of binding of the fragments bound at the active sites provides additional insight into how the long-chain acyl moiety of the substrates can be accommodated at their proposed binding pockets. In addition, the 20 fragment-binding events between the active sites identify potential transient binding sites of reaction intermediates relevant to the possible channeling of substrates between these active sites. These results provide a basis for further studies to understand the functional relevance of the latter binding sites and to identify substrates for which channeling is crucial.
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Affiliation(s)
- Subhadra Dalwani
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Franziska U Huschmann
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin, Germany
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Rajaram Venkatesan
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
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9
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Hwang IS, Oh EJ, Oh CS. A novel virulence gene, cviA1 of Clavibacter michiganensis for necrosis development in the Nicotiana benthamiana plant. Microbiol Res 2024; 285:127743. [PMID: 38733725 DOI: 10.1016/j.micres.2024.127743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/06/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Clavibacter michiganensis is a Gram-positive bacterium that causes diverse disease symptoms in tomatoes and Nicotiana benthamiana, a surrogate host plant, including canker, blister lesions, and wilting. Previously, we reported that C. michiganensis also causes necrosis in N. benthamiana leaves. Here, to identify novel virulence genes of C. michiganensis required for necrosis development in N. benthamiana leaves, we screened 1,862 transposon-inserted mutants and identified a mutant strain that exhibited weak and delayed necrosis, whereas there was no discernible difference in blister lesions, canker, or wilting symptoms. Notably, this mutant caused canker similar to that of the wild-type strain, but caused mild wilting in tomato. This mutant carried a transposon in a chromosomal gene, called Clavibactervirulence gene A1 (cviA1). CviA1 encodes a 180-amino acid protein with a signal peptide (SP) at the N-terminus and two putative transmembrane domains (TMs) at the C-terminus. Interestingly, deletion of the SP or the C-terminus, including the two putative TMs, in CviA1 failed to restore full necrosis in the mutant, highlighting the importance of protein secretion and the putative TMs for necrosis. A paralog of cviA1, cviA2 is located on the large plasmid pCM2 of C. michiganensis. Despite its high similarity to cviA1, the introduction of cviA2 into the cviA1 mutant strain did not restore virulence. Similarly, the introduction of cviA1 into the Clavibacter capsici type strain PF008, which initially lacks cviA1, did not enhance necrosis symptoms. These results reveals that the chromosomal cviA1 gene in C. michiganensis plays an important role in necrosis development in N. benthamiana leaves.
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Affiliation(s)
- In Sun Hwang
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, the Republic of Korea
| | - Eom-Ji Oh
- Plant Immunity Research Center, Seoul National University, Seoul 08826, the Republic of Korea
| | - Chang-Sik Oh
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, the Republic of Korea; Plant Immunity Research Center, Seoul National University, Seoul 08826, the Republic of Korea; Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, the Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, the Republic of Korea.
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10
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Sutherland‐Smith AJ, Carbone V, Schofield LR, Cronin B, Duin EC, Ronimus RS. The crystal structure of methanogen McrD, a methyl-coenzyme M reductase-associated protein. FEBS Open Bio 2024; 14:1222-1229. [PMID: 38877345 PMCID: PMC11301259 DOI: 10.1002/2211-5463.13848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/16/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
Methyl-coenzyme M reductase (MCR) is a multi-subunit (α2β2γ2) enzyme responsible for methane formation via its unique F430 cofactor. The genes responsible for producing MCR (mcrA, mcrB and mcrG) are typically colocated with two other highly conserved genes mcrC and mcrD. We present here the high-resolution crystal structure for McrD from a human gut methanogen Methanomassiliicoccus luminyensis strain B10. The structure reveals that McrD comprises a ferredoxin-like domain assembled into an α + β barrel-like dimer with conformational flexibility exhibited by a functional loop. The description of the M. luminyensis McrD crystal structure contributes to our understanding of this key conserved methanogen protein typically responsible for promoting MCR activity and the production of methane, a greenhouse gas.
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Affiliation(s)
| | | | | | - Bryan Cronin
- Department of Chemistry and BiochemistryAuburn UniversityALUSA
| | - Evert C. Duin
- Department of Chemistry and BiochemistryAuburn UniversityALUSA
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11
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Qin C, Graf LG, Striska K, Janetzky M, Geist N, Specht R, Schulze S, Palm GJ, Girbardt B, Dörre B, Berndt L, Kemnitz S, Doerr M, Bornscheuer UT, Delcea M, Lammers M. Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule. Nat Commun 2024; 15:6002. [PMID: 39019872 PMCID: PMC11255334 DOI: 10.1038/s41467-024-49952-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/24/2024] [Indexed: 07/19/2024] Open
Abstract
The AMP-forming acetyl-CoA synthetase is regulated by lysine acetylation both in bacteria and eukaryotes. However, the underlying mechanism is poorly understood. The Bacillus subtilis acetyltransferase AcuA and the AMP-forming acetyl-CoA synthetase AcsA form an AcuA•AcsA complex, dissociating upon lysine acetylation of AcsA by AcuA. Crystal structures of AcsA from Chloroflexota bacterium in the apo form and in complex with acetyl-adenosine-5'-monophosphate (acetyl-AMP) support the flexible C-terminal domain adopting different conformations. AlphaFold2 predictions suggest binding of AcuA stabilizes AcsA in an undescribed conformation. We show the AcuA•AcsA complex dissociates upon acetyl-coenzyme A (acetyl-CoA) dependent acetylation of AcsA by AcuA. We discover an intrinsic phosphotransacetylase activity enabling AcuA•AcsA generating acetyl-CoA from acetyl-phosphate (AcP) and coenzyme A (CoA) used by AcuA to acetylate and inactivate AcsA. Here, we provide mechanistic insights into the regulation of AMP-forming acetyl-CoA synthetases by lysine acetylation and discover an intrinsic phosphotransacetylase allowing modulation of its activity based on AcP and CoA levels.
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Affiliation(s)
- Chuan Qin
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Leonie G Graf
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Kilian Striska
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Markus Janetzky
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Norman Geist
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Robin Specht
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Britta Girbardt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Babett Dörre
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Leona Berndt
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Stefan Kemnitz
- Department for High Performance Computing, University Computing Center, University of Greifswald, 17489, Greifswald, Germany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Department of Biophysical Chemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Michael Lammers
- Department of Synthetic and Structural Biochemistry, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany.
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12
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Prajapati A, Palva A, von Ossowski I, Krishnan V. The crystal structure of the N-terminal domain of the backbone pilin LrpA reveals a new closure-and-twist motion for assembling dynamic pili in Ligilactobacillus ruminis. Acta Crystallogr D Struct Biol 2024; 80:474-492. [PMID: 38935340 DOI: 10.1107/s2059798324005114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Sortase-dependent pili are long surface appendages that mediate attachment, colonization and biofilm formation in certain genera and species of Gram-positive bacteria. Ligilactobacillus ruminis is an autochthonous gut commensal that relies on sortase-dependent LrpCBA pili for host adherence and persistence. X-ray crystal structure snapshots of the backbone pilin LrpA were captured in two atypical bent conformations leading to a zigzag morphology in the LrpCBA pilus structure. Small-angle X-ray scattering and structural analysis revealed that LrpA also adopts the typical linear conformation, resulting in an elongated pilus morphology. Various conformational analyses and biophysical experiments helped to demonstrate that a hinge region located at the end of the flexible N-terminal domain of LrpA facilitates a new closure-and-twist motion for assembling dynamic pili during the assembly process and host attachment. Further, the incongruent combination of flexible domain-driven conformational dynamics and rigid isopeptide bond-driven stability observed in the LrpCBA pilus might also extend to the sortase-dependent pili of other bacteria colonizing a host.
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Affiliation(s)
- Amar Prajapati
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR, Biotech Science Cluster, Faridabad 121 001, India
| | - Airi Palva
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR, Biotech Science Cluster, Faridabad 121 001, India
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13
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Li Z, Pickles IB, Sharma M, Melling B, Pallasdies L, Codée JDC, Williams SJ, Overkleeft HS, Davies GJ. Detection of Sulfoquinovosidase Activity in Cell Lysates Using Activity-Based Probes. Angew Chem Int Ed Engl 2024; 63:e202401358. [PMID: 38647177 DOI: 10.1002/anie.202401358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
The sulfolipid sulfoquinovosyl diacylglycerol (SQDG), produced by plants, algae, and cyanobacteria, constitutes a major sulfur reserve in the biosphere. Microbial breakdown of SQDG is critical for the biological utilization of its sulfur. This commences through release of the parent sugar, sulfoquinovose (SQ), catalyzed by sulfoquinovosidases (SQases). These vanguard enzymes are encoded in gene clusters that code for diverse SQ catabolic pathways. To identify, visualize and isolate glycoside hydrolase CAZY-family 31 (GH31) SQases in complex biological environments, we introduce SQ cyclophellitol-aziridine activity-based probes (ABPs). These ABPs label the active site nucleophile of this enzyme family, consistent with specific recognition of the SQ cyclophellitol-aziridine in the active site, as evidenced in the 3D structure of Bacillus megaterium SQase. A fluorescent Cy5-probe enables visualization of SQases in crude cell lysates from bacteria harbouring different SQ breakdown pathways, whilst a biotin-probe enables SQase capture and identification by proteomics. The Cy5-probe facilitates monitoring of active SQase levels during different stages of bacterial growth which show great contrast to more traditional mRNA analysis obtained by RT-qPCR. Given the importance of SQases in global sulfur cycling and in human microbiota, these SQase ABPs provide a new tool with which to study SQase occurrence, activity and stability.
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Affiliation(s)
- Zirui Li
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Isabelle B Pickles
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Mahima Sharma
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Benjamin Melling
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Luise Pallasdies
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Jeroen D C Codée
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Spencer J Williams
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Herman S Overkleeft
- Department of Bio-organic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK
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14
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Williams HM, Thorkelsson S, Vogel D, Busch C, Milewski M, Cusack S, Grünewald K, Quemin EJ, Rosenthal M. Structural snapshots of phenuivirus cap-snatching and transcription. Nucleic Acids Res 2024; 52:6049-6065. [PMID: 38709882 PMCID: PMC11162785 DOI: 10.1093/nar/gkae330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/10/2024] [Accepted: 04/19/2024] [Indexed: 05/08/2024] Open
Abstract
Severe fever with thrombocytopenia syndrome virus (SFTSV) is a human pathogen that is now endemic to several East Asian countries. The viral large (L) protein catalyzes viral transcription by stealing host mRNA caps via a process known as cap-snatching. Here, we establish an in vitro cap-snatching assay and present three high-quality electron cryo-microscopy (cryo-EM) structures of the SFTSV L protein in biologically relevant, transcription-specific states. In a priming-state structure, we show capped RNA bound to the L protein cap-binding domain (CBD). The L protein conformation in this priming structure is significantly different from published replication-state structures, in particular the N- and C-terminal domains. The capped-RNA is positioned in a way that it can feed directly into the RNA-dependent RNA polymerase (RdRp) ready for elongation. We also captured the L protein in an early-elongation state following primer-incorporation demonstrating that this priming conformation is retained at least in the very early stages of primer extension. This structural data is complemented by in vitro biochemical and cell-based assays. Together, these insights further our mechanistic understanding of how SFTSV and other bunyaviruses incorporate stolen host mRNA fragments into their viral transcripts thereby allowing the virus to hijack host cell translation machinery.
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Affiliation(s)
- Harry M Williams
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
| | - Sigurdur R Thorkelsson
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Dominik Vogel
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Carola Busch
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Morlin Milewski
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | | | - Kay Grünewald
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Emmanuelle R J Quemin
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Leibniz Institute of Virology, Hamburg, Germany
- Department of Virology, Institute for Integrative Biology of the Cell (I2BC), Centre National de la Recherche Scientifique (CNRS) UMR9198, Gif-sur-Yvette, France
| | - Maria Rosenthal
- Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
- Centre for Structural Systems Biology (CSSB), Hamburg, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
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15
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Rizzi G, Digiovanni S, Degani G, Barbiroli A, Di Pisa F, Popolo L, Visentin C, Vanoni MA, Ricagno S. Site-directed mutagenesis reveals the interplay between stability, structure, and enzymatic activity in RidA from Capra hircus. Protein Sci 2024; 33:e5036. [PMID: 38801230 PMCID: PMC11129622 DOI: 10.1002/pro.5036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Reactive intermediate deaminase A (RidA) is a highly conserved enzyme that catalyzes the hydrolysis of 2-imino acids to the corresponding 2-keto acids and ammonia. RidA thus prevents the accumulation of such potentially harmful compounds in the cell, as exemplified by its role in the degradation of 2-aminoacrylate, formed during the metabolism of cysteine and serine, catalyzing the conversion of its stable 2-iminopyruvate tautomer into pyruvate. Capra hircus (goat) RidA (ChRidA) was the first mammalian RidA to be isolated and described. It has the typical homotrimeric fold of the Rid superfamily, characterized by remarkably high thermal stability, with three active sites located at the interface between adjacent subunits. ChRidA exhibits a broad substrate specificity with a preference for 2-iminopyruvate and other 2-imino acids derived from amino acids with non-polar non-bulky side chains. Here we report a biophysical and biochemical characterization of eight ChRidA variants obtained by site-directed mutagenesis to gain insight into the role of specific residues in protein stability and catalytic activity. Each mutant was produced in Escherichia coli cells, purified and characterized in terms of quaternary structure, thermal stability and substrate specificity. The results are rationalized in the context of the high-resolution structures obtained by x-ray crystallography.
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Affiliation(s)
- Giulia Rizzi
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
| | | | - Genny Degani
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
| | - Alberto Barbiroli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'AmbienteUniversità degli Studi di MilanoMilanItaly
| | - Flavio Di Pisa
- Istituto di BiofisicaConsiglio Nazionale delle RicercheMilanItaly
| | - Laura Popolo
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
| | - Cristina Visentin
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
| | | | - Stefano Ricagno
- Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanItaly
- Institute of Molecular and Translational CardiologyI.R.C.C.S. Policlinico San DonatoSan Donato MilaneseItaly
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16
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Burge RJ, Jameson KH, Geoghegan V, Dowle AA, Mottram JC, Wilkinson AJ. Formation of functional E3 ligase complexes with UBC2 and UEV1 of Leishmania mexicana. Mol Biochem Parasitol 2024; 258:111619. [PMID: 38556171 DOI: 10.1016/j.molbiopara.2024.111619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
In eukaryotic cells, molecular fate and cellular responses are shaped by multicomponent enzyme systems which reversibly attach ubiquitin and ubiquitin-like modifiers to target proteins. The extent of the ubiquitin proteasome system in Leishmania mexicana and its importance for parasite survival has recently been established through deletion mutagenesis and life-cycle phenotyping studies. The ubiquitin conjugating E2 enzyme UBC2, and the E2 enzyme variant UEV1, with which it forms a stable complex in vitro, were shown to be essential for the differentiation of promastigote parasites to the infectious amastigote form. To investigate further, we used immunoprecipitation of Myc-UBC2 or Myc-UEV1 to identify interacting proteins in L. mexicana promastigotes. The interactome of UBC2 comprises multiple ubiquitin-proteasome components including UEV1 and four RING E3 ligases, as well as potential substrates predicted to have roles in carbohydrate metabolism and intracellular trafficking. The smaller UEV1 interactome comprises six proteins, including UBC2 and shared components of the UBC2 interactome consistent with the presence of intracellular UBC2-UEV1 complexes. Recombinant RING1, RING2 and RING4 E3 ligases were shown to support ubiquitin transfer reactions involving the E1, UBA1a, and UBC2 to available substrate proteins or to unanchored ubiquitin chains. These studies define additional components of a UBC2-dependent ubiquitination pathway shown previously to be essential for promastigote to amastigote differentiation.
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Affiliation(s)
- Rebecca J Burge
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK
| | - Katie H Jameson
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Vincent Geoghegan
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK
| | - Adam A Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, UK.
| | - Anthony J Wilkinson
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK.
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17
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Cornish K, Huo J, Jones L, Sharma P, Thrush JW, Abdelkarim S, Kipar A, Ramadurai S, Weckener M, Mikolajek H, Liu S, Buckle I, Bentley E, Kirby A, Han X, Laidlaw SM, Hill M, Eyssen L, Norman C, Le Bas A, Clarke J, James W, Stewart JP, Carroll M, Naismith JH, Owens RJ. Structural and functional characterization of nanobodies that neutralize Omicron variants of SARS-CoV-2. Open Biol 2024; 14:230252. [PMID: 38835241 DOI: 10.1098/rsob.230252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/22/2024] [Indexed: 06/06/2024] Open
Abstract
The Omicron strains of SARS-CoV-2 pose a significant challenge to the development of effective antibody-based treatments as immune evasion has compromised most available immune therapeutics. Therefore, in the 'arms race' with the virus, there is a continuing need to identify new biologics for the prevention or treatment of SARS-CoV-2 infections. Here, we report the isolation of nanobodies that bind to the Omicron BA.1 spike protein by screening nanobody phage display libraries previously generated from llamas immunized with either the Wuhan or Beta spike proteins. The structure and binding properties of three of these nanobodies (A8, H6 and B5-5) have been characterized in detail providing insight into their binding epitopes on the Omicron spike protein. Trimeric versions of H6 and B5-5 neutralized the SARS-CoV-2 variant of concern BA.5 both in vitro and in the hamster model of COVID-19 following nasal administration. Thus, either alone or in combination could serve as starting points for the development of new anti-viral immunotherapeutics.
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Affiliation(s)
- Katy Cornish
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford , Oxford, UK
| | - Luke Jones
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford , Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford , Oxford, UK
| | - Parul Sharma
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Joseph W Thrush
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Sahar Abdelkarim
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Anja Kipar
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
- Vetsuisse Faculty, Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, University of Zurich , Zurich, Switzerland
| | - Siva Ramadurai
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Miriam Weckener
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | | | - Sai Liu
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford , Oxford, UK
| | - Imogen Buckle
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Eleanor Bentley
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Ximeng Han
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Stephen M Laidlaw
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford , Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford , Oxford, UK
| | - Michelle Hill
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford , Oxford, UK
| | - Lauren Eyssen
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Chelsea Norman
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - Audrey Le Bas
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - John Clarke
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
| | - William James
- James & Lillian Martin Centre, Sir William Dunn School of Pathology, University of Oxford , Oxford, UK
| | - James P Stewart
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool , Liverpool, UK
| | - Miles Carroll
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford , Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford , Oxford, UK
| | - James H Naismith
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford , Oxford, UK
| | - Raymond J Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus , Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford , Oxford, UK
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18
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Nonne F, Iacono LD, Bertuzzi S, Unione L, Proietti D, Norais N, Margarit I, Adamo R, Jiménez-Barbero J, Carboni F, Romano MR. A Multidisciplinary Structural Approach to the Identification of the Haemophilus influenzae Type b Capsular Polysaccharide Protective Epitope. ACS CENTRAL SCIENCE 2024; 10:978-987. [PMID: 38799664 PMCID: PMC11117310 DOI: 10.1021/acscentsci.3c01515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 05/29/2024]
Abstract
Glycoconjugate vaccines so far licensed are generally composed of a native or size-reduced capsular polysaccharide conjugated to carrier proteins. Detailed information on the structural requirements necessary for CPS recognition is becoming the key to accelerating the development of next-generation improved glycoconjugate vaccines. Structural glycobiology studies using oligosaccharides (OS) complexed with functional monoclonal antibodies represent a powerful tool for gaining information on CPS immunological determinants at the atomic level. Herein, the minimal structural epitope of Haemophilus influenzae type b (Hib) CPS recognized by a functional human monoclonal antibody (hmAb) is reported. Short and well-defined Hib oligosaccharides originating from the depolymerization of the native CPS have been used to elucidate saccharide-mAb interactions by using a multidisciplinary approach combining surface plasmon resonance (SPR), saturation transfer difference-nanomagnetic resonance (STD-NMR), and X-ray crystallography. Our study demonstrates that the minimal structural epitope of Hib is comprised within two repeating units (RUs) where ribose and ribitol are directly engaged in the hmAb interaction, and the binding pocket fully accommodates two RUs without any additional involvement of a third one. Understanding saccharide antigen structural characteristics can provide the basis for the design of innovative glycoconjugate vaccines based on alternative technologies, such as synthetic or enzymatic approaches.
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Affiliation(s)
- Francesca Nonne
- GSK
Vaccines Institute for Global Health, 53100 Siena, Italy
| | | | - Sara Bertuzzi
- CIC
bioGUNE, Basque Research
Technology Alliance, BRTA, Bizkaia Technology Park, 48160 Derio, Spain
| | - Luca Unione
- CIC
bioGUNE, Basque Research
Technology Alliance, BRTA, Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science and Technology, Euskadi Plaza 5, 48009 Bilbao, Spain
| | | | | | | | | | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research
Technology Alliance, BRTA, Bizkaia Technology Park, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science and Technology, Euskadi Plaza 5, 48009 Bilbao, Spain
- Department
of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain
- Centro de
Investigación Biomédica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain
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19
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Rajapaksha N, Yao H, Cook A, Seibold S, Liu L, Battaile KP, Fontenot L, Donnarumma F, Lovell S, Rivera M. Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity. Front Mol Biosci 2024; 11:1390745. [PMID: 38841187 PMCID: PMC11150526 DOI: 10.3389/fmolb.2024.1390745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
We report the biochemical, structural, and functional characterization of the protein coded by gene PA4880 in the P. aeruginosa PAO1 genome. The PA4880 gene had been annotated as coding a probable bacterioferritin. Our structural work shows that the product of gene PA4880 is a protein that adopts the Dps subunit fold, which oligomerizes into a 12-mer quaternary structure. Unlike Dps, however, the ferroxidase di-iron centers and iron coordinating ligands are buried within each subunit, in a manner identical to that observed in the ferroxidase center of P. aeruginosa bacterioferritin. Since these structural characteristics correspond to Dps-like proteins, we term the protein as P. aeruginosa Dps-like, or Pa DpsL. The ferroxidase centers in Pa DpsL catalyze the oxidation of Fe2+ utilizing O2 or H2O2 as oxidant, and the resultant Fe3+ is compartmentalized in the interior cavity. Interestingly, incubating Pa DpsL with plasmid DNA results in efficient nicking of the DNA and at higher concentrations of Pa DpsL the DNA is linearized and eventually degraded. The nickase and endonuclease activities suggest that Pa DpsL, in addition to participating in the defense of P. aeruginosa cells against iron-induced toxicity, may also participate in the innate immune mechanisms consisting of restriction endonucleases and cognate methyl transferases.
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Affiliation(s)
- Nimesha Rajapaksha
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Huili Yao
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Aisha Cook
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Steve Seibold
- Protein Structure & X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, United States
| | - Lijun Liu
- Protein Structure & X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, United States
| | | | - Leo Fontenot
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
| | - Scott Lovell
- Protein Structure & X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS, United States
| | - Mario Rivera
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, United States
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20
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Urbániková Ľ, Janeček Š. Trehalose synthases from the subfamily GH13_16 involved in α-glucan biosynthesis - a focus on their maltokinase domain. Int J Biol Macromol 2024; 268:131680. [PMID: 38641282 DOI: 10.1016/j.ijbiomac.2024.131680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
The subfamily GH13_16 trehalose synthase (TreS) converts maltose to trehalose and vice versa. Typically, it consists of three domains, but it may contain a C-terminal extension exhibiting clear sequence features of a maltokinase (MaK). The present in silico study was focused on collection of naturally fused TreS-MaKs and their subsequent detailed bioinformatics analysis. Hence a set of total 3354 unique sequences was compared consisting of 1900 single TreSs, 1426 fused TreS-MaKs and 28 single MaKs. Fused TreS-MaKs were divided into five groups, namely with a standard MaK, with mutations in the maltose-binding site, of the catalytic nucleophile, of the general acid/base and of both catalytic residues. Sequence logos bearing the best conserved sequence regions were prepared for both TreSs and MaKs in an effort to find unique sequence features. In addition, linkers connecting the TreS and MaK parts in the fused enzymes were analysed. This analysis revealed that MaKs in fused enzymes have an extended N-terminal regions compared to single MaKs. Finally, the evolutionary relationships were demonstrated by phylogenetic trees of TreS parts from single TreSs and fused TreS-MaKs from the same organism as well as of single TreSs existing in multiple isoforms in the same organism.
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Affiliation(s)
- Ľubica Urbániková
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia
| | - Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, SK-84551 Bratislava, Slovakia; Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius in Trnava, SK-91701 Trnava, Slovakia.
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21
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Bradshaw WJ, Kennedy EC, Moreira T, Smith LA, Chalk R, Katis VL, Benesch JLP, Brennan PE, Murphy EJ, Gileadi O. Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2. Structure 2024; 32:453-466.e6. [PMID: 38309262 PMCID: PMC10997489 DOI: 10.1016/j.str.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
SHIP1, an inositol 5-phosphatase, plays a central role in cellular signaling. As such, it has been implicated in many conditions. Exploiting SHIP1 as a drug target will require structural knowledge and the design of selective small molecules. We have determined apo, and magnesium and phosphate-bound structures of the phosphatase and C2 domains of SHIP1. The C2 domains of SHIP1 and the related SHIP2 modulate the activity of the phosphatase domain. To understand the mechanism, we performed activity assays, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics on SHIP1 and SHIP2. Our findings demonstrate that the influence of the C2 domain is more pronounced for SHIP2 than SHIP1. We determined 91 structures of SHIP1 with fragments bound, with some near the interface between the two domains. We performed a mass spectrometry screen and determined four structures with covalent fragments. These structures could act as starting points for the development of potent, selective probes.
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Affiliation(s)
- William J Bradshaw
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
| | - Emma C Kennedy
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Tiago Moreira
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Luke A Smith
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Rod Chalk
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Vittorio L Katis
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Justin L P Benesch
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Paul E Brennan
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Emma J Murphy
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK
| | - Opher Gileadi
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, University of Oxford, Oxford OX3 7FZ, UK.
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22
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Shahsavani MB, Hoshino M, Kumar A, Yousefi R. Charge manipulation of the human insulin B chain C-terminal to shed light on the complex mechanism of insulin fibrillation. Biochim Biophys Acta Gen Subj 2024; 1868:130578. [PMID: 38278307 DOI: 10.1016/j.bbagen.2024.130578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 01/28/2024]
Abstract
Insulin fibrillation poses a significant challenge in the development and treatment of diabetes. Current efforts to unravel its mechanisms have thus far remained incomplete. To shed light on the intricate processes behind insulin fibrillation, we employed mutagenesis techniques to introduce additional positive charge residues into the C-terminal region of the insulin B chain which plays an important role in insulin dimerization. We employed our investigation with various spectroscopic methods, electron microscopy, and molecular dynamics simulations. These methods allowed us to explore the structure and fibrillation behavior of the engineered B chains following their expression in a bacterial host and successful purification. This manipulation had a pronounced impact on the oligomerization behavior of the insulin B chain. It appears that these mutations delay the formation of the dimeric state in the process of transitioning to larger oligomers, consequently, leading to an alteration in the kinetics of fibrillation. Our findings also indicated that the mutant insulin B chains (Di-R, Di-K, and Di-H) displayed resistance to the initiation of fibrillation. This resistance can be attributed to the repulsive forces generated by the introduced positive charges, which disrupt the attractive interactions favoring nucleation. Notably, the mutant B chains formed shorter and less abundant oligomers and fibrils, which can be ascribed to the alterations induced by repulsion. Our engineered mutant B chains exhibited enhanced stability against stress-induced fibrillation, hinting at their potential utility in the development of new insulin analogs. This study underscores the significance of the C-terminal region in the initial stages of insulin B chain fibrillation, providing valuable insights into the intricate mechanisms involved and their potential pharmaceutical applications.
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Affiliation(s)
- Mohammad Bagher Shahsavani
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Masaru Hoshino
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, India
| | - Reza Yousefi
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran; Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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23
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Oh EJ, Hwang IS, Kwon CT, Oh CS. A Putative Apoplastic Effector of Clavibacter capsici, ChpG Cc as Hypersensitive Response and Virulence (Hrv) Protein in Plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:370-379. [PMID: 38148291 DOI: 10.1094/mpmi-09-23-0145-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Clavibacter bacteria use secreted apoplastic effectors, such as putative serine proteases, for virulence in host plants and for hypersensitive response (HR) induction in nonhost plants. Previously, we have shown that Clavibacter capsici ChpGCc is important for the necrosis development in pepper (Capsicum annuum) leaves. Here, we determine the function of ChpGCc, along with three paralogous proteins, for HR induction in the apoplastic space of a nonhost plant, Nicotiana tabacum. The full-length and signal peptide-deleted (ΔSP) mature forms of all proteins fused with the tobacco PR1b signal sequence were generated. The full-length and ΔSP forms of ChpGCc and only the ΔSP forms of ChpECc and Pat-1Cc, but none of the ChpCCc, triggered HR. Based on the predicted protein structures, ChpGCc carries amino acids for a catalytic triad and a disulfide bridge in positions like Pat-1Cm. Substituting these amino acids of ChpGCc with alanine abolished or reduced HR-inducing activity. To determine whether these residues are important for necrosis development in pepper, alanine-substituted chpGCc genes were transformed into the C. capsici PF008ΔpCM1 strain, which lacks the intact chpGCc gene. The strain with any variants failed to restore the necrosis-causing ability. These results suggest that ChpGCc has a dual function as a virulence factor in host plants and an HR elicitor in nonhost plants. Based on our findings and previous results, we propose Clavibacter apoplastic effectors, such as ChpGCc, Pat-1Cm, Chp-7Cs, and ChpGCm, as hypersensitive response and virulence (Hrv) proteins that display phenotypic similarities to the hypersensitive response and pathogenicity (Hrp) proteins found in gram-negative bacteria. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Eom-Ji Oh
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
| | - In Sun Hwang
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Choon-Tak Kwon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin 17104, Korea
| | - Chang-Sik Oh
- Plant Immunity Research Center, Seoul National University, Seoul 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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24
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Suzuki M, Saito A, Kobayashi M, Yokoyama T, Omiya S, Li J, Sugita K, Miki K, Saito JI, Ando A. Crystal structure of the GH-46 subclass III chitosanase from Bacillus circulans MH-K1 in complex with chitotetraose. Biochim Biophys Acta Gen Subj 2024; 1868:130549. [PMID: 38158023 DOI: 10.1016/j.bbagen.2023.130549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Chitosanases (EC 3.2.1.132) hydrolyze chitosan which is a polymer of glucosamine (GlcN) linked by β - 1,4 bonds, and show cleavage specificity against partially acetylated chitosan containing N-acetylglucosamine (GlcNAc) residues. Chitosanases' structural underpinnings for cleavage specificity and the conformational switch from open to closed structures are still a mystery. METHODS The GH-46 subclass III chitosanase from Bacillus circulans MH-K1 (MH-K1 chitosanase), which also catalyzes the hydrolysis of GlcN-GlcNAc bonds in addition to GlcN-GlcN, has had its chitotetraose [(GlcN)4]-complexed crystal structure solved at 1.35 Å resolution. RESULTS The MH-K1 chitosanase's (GlcN)4-bound structure has numerous structural similarities to other GH-46 chitosanases in terms of substrate binding and catalytic processes. However, subsite -1, which is absolutely specific for GlcN, seems to characterize the structure of a subclass III chitosanase due to its distinctive length and angle of a flexible loop. According to a comparison of the (GlcN)4-bound and apo-form structures, the particular binding of a GlcN residue at subsite -2 through Asp77 causes the backbone helix to kink, which causes the upper- and lower-domains to approach closely when binding a substrate. CONCLUSIONS Although GH-46 chitosanases vary in the finer details of the subsites defining cleavage specificity, they share similar structural characteristics in substrate-binding, catalytic processes, and potentially in conformational change. GENERAL SIGNIFICANCE The precise binding of a GlcN residue to the -2 subsite is essential for the conformational shift that occurs in all GH-46 chitosanases, as shown by the crystal structures of the apo- and substrate-bound forms of MH-K1 chitosanase.
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Affiliation(s)
- Michihiko Suzuki
- Molecular Analysis Center, Research Unit, R&D Division, Kyowa Kirin, Sunto-gun, Shizuoka 411-8731, Japan
| | - Akihiro Saito
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan; Department of Materials and Life Science, Faculty of Science and Technology, Shizuoka Institute of Science and Technology, Fukuroi, Shizuoka 437-8555, Japan.
| | - Mariko Kobayashi
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Tomofumi Yokoyama
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Shoko Omiya
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Jian Li
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Kei Sugita
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Jun-Ichi Saito
- Molecular Analysis Center, Research Unit, R&D Division, Kyowa Kirin, Sunto-gun, Shizuoka 411-8731, Japan
| | - Akikazu Ando
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
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25
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Wu Y, Bell A, Thomas GH, Bolam DN, Sargent F, Juge N, Palmer T, Severi E. Characterisation of anhydro-sialic acid transporters from mucosa-associated bacteria. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001448. [PMID: 38488830 PMCID: PMC10955332 DOI: 10.1099/mic.0.001448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
Sialic acid (Sia) transporters are critical to the capacity of host-associated bacteria to utilise Sia for growth and/or cell surface modification. While N-acetyl-neuraminic acid (Neu5Ac)-specific transporters have been studied extensively, little is known on transporters dedicated to anhydro-Sia forms such as 2,7-anhydro-Neu5Ac (2,7-AN) or 2,3-dehydro-2-deoxy-Neu5Ac (Neu5Ac2en). Here, we used a Sia-transport-null strain of Escherichia coli to investigate the function of members of anhydro-Sia transporter families previously identified by computational studies. First, we showed that the transporter NanG, from the Glycoside-Pentoside-Hexuronide:cation symporter family, is a specific 2,7-AN transporter, and identified by mutagenesis a crucial functional residue within the putative substrate-binding site. We then demonstrated that NanX transporters, of the Major Facilitator Superfamily, also only transport 2,7-AN and not Neu5Ac2en nor Neu5Ac. Finally, we provided evidence that SiaX transporters, of the Sodium-Solute Symporter superfamily, are promiscuous Neu5Ac/Neu5Ac2en transporters able to acquire either substrate equally well. The characterisation of anhydro-Sia transporters expands our current understanding of prokaryotic Sia metabolism within host-associated microbial communities.
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Affiliation(s)
- Yunhan Wu
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew Bell
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Gavin H. Thomas
- Department of Biology and York Biomedical Research Institute (YBRI), Wentworth Way, University of York, York YO10 5DD, UK
| | - David N. Bolam
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Frank Sargent
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Nathalie Juge
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Tracy Palmer
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Emmanuele Severi
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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26
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Mycroft-West CJ, Abdelkarim S, Duyvesteyn HME, Gandhi NS, Skidmore MA, Owens RJ, Wu L. Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1. Nat Commun 2024; 15:1326. [PMID: 38351061 PMCID: PMC10864358 DOI: 10.1038/s41467-024-45419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Heparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, non-templated patterns of sulfation and epimerization, which mediate interactions with diverse protein partners. Complex HS modifications form around initial clusters of glucosamine-N-sulfate (GlcNS) on nascent polysaccharide chains, but the mechanistic basis underpinning incorporation of GlcNS itself into HS remains unclear. Here, we determine cryo-electron microscopy structures of human N-deacetylase-N-sulfotransferase (NDST)1, the bifunctional enzyme primarily responsible for initial GlcNS modification of HS. Our structures reveal the architecture of both NDST1 deacetylase and sulfotransferase catalytic domains, alongside a non-catalytic N-terminal domain. The two catalytic domains of NDST1 adopt a distinct back-to-back topology that limits direct cooperativity. Binding analyses, aided by activity-modulating nanobodies, suggest that anchoring of the substrate at the sulfotransferase domain initiates the NDST1 catalytic cycle, providing a plausible mechanism for cooperativity despite spatial domain separation. Our data shed light on key determinants of NDST1 activity, and describe tools to probe NDST1 function in vitro and in vivo.
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Affiliation(s)
| | - Sahar Abdelkarim
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK
| | - Neha S Gandhi
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- School of Chemistry and Physics, Queensland University of Technology, QLD 4000, Brisbane, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Mark A Skidmore
- Centre for Glycoscience Research and Training, Keele University, ST5 5BG, Newcastle-Under-Lyme, UK
| | - Raymond J Owens
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK
| | - Liang Wu
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK.
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27
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Shannon A, Chazot A, Feracci M, Falcou C, Fattorini V, Selisko B, Good S, Moussa A, Sommadossi JP, Ferron F, Alvarez K, Canard B. An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex. Nucleic Acids Res 2024; 52:1325-1340. [PMID: 38096103 PMCID: PMC10853775 DOI: 10.1093/nar/gkad1194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024] Open
Abstract
Nucleotide analogues (NA) are currently employed for treatment of several viral diseases, including COVID-19. NA prodrugs are intracellularly activated to the 5'-triphosphate form. They are incorporated into the viral RNA by the viral polymerase (SARS-CoV-2 nsp12), terminating or corrupting RNA synthesis. For Coronaviruses, natural resistance to NAs is provided by a viral 3'-to-5' exonuclease heterodimer nsp14/nsp10, which can remove terminal analogues. Here, we show that the replacement of the α-phosphate of Bemnifosbuvir 5'-triphosphate form (AT-9010) by an α-thiophosphate renders it resistant to excision. The resulting α-thiotriphosphate, AT-9052, exists as two epimers (RP/SP). Through co-crystallization and activity assays, we show that the Sp isomer is preferentially used as a substrate by nucleotide diphosphate kinase (NDPK), and by SARS-CoV-2 nsp12, where its incorporation causes immediate chain-termination. The same -Sp isomer, once incorporated by nsp12, is also totally resistant to the excision by nsp10/nsp14 complex. However, unlike AT-9010, AT-9052-RP/SP no longer inhibits the N-terminal nucleotidylation domain of nsp12. We conclude that AT-9052-Sp exhibits a unique mechanism of action against SARS-CoV-2. Moreover, the thio modification provides a general approach to rescue existing NAs whose activity is hampered by coronavirus proofreading capacity.
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Affiliation(s)
- Ashleigh Shannon
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Aurélie Chazot
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Mikael Feracci
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Camille Falcou
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Véronique Fattorini
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Barbara Selisko
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Steven Good
- ATEA Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA 02110, USA
| | - Adel Moussa
- ATEA Pharmaceuticals, Inc., 225 Franklin St., Suite 2100, Boston, MA 02110, USA
| | | | - François Ferron
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Karine Alvarez
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, Case 925, 163 Avenue de Luminy, 13288, Marseille Cedex 09, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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28
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Yu X, Matico RE, Miller R, Chauhan D, Van Schoubroeck B, Grauwen K, Suarez J, Pietrak B, Haloi N, Yin Y, Tresadern GJ, Perez-Benito L, Lindahl E, Bottelbergs A, Oehlrich D, Van Opdenbosch N, Sharma S. Structural basis for the oligomerization-facilitated NLRP3 activation. Nat Commun 2024; 15:1164. [PMID: 38326375 PMCID: PMC10850481 DOI: 10.1038/s41467-024-45396-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
The NACHT-, leucine-rich-repeat-, and pyrin domain-containing protein 3 (NLRP3) is a critical intracellular inflammasome sensor and an important clinical target against inflammation-driven human diseases. Recent studies have elucidated its transition from a closed cage to an activated disk-like inflammasome, but the intermediate activation mechanism remains elusive. Here we report the cryo-electron microscopy structure of NLRP3, which forms an open octamer and undergoes a ~ 90° hinge rotation at the NACHT domain. Mutations on open octamer's interfaces reduce IL-1β signaling, highlighting its essential role in NLRP3 activation/inflammasome assembly. The centrosomal NIMA-related kinase 7 (NEK7) disrupts large NLRP3 oligomers and forms NEK7/NLRP3 monomers/dimers which is a critical step preceding the assembly of the disk-like inflammasome. These data demonstrate an oligomeric cooperative activation of NLRP3 and provide insight into its inflammasome assembly mechanism.
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Affiliation(s)
- Xiaodi Yu
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA.
| | - Rosalie E Matico
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | - Robyn Miller
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | - Dhruv Chauhan
- Johnson & Johnson Innovation Medicine, J&J Interventional Oncology, Beerse, Belgium
| | | | - Karolien Grauwen
- Johnson & Johnson Innovation Medicine, J&J Interventional Oncology, Beerse, Belgium
| | - Javier Suarez
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | - Beth Pietrak
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | - Nandan Haloi
- Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yanting Yin
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
| | | | - Laura Perez-Benito
- Johnson & Johnson Innovation Medicine, Discovery Sciences, Beerse, Belgium
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Astrid Bottelbergs
- Johnson & Johnson Innovation Medicine, Discovery Sciences, Beerse, Belgium
| | - Daniel Oehlrich
- Johnson & Johnson Innovation Medicine, Discovery Sciences, Beerse, Belgium
| | - Nina Van Opdenbosch
- Johnson & Johnson Innovation Medicine, J&J Interventional Oncology, Beerse, Belgium
| | - Sujata Sharma
- Johnson & Johnson Innovation Medicine, Spring House, PA, 19044, USA
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29
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Dialpuri JS, Bagdonas H, Schofield LC, Pham PT, Holland L, Bond PS, Sánchez Rodríguez F, McNicholas SJ, Agirre J. Online carbohydrate 3D structure validation with the Privateer web app. Acta Crystallogr F Struct Biol Commun 2024; 80:30-35. [PMID: 38265073 PMCID: PMC10836424 DOI: 10.1107/s2053230x24000359] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code. Here, the Privateer web app is presented, which is always up to date and available to be used online (https://privateer.york.ac.uk) without installation. This self-updating tool, which runs locally on the user's machine, will allow structural biologists to simply and quickly analyse carbohydrate ligands and protein glycosylation from a web browser whilst retaining all confidential information on their devices.
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Affiliation(s)
- Jordan S. Dialpuri
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom
| | - Haroldas Bagdonas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom
| | - Lucy C. Schofield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom
| | - Phuong Thao Pham
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom
| | - Lou Holland
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom
| | - Paul S. Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom
| | - Filomeno Sánchez Rodríguez
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom
| | - Stuart J. McNicholas
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 3BG, United Kingdom
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Yusof NY, Quay DHX, Kamaruddin S, Jonet MA, Md Illias R, Mahadi NM, Firdaus-Raih M, Abu Bakar FD, Abdul Murad AM. Biochemical and in silico structural characterization of a cold-active arginase from the psychrophilic yeast, Glaciozyma antarctica PI12. Extremophiles 2024; 28:15. [PMID: 38300354 DOI: 10.1007/s00792-024-01333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/30/2023] [Indexed: 02/02/2024]
Abstract
Glaciozyma antarctica PI12 is a psychrophilic yeast isolated from Antarctica. In this work, we describe the heterologous production, biochemical properties and in silico structure analysis of an arginase from this yeast (GaArg). GaArg is a metalloenzyme that catalyses the hydrolysis of L-arginine to L-ornithine and urea. The cDNA of GaArg was reversed transcribed, cloned, expressed and purified as a recombinant protein in Escherichia coli. The purified protein was active against L-arginine as its substrate in a reaction at 20 °C, pH 9. At 10-35 °C and pH 7-9, the catalytic activity of the protein was still present around 50%. Mn2+, Ni2+, Co2+ and K+ were able to enhance the enzyme activity more than two-fold, while GaArg is most sensitive to SDS, EDTA and DTT. The predicted structure model of GaArg showed a very similar overall fold with other known arginases. GaArg possesses predominantly smaller and uncharged amino acids, fewer salt bridges, hydrogen bonds and hydrophobic interactions compared to the other counterparts. GaArg is the first reported arginase that is cold-active, facilitated by unique structural characteristics for its adaptation of catalytic functions at low-temperature environments. The structure and function of cold-active GaArg provide insights into the potentiality of new applications in various biotechnology and pharmaceutical industries.
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Affiliation(s)
- Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia.
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
| | - Doris Huai Xia Quay
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
| | - Shazilah Kamaruddin
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Mohd Anuar Jonet
- Malaysia Genome and Vaccine Institute, Jalan Bangi Lama, 43000, Kajang, Selangor, Malaysia
| | - Rosli Md Illias
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81300, Skudai, Johor, Malaysia
| | - Nor Muhammad Mahadi
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Mohd Firdaus-Raih
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM, 43600, Bangi, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences & Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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31
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Ackroyd BK, Dodson EJ, Mehboob J, Dowle AA, Thomas GH, Wilkinson AJ. Structure and ligand binding in the putative anti-microbial peptide transporter protein, YejA. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001430. [PMID: 38334478 PMCID: PMC10924461 DOI: 10.1099/mic.0.001430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024]
Abstract
YejABEF is an ATP-binding cassette transporter that is implicated in the sensitivity of Escherichia coli to anti-microbial peptides, the best-characterized example being microcin C, a peptide-nucleotide antibiotic that targets aspartyl-tRNA synthetase. Here the structure of the extracellular solute binding protein, YejA, has been determined, revealing an oligopeptide-binding protein fold enclosing a ligand-binding pocket larger than those of other peptide-binding proteins of known structure. Prominent electron density in this cavity defines an undecapeptide sequence LGEPRYAFNFN, an observation that is confirmed by mass spectrometry. In the structure, the peptide interactions with the protein are mediated by main chain hydrogen bonds with the exception of Arg5 whose guanidinium side chain makes a set of defining polar interactions with four YejA residues. More detailed characterization of purified recombinant YejA, by a combination of ESI and MALDI-mass spectrometry as well as thermal shift assays, reveals a set of YejA complexes containing overlapping peptides 10-19 residues in length. All contain the sequence LGEPRYAFN. Curiously, these peptides correspond to residues 8-26 of the mature YejA protein, which belong to a unique N-terminal extension that distinguishes YejA from other cluster C oligopeptide binding proteins of known structure. This 35-residue extension is well-ordered and packs across the surface of the protein. The undecapeptide ligand occupies only a fraction of the enclosed pocket volume suggesting the possibility that much larger peptides or peptide conjugates could be accommodated, though thermal shift assays of YejA binding to antimicrobial peptides and peptides unrelated to LGEPRYAFNFN have not provided evidence of binding. While the physiological significance of this 'auto-binding' is not clear, the experimental data suggest that it is not an artefact of the crystallization process and that it may have a function in the sensing of periplasmic or membrane stress.
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Affiliation(s)
- Bryony K. Ackroyd
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
- Department of Biology and York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Eleanor J. Dodson
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Javeria Mehboob
- Department of Biology and York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Adam A. Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK
| | - Gavin H. Thomas
- Department of Biology and York Biomedical Research Institute, University of York, York YO10 5DD, UK
| | - Anthony J. Wilkinson
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, York YO10 5DD, UK
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32
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Mayer AB, Amaral HDO, de Oliveira DGR, Campos GAA, Ribeiro PG, Fernandes SCR, de Souza ACB, de Castro RJA, Bocca AL, Mortari MR. New fraternine analogues: Evaluation of the antiparkinsonian effect in the model of Parkinson's disease. Neuropeptides 2024; 103:102390. [PMID: 37984248 DOI: 10.1016/j.npep.2023.102390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
Venom-derived peptides are important sources for the development of new therapeutic molecules, especially due to their broad pharmacological activity. Previously, our research group identified a novel natural peptide, named fraternine, with promising effects for the treatment of Parkinson's disease. In the present paper, we synthesized three peptides bioinspired in fraternine: fra-10, fra-14, and fra-24. They were tested in the 6-OHDA-induced model of parkinsonism, quantifying motor coordination, levels of TH+ neurons in the substantia nigra pars compacta (SN), and inflammation mediators TNF-α, IL-6, and IL-1ß in the cortex. Peptides fra-14 and fra-10 improved the motor coordination in relation to 6-OHDA lesioned animals. However, most of the peptides were toxic in the doses applied. All three peptides reduced the intensity of the lesion induced rotations in the apomorphine test. Fra-24 higher dose increased the number of TH+ neurons in SN and reduced the concentration of TNF-α in the cortex of 6-OHDA lesioned mice. Overall, only the peptide fra-24 presented a neuroprotection effect on dopaminergic neurons of SN and a reduction of cytokine TNF-α levels, making it worthy of consideration for the treatment of PD.
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Affiliation(s)
- Andréia Biolchi Mayer
- Laboratory of Neuropharmacology, Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Henrique de Oliveira Amaral
- Laboratory of Neuropharmacology, Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Danilo Gustavo R de Oliveira
- Laboratory of Neuropharmacology, Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Gabriel Avohay Alves Campos
- Laboratory of Neuropharmacology, Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Priscilla Galante Ribeiro
- Laboratory of Neuropharmacology, Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Solange Cristina Rego Fernandes
- Laboratory of Neuropharmacology, Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Adolfo Carlos Barros de Souza
- Laboratory of Neuropharmacology, Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Raffael Júnio Araújo de Castro
- Laboratory of Applied Immunology, Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Anamélia Lorenzetti Bocca
- Laboratory of Applied Immunology, Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Márcia Renata Mortari
- Laboratory of Neuropharmacology, Department of Physiological Sciences, Institute of Biological Sciences, University of Brasília, Brasília, DF, 70910-900, Brazil.
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33
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Hung L, Terwilliger TC, Waldo GS, Nguyen HB. Engineering highly stable variants of Corynactis californica green fluorescent proteins. Protein Sci 2024; 33:e4886. [PMID: 38151801 PMCID: PMC10804665 DOI: 10.1002/pro.4886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/30/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023]
Abstract
Fluorescent proteins (FPs) are versatile biomarkers that facilitate effective detection and tracking of macromolecules of interest in real time. Engineered FPs such as superfolder green fluorescent protein (sfGFP) and superfolder Cherry (sfCherry) have exceptional refolding capability capable of delivering fluorescent readout in harsh environments where most proteins lose their native functions. Our recent work on the development of a split FP from a species of strawberry anemone, Corynactis californica, delivered pairs of fragments with up to threefold faster complementation than split GFP. We present the biophysical, biochemical, and structural characteristics of five full-length variants derived from these split C. californica GFP (ccGFP). These ccGFP variants are more tolerant under chemical denaturation with up to 8 kcal/mol lower unfolding free energy than that of the sfGFP. It is likely that some of these ccGFP variants could be suitable as biomarkers under more adverse environments where sfGFP fails to survive. A structural analysis suggests explanations of the variations in stabilities among the ccGFP variants.
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Affiliation(s)
- Li‐Wei Hung
- Bioscience DivisionMS M888, Los Alamos National LaboratoryLos AlamosNew MexicoUSA
| | - Thomas C. Terwilliger
- Bioscience DivisionMS M888, Los Alamos National LaboratoryLos AlamosNew MexicoUSA
- New Mexico ConsortiumLos AlamosNew MexicoUSA
| | - Geoffrey S. Waldo
- Bioscience DivisionMS M888, Los Alamos National LaboratoryLos AlamosNew MexicoUSA
| | - Hau B. Nguyen
- Bioscience DivisionMS M888, Los Alamos National LaboratoryLos AlamosNew MexicoUSA
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34
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Lykins J, Moschitto MJ, Zhou Y, Filippova EV, Le HV, Tomita T, Fox BA, Bzik DJ, Su C, Rajagopala SV, Flores K, Spano F, Woods S, Roberts CW, Hua C, El Bissati K, Wheeler KM, Dovgin S, Muench SP, McPhillie M, Fishwick CW, Anderson WF, Lee PJ, Hickman M, Weiss LM, Dubey JP, Lorenzi HA, Silverman RB, McLeod RL. From TgO/GABA-AT, GABA, and T-263 Mutant to Conception of Toxoplasma. iScience 2024; 27:108477. [PMID: 38205261 PMCID: PMC10776954 DOI: 10.1016/j.isci.2023.108477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 04/28/2023] [Accepted: 11/13/2023] [Indexed: 01/12/2024] Open
Abstract
Toxoplasma gondii causes morbidity, mortality, and disseminates widely via cat sexual stages. Here, we find T. gondii ornithine aminotransferase (OAT) is conserved across phyla. We solve TgO/GABA-AT structures with bound inactivators at 1.55 Å and identify an inactivator selective for TgO/GABA-AT over human OAT and GABA-AT. However, abrogating TgO/GABA-AT genetically does not diminish replication, virulence, cyst-formation, or eliminate cat's oocyst shedding. Increased sporozoite/merozoite TgO/GABA-AT expression led to our study of a mutagenized clone with oocyst formation blocked, arresting after forming male and female gametes, with "Rosetta stone"-like mutations in genes expressed in merozoites. Mutations are similar to those in organisms from plants to mammals, causing defects in conception and zygote formation, affecting merozoite capacitation, pH/ionicity/sodium-GABA concentrations, drawing attention to cyclic AMP/PKA, and genes enhancing energy or substrate formation in TgO/GABA-AT-related-pathways. These candidates potentially influence merozoite's capacity to make gametes that fuse to become zygotes, thereby contaminating environments and causing disease.
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Affiliation(s)
- Joseph Lykins
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Matthew J. Moschitto
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
| | - Ying Zhou
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Ekaterina V. Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Hoang V. Le
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
| | - Tadakimi Tomita
- Division of Parasitology, Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Barbara A. Fox
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - David J. Bzik
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Chunlei Su
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Seesandra V. Rajagopala
- Department of Infectious Diseases, The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Kristin Flores
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Furio Spano
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stuart Woods
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow Scotland, UK
| | - Craig W. Roberts
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow Scotland, UK
| | - Cong Hua
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Kamal El Bissati
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Kelsey M. Wheeler
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Sarah Dovgin
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
| | - Stephen P. Muench
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, The University of Leeds, Leeds, West York LS2 9JT, UK
| | - Martin McPhillie
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Colin W.G. Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Wayne F. Anderson
- Center for Structural Genomics of Infectious Diseases and the Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Patricia J. Lee
- Division of Experimental Therapeutics, Military Malaria Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Mark Hickman
- Division of Experimental Therapeutics, Military Malaria Research Program, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Louis M. Weiss
- Division of Parasitology, Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jitender P. Dubey
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Hernan A. Lorenzi
- Department of Infectious Diseases, The J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Richard B. Silverman
- Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, and Center for Developmental Therapeutics, Northwestern University, Evanston, IL 60208-3113, USA
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Rima L. McLeod
- Department of Ophthalmology and Visual Sciences, The University of Chicago, Chicago, IL 60637, USA
- Department of Pediatrics (Infectious Diseases), Institute of Genomics, Genetics, and Systems Biology, Global Health Center, Toxoplasmosis Center, CHeSS, The College, University of Chicago, Chicago, IL 60637, USA
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35
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Linciano P, Pozzi C, Tassone G, Landi G, Mangani S, Santucci M, Luciani R, Ferrari S, Santarem N, Tagliazucchi L, Cordeiro-da-Silva A, Tonelli M, Tondi D, Bertarini L, Gul S, Witt G, Moraes CB, Costantino L, Costi MP. The discovery of aryl-2-nitroethyl triamino pyrimidines as anti-Trypanosoma brucei agents. Eur J Med Chem 2024; 264:115946. [PMID: 38043491 DOI: 10.1016/j.ejmech.2023.115946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/05/2023]
Abstract
Pteridine reductase 1 (PTR1) is a catalytic protein belonging to the folate metabolic pathway in Trypanosmatidic parasites. PTR1 is a known target for the medicinal chemistry development of antiparasitic agents against Trypanosomiasis and Leishmaniasis. In previous studies, new nitro derivatives were elaborated as PTR1 inhibitors. The compounds showing a diamino-pyrimidine core structure were previously developed but they showed limited efficacy. Therefore, a new class of phenyl-, heteroaryl- and benzyloxy-nitro derivatives based on the 2-nitroethyl-2,4,6-triaminopyrimidine scaffold were designed and tested. The compounds were assayed for their ability to inhibit T. brucei and L. major PTR1 enzymes and for their antiparasitic activity towards T. brucei and L. infantum parasites. To understand the structure-activity relationships of the compounds against TbPTR1, the X-ray crystallographic structure of the 2,4,6-triaminopyrimidine (TAP) was obtained and molecular modelling studies were performed. As a next step, only the most effective compounds against T. brucei were then tested against the amastigote cellular stage of T. cruzi, searching for a broad-spectrum antiprotozoal agent. An early ADME-Tox profile evaluation was performed. The early toxicity profile of this class of compounds was investigated by measuring their inhibition of hERG and five cytochrome P450 isoforms (CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4), cytotoxicity towards A549 cells and mitochondrial toxicity. Pharmacokinetic studies (SNAP-PK) were performed on selected compounds using hydroxypropyl-β-cyclodextrins (50 % w/v) to preliminarily study their plasma concentration when administered per os at a dose of 20 mg/kg. Compound 1p, showed the best pharmacodynamic and pharmacokinetic properties, can be considered a good candidate for further bioavailability and efficacy studies.
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Affiliation(s)
- Pasquale Linciano
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy; Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugual
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Rosaria Luciani
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Nuno Santarem
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugual; Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge ViterboFerreira 228, 4050-313 Porto, Portugal
| | - Lorenzo Tagliazucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy; Clinical and Experimental Medicine (CEM) PhD Program, University of Modena and Reggio Emilia, Via Campi 278, 41125, Modena, Italy
| | - Anabela Cordeiro-da-Silva
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugual; Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge ViterboFerreira 228, 4050-313 Porto, Portugal
| | - Michele Tonelli
- Department of Pharmacy, University of Genoa, Viale Benedetto XV, 3, 16132, Genoa, Italy
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Laura Bertarini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Hamburg, Germany
| | - Gesa Witt
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Hamburg, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Hamburg, Germany
| | - Carolina B Moraes
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), 13083-100, Campinas, SP, Brazil
| | - Luca Costantino
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125, Modena, Italy.
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Eymery MC, Nguyen KA, Basu S, Hausmann J, Tran-Nguyen VK, Seidel HP, Gutierrez L, Boumendjel A, McCarthy AA. Discovery of potent chromone-based autotaxin inhibitors inspired by cannabinoids. Eur J Med Chem 2024; 263:115944. [PMID: 37976710 DOI: 10.1016/j.ejmech.2023.115944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Autotaxin (ATX) is an enzyme primarily known for the production of lysophosphatidic acid. Being involved in the development of major human diseases, such as cancer and neurodegenerative diseases, the enzyme has been featured in multiple studies as a pharmacological target. We previously found that the cannabinoid tetrahydrocannabinol (THC) could bind and act as an excellent inhibitor of ATX. This study aims to use the cannabinoid scaffold as a starting point to find cannabinoid-unrelated ATX inhibitors, following a funnel down approach in which large chemical libraries sharing chemical similarities with THC were screened to identify lead scaffold types for optimization. This approach allowed us to identify compounds bearing chromone and indole scaffolds as promising ATX inhibitors. Further optimization led to MEY-003, which is characterized by the direct linkage of an N-pentyl indole to the 5,7-dihydroxychromone moiety. This molecule has potent inhibitory activity towards ATX-β and ATX-ɣ as evidenced by enzymatic studies and its mode of action was rationalized by structural biology studies using macromolecular X-ray crystallography.
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Affiliation(s)
- Mathias Christophe Eymery
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France; Univ. Grenoble Alpes, INSERM U1039, LRB, 38000, Grenoble, France
| | - Kim-Anh Nguyen
- Univ. Grenoble Alpes, INSERM U1039, LRB, 38000, Grenoble, France
| | - Shibom Basu
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Jens Hausmann
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Viet-Khoa Tran-Nguyen
- Unité de Biologie Fonctionnelle et Adaptative (BFA), Université Paris Cité, 75013, Paris, France
| | - Hans Peter Seidel
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Lola Gutierrez
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
| | | | - Andrew Aloysius McCarthy
- European Molecular Biology Laboratory, EMBL Grenoble, 71 Avenue des Martyrs, 38000, Grenoble, France
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37
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Alkan C, O’Brien T, Kenyon V, Ikegami T. Computer-Selected Antiviral Compounds: Assessing In Vitro Efficacies against Rift Valley Fever Virus. Viruses 2024; 16:88. [PMID: 38257788 PMCID: PMC10818293 DOI: 10.3390/v16010088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Rift Valley fever is a zoonotic viral disease transmitted by mosquitoes, impacting both humans and livestock. Currently, there are no approved vaccines or antiviral treatments for humans. This study aimed to evaluate the in vitro efficacy of chemical compounds targeting the Gc fusion mechanism. These compounds were identified through virtual screening of millions of commercially available small molecules using a structure-based artificial intelligence bioactivity predictor. In our experiments, a pretreatment with small molecule compounds revealed that 3 out of 94 selected compounds effectively inhibited the replication of the Rift Valley fever virus MP-12 strain in Vero cells. As anticipated, these compounds did not impede viral RNA replication when administered three hours after infection. However, significant inhibition of viral RNA replication occurred upon viral entry when cells were pretreated with these small molecules. Furthermore, these compounds exhibited significant inhibition against Arumowot virus, another phlebovirus, while showing no antiviral effects on tick-borne bandaviruses. Our study validates AI-based virtual high throughput screening as a rational approach for identifying effective antiviral candidates for Rift Valley fever virus and other bunyaviruses.
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Affiliation(s)
- Cigdem Alkan
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA;
| | - Terrence O’Brien
- Discovery Chemistry, Genentech, Inc., South San Francisco, CA 94080, USA;
| | | | - Tetsuro Ikegami
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA;
- Sealy Institute for Vaccine Sciences, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, The University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
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38
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Gregory KS, Cozier GE, Schwager SLU, Sturrock ED, Acharya KR. Structural insights into the inhibitory mechanism of angiotensin-I-converting enzyme by the lactotripeptides IPP and VPP. FEBS Lett 2024; 598:242-251. [PMID: 37904282 PMCID: PMC10952540 DOI: 10.1002/1873-3468.14768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/12/2023] [Accepted: 10/15/2023] [Indexed: 11/01/2023]
Abstract
Human somatic angiotensin-1-converting enzyme (sACE) is composed of a catalytic N-(nACE) and C-domain (cACE) of similar size with different substrate specificities. It is involved in the regulation of blood pressure by converting angiotensin I to the vasoconstrictor angiotensin II and has been a major focus in the development of therapeutics for hypertension. Bioactive peptides from various sources, including milk, have been identified as natural ACE inhibitors. We report the structural basis for the role of two lacototripeptides, Val-Pro-Pro and Ile-Pro-Pro, in domain-specific inhibition of ACE using X-ray crystallography and kinetic analysis. The lactotripeptides have preference for nACE due to altered polar interactions distal to the catalytic zinc ion. Elucidating the mechanism of binding and domain selectivity of these peptides also provides important insights into the functional roles of ACE.
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Affiliation(s)
| | | | - Sylva L. U. Schwager
- Department of Integrative Biomedical SciencesInstitute of Infectious Disease and Molecular Medicine, University of Cape TownSouth Africa
| | - Edward D. Sturrock
- Department of Integrative Biomedical SciencesInstitute of Infectious Disease and Molecular Medicine, University of Cape TownSouth Africa
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39
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Tyagi S, Yadav RK, Krishnan V. Determination of the Crystal Structure of the Cell Wall-Anchored Proteins and Pilins. Methods Mol Biol 2024; 2727:159-191. [PMID: 37815717 DOI: 10.1007/978-1-0716-3491-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Surface proteins and pili (or pilus) anchored on the Gram-positive bacterial cell wall play a vital role in adhesion, colonization, biofilm formation, and immunomodulation. The pilus consists of building blocks called pilins or pilus subunits. The surface proteins and pilins share some common sequences and structural features. They contain an N-terminal signal sequence and the C-terminal cell wall sorting region, enabling their transportation across the membrane and covalent attachment to the bacterial cell wall, respectively. The transpeptidase enzymes called sortases facilitate the covalent links between the pilins during the pilus assembly and between surface proteins or basal subunits of pili and peptidoglycan-bridge during the cell wall anchoring. Thus, elucidating three-dimensional structures for the surface proteins and pilins at the atomic level is essential for understanding the mechanism of adhesion, pilus assembly, and host interaction. This chapter aims to provide a general protocol for crystal structure determination of surface proteins and pilins anchored on the Gram-positive bacterial cell wall and substrates for sortases. The protocol involves the production of recombinant protein, crystallization, and structure determination by X-ray crystallography technique.
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Affiliation(s)
- Shivangi Tyagi
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Rajnesh Kumari Yadav
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Vengadesan Krishnan
- Laboratory of Structural Biology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India.
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40
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Williams HM, Moeller JB, Burns I, Schlosser A, Sorensen GL, Greenhough TJ, Holmskov U, Shrive AK. Crystal structures of human immune protein FIBCD1 suggest an extended binding site compatible with recognition of pathogen-associated carbohydrate motifs. J Biol Chem 2024; 300:105552. [PMID: 38072065 PMCID: PMC10825690 DOI: 10.1016/j.jbc.2023.105552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/14/2024] Open
Abstract
Fibrinogen C domain-containing protein 1 (FIBCD1) is an immune protein proposed to be involved in host recognition of chitin on the surface of pathogens. As FIBCD1 readily binds acetylated molecules, we have determined the high-resolution crystal structures of a recombinant fragment of the FIBCD1 C-terminal domain complexed with small N-acetyl-containing ligands to determine the mode of recognition. All ligands bind at the conserved N-acetyl-binding site (S1) with galactose and glucose-derived ligands rotated 180° relative to each other. One subunit of a native structure derived from protein expressed in mammalian cells binds glycosylation from a neighboring subunit, in an extended binding site. Across the various structures, the primary S1 binding pocket is occupied by N-acetyl-containing ligands or acetate, with N-acetyl, acetate, or sulfate ion in an adjacent pocket S1(2). Inhibition binding studies of N-acetylglucosamine oligomers, (GlcNAc)n, n = 1, 2, 3, 5, 11, via ELISA along with microscale thermophoresis affinity assays indicate a strong preference of FIBCD1 for longer N-acetylchitooligosaccharides. Binding studies of mutant H396A, located beyond the S1(2) site, showed no significant difference from wildtype, but K381L, within the S1(2) pocket, blocked binding to the model ligand acetylated bovine serum albumin, suggesting that S1(2) may have functional importance in ligand binding. The binding studies, alongside structural definition of diverse N-acetyl monosaccharide binding in the primary S1 pocket and of additional, adjacent binding pockets, able to accommodate both carbohydrate and sulfate functional groups, suggest a versatility in FIBCD1 to recognize chitin oligomers and other pathogen-associated carbohydrate motifs across an extended surface.
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Affiliation(s)
- Harry M Williams
- School of Life Sciences, Keele University, Staffordshire, United Kingdom
| | - Jesper B Moeller
- Cancer and Inflammation Research Unit, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark; Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Ian Burns
- School of Life Sciences, Keele University, Staffordshire, United Kingdom
| | - Anders Schlosser
- Cancer and Inflammation Research Unit, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Grith L Sorensen
- Cancer and Inflammation Research Unit, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | | | - Uffe Holmskov
- Cancer and Inflammation Research Unit, Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Annette K Shrive
- School of Life Sciences, Keele University, Staffordshire, United Kingdom.
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Bruce HA, Singer AU, Filippova EV, Blazer LL, Adams JJ, Enderle L, Ben‐David M, Radley EH, Mao DYL, Pau V, Orlicky S, Sicheri F, Kurinov I, Atwell S, Kossiakoff AA, Sidhu SS. Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes. Protein Sci 2024; 33:e4824. [PMID: 37945533 PMCID: PMC10731619 DOI: 10.1002/pro.4824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/09/2023] [Accepted: 10/28/2023] [Indexed: 11/12/2023]
Abstract
The atomic-resolution structural information that X-ray crystallography can provide on the binding interface between a Fab and its cognate antigen is highly valuable for understanding the mechanism of interaction. However, many Fab:antigen complexes are recalcitrant to crystallization, making the endeavor a considerable effort with no guarantee of success. Consequently, there have been significant steps taken to increase the likelihood of Fab:antigen complex crystallization by altering the Fab framework. In this investigation, we applied the surface entropy reduction strategy coupled with phage-display technology to identify a set of surface substitutions that improve the propensity of a human Fab framework to crystallize. In addition, we showed that combining these surface substitutions with previously reported Crystal Kappa and elbow substitutions results in an extraordinary improvement in Fab and Fab:antigen complex crystallizability, revealing a strong synergistic relationship between these sets of substitutions. Through comprehensive Fab and Fab:antigen complex crystallization screenings followed by structure determination and analysis, we defined the roles that each of these substitutions play in facilitating crystallization and how they complement each other in the process.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Daniel Y. L. Mao
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoCanada
| | - Victor Pau
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoCanada
| | - Stephen Orlicky
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoCanada
| | - Frank Sicheri
- Lunenfeld‐Tanenbaum Research InstituteSinai Health SystemTorontoCanada
- Departments of Biochemistry and Molecular GeneticsUniversity of TorontoOntarioCanada
| | | | | | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinoisUSA
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Salo AM, Rappu P, Koski MK, Karjalainen E, Izzi V, Drushinin K, Miinalainen I, Käpylä J, Heino J, Myllyharju J. Collagen prolyl 4-hydroxylase isoenzymes I and II have sequence specificity towards different X-Pro-Gly triplets. Matrix Biol 2024; 125:73-87. [PMID: 38081527 DOI: 10.1016/j.matbio.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 02/12/2024]
Abstract
Collagen biosynthesis requires several co- and post-translational modifications of lysine and proline residues to form structurally and functionally competent collagen molecules. Formation of 4-hydroxyproline (4Hyp) in Y-position prolines of the repetitive -X-Y-Gly- sequences provides thermal stability for the triple-helical collagen molecules. 4Hyp formation is catalyzed by a collagen prolyl 4-hydroxylase (C-P4H) family consisting of three isoenzymes. Here we identify specific roles for the two main C-P4H isoenzymes in collagen hydroxylation by a detailed 4Hyp analysis of type I and IV collagens derived from cell and tissue samples. Loss of C-P4H-I results in underhydroxylation of collagen where the affected prolines are not uniformly distributed, but mainly present in sites where the adjacent X-position amino acid has a positively charged or a polar uncharged side chain. In contrast, loss of C-P4H-II results in underhydroxylation of triplets where the X-position is occupied by a negatively charged amino acid glutamate or aspartate. Hydroxylation of these triplets was found to be important as loss of C-P4H-II alone resulted in reduced collagen melting temperature and altered assembly of collagen fibrils and basement membrane. The observed C-P4H isoenzyme differences in substrate specificity were explained by selective binding of the substrate to the active site resulting in distinct differences in Km and Vmax values. Furthermore, our results clearly show that the substrate proline selection is not dependent on the collagen type, but the main determinant is the X-position amino acid of the -X-Pro-Gly- triplet. Although our data clearly shows the necessity of both C-P4H-I and II for normal prolyl 4-hydroxylation and function of collagens, the mRNA expression of the isoenzymes with various procollagens was, surprisingly, not tightly coordinated, suggesting additional levels of control. In conclusion, this study provides a molecular level explanation for the need of multiple C-P4H isoenzymes to generate collagen molecules capable to assemble into intact extracellular matrix structures.
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Affiliation(s)
- Antti M Salo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Pekka Rappu
- Department of Life Technologies, University of Turku, Turku, Finland
| | - M Kristian Koski
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Emma Karjalainen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Valerio Izzi
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Faculty of Medicine, BioIM Research Unit, University of Oulu, Oulu, Finland
| | - Kati Drushinin
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Jarmo Käpylä
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Jyrki Heino
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Johanna Myllyharju
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
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43
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Casanova-Sepúlveda G, Sexton JA, Turk BE, Boggon TJ. Autoregulation of the LIM kinases by their PDZ domain. Nat Commun 2023; 14:8441. [PMID: 38114480 PMCID: PMC10730565 DOI: 10.1038/s41467-023-44148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
LIM domain kinases (LIMK) are important regulators of actin cytoskeletal remodeling. These protein kinases phosphorylate the actin depolymerizing factor cofilin to suppress filament severing, and are key nodes between Rho GTPase cascades and actin. The two mammalian LIMKs, LIMK1 and LIMK2, contain consecutive LIM domains and a PDZ domain upstream of the C-terminal kinase domain. The roles of the N-terminal regions are not fully understood, and the function of the PDZ domain remains elusive. Here, we determine the 2.0 Å crystal structure of the PDZ domain of LIMK2 and reveal features not previously observed in PDZ domains including a core-facing arginine residue located at the second position of the 'x-Φ-G-Φ' motif, and that the expected peptide binding cleft is shallow and poorly conserved. We find a distal extended surface to be highly conserved, and when LIMK1 was ectopically expressed in yeast we find targeted mutagenesis of this surface decreases growth, implying increased LIMK activity. PDZ domain LIMK1 mutants expressed in yeast are hyperphosphorylated and show elevated activity in vitro. This surface in both LIMK1 and LIMK2 is critical for autoregulation independent of activation loop phosphorylation. Overall, our study demonstrates the functional importance of the PDZ domain to autoregulation of LIMKs.
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Affiliation(s)
| | - Joel A Sexton
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA
| | - Benjamin E Turk
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA
| | - Titus J Boggon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Pharmacology, Yale University, New Haven, CT, 06520, USA.
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44
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Liu Q, Maqbool A, Mirkin FG, Singh Y, Stevenson CEM, Lawson DM, Kamoun S, Huang W, Hogenhout SA. Bimodular architecture of bacterial effector SAP05 that drives ubiquitin-independent targeted protein degradation. Proc Natl Acad Sci U S A 2023; 120:e2310664120. [PMID: 38039272 DOI: 10.1073/pnas.2310664120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/19/2023] [Indexed: 12/03/2023] Open
Abstract
In eukaryotes, targeted protein degradation (TPD) typically depends on a series of interactions among ubiquitin ligases that transfer ubiquitin molecules to substrates leading to degradation by the 26S proteasome. We previously identified that the bacterial effector protein SAP05 mediates ubiquitin-independent TPD. SAP05 forms a ternary complex via interactions with the von Willebrand Factor Type A (vWA) domain of the proteasomal ubiquitin receptor Rpn10 and the zinc-finger (ZnF) domains of the SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) and GATA BINDING FACTOR (GATA) transcription factors (TFs). This leads to direct TPD of the TFs by the 26S proteasome. Here, we report the crystal structures of the SAP05-Rpn10vWA complex at 2.17 Å resolution and of the SAP05-SPL5ZnF complex at 2.20 Å resolution. Structural analyses revealed that SAP05 displays a remarkable bimodular architecture with two distinct nonoverlapping surfaces, a "loop surface" with three protruding loops that form electrostatic interactions with ZnF, and a "sheet surface" featuring two β-sheets, loops, and α-helices that establish polar interactions with vWA. SAP05 binding to ZnF TFs involves single amino acids responsible for multiple contacts, while SAP05 binding to vWA is more stable due to the necessity of multiple mutations to break the interaction. In addition, positioning of the SAP05 complex on the 26S proteasome points to a mechanism of protein degradation. Collectively, our findings demonstrate how a small bacterial bimodular protein can bypass the canonical ubiquitin-proteasome proteolysis pathway, enabling ubiquitin-independent TPD in eukaryotic cells. This knowledge holds significant potential for the creation of TPD technologies.
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Affiliation(s)
- Qun Liu
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Abbas Maqbool
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Federico G Mirkin
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Yeshveer Singh
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Clare E M Stevenson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - David M Lawson
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich NR4 7UH, United Kingdom
| | - Weijie Huang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Centre for Plant Stress Biology, Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 20032, China
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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45
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Arita GS, Ma Q, Leaves I, Pradhan A, Hickey E, Dambuza I, Bebes A, Vincenzi Conrado PC, Barros Galinari C, Vicente Seixas FA, Kioshima ÉS, de Souza Bonfim-Mendonça P, Svidzinski TIE, Brown AJP. The impact of ORF19.36.1 in the pathobiology of Candida albicans. Microb Pathog 2023; 185:106437. [PMID: 37913825 DOI: 10.1016/j.micpath.2023.106437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Our previous proteomics data obtained from Candida albicans recovered after serial passage in a murine model of systemic infection revealed that Orf19.36.1 expression correlates with the virulence of the fungus. Therefore, the impact of ORF19.36.1 upon virulence was tested in this study. MATERIALS & METHODS CRISPR-Cas9 technology was used to construct homozygous C. albicans orf19.36.1 null mutants and the phenotypes of these mutants examined in vitro (filamentation, invasion, adhesion, biofilm formation, hydrolase activities) and in vivo assays. RESULTS The deletion of ORF19.36.1 did not significantly impact the phenotypes examined or the virulence of C. albicans in two infection models. CONCLUSION These results suggest that, although Orf19.36.1 expression correlates with virulence, this protein is not essential for C. albicans pathobiology.
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Affiliation(s)
- Glaucia Sayuri Arita
- Department of Clinical Analysis and Biomedicine, Laboratory of Medical Mycology, State University of Maringa, T20 Building, Room 203, Colombo Avenue, 5790 - Zone 7, Maringá, PR, 87020-900, Brazil
| | - Qinxi Ma
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Ian Leaves
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Arnab Pradhan
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Emer Hickey
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Ivy Dambuza
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Attila Bebes
- Centre for Cytomics, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Pollyanna Cristina Vincenzi Conrado
- Department of Clinical Analysis and Biomedicine, Laboratory of Medical Mycology, State University of Maringa, T20 Building, Room 203, Colombo Avenue, 5790 - Zone 7, Maringá, PR, 87020-900, Brazil
| | - Camila Barros Galinari
- Department of Clinical Analysis and Biomedicine, Laboratory of Medical Mycology, State University of Maringa, T20 Building, Room 203, Colombo Avenue, 5790 - Zone 7, Maringá, PR, 87020-900, Brazil
| | - Flávio Augusto Vicente Seixas
- Department of Technology, State University of Maringa, Ângelo Moreira da Fonseca Avenue, 1800 - Danielle Park, Umuarama, PR, 87506-370, Brazil
| | - Érika Seki Kioshima
- Department of Clinical Analysis and Biomedicine, Laboratory of Medical Mycology, State University of Maringa, T20 Building, Room 203, Colombo Avenue, 5790 - Zone 7, Maringá, PR, 87020-900, Brazil
| | - Patrícia de Souza Bonfim-Mendonça
- Department of Clinical Analysis and Biomedicine, Laboratory of Medical Mycology, State University of Maringa, T20 Building, Room 203, Colombo Avenue, 5790 - Zone 7, Maringá, PR, 87020-900, Brazil
| | - Terezinha Inez Estivalet Svidzinski
- Department of Clinical Analysis and Biomedicine, Laboratory of Medical Mycology, State University of Maringa, T20 Building, Room 203, Colombo Avenue, 5790 - Zone 7, Maringá, PR, 87020-900, Brazil.
| | - Alistair J P Brown
- Medical Research Council Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
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46
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Evic V, Soic R, Mocibob M, Kekez M, Houser J, Wimmerová M, Matković-Čalogović D, Gruic-Sovulj I, Kekez I, Rokov-Plavec J. Evolutionarily conserved cysteines in plant cytosolic seryl-tRNA synthetase are important for its resistance to oxidation. FEBS Lett 2023; 597:2975-2992. [PMID: 37804069 DOI: 10.1002/1873-3468.14748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/08/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
We have previously identified a unique disulfide bond in the crystal structure of Arabidopsis cytosolic seryl-tRNA synthetase involving cysteines evolutionarily conserved in all green plants. Here, we discovered that both cysteines are important for protein stability, but with opposite effects, and that their microenvironment may promote disulfide bond formation in oxidizing conditions. The crystal structure of the C244S mutant exhibited higher rigidity and an extensive network of noncovalent interactions correlating with its higher thermal stability. The activity of the wild-type showed resistance to oxidation with H2 O2 , while the activities of cysteine-to-serine mutants were impaired, indicating that the disulfide link may enable the protein to function under oxidative stress conditions which can be beneficial for an efficient plant stress response.
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Affiliation(s)
- Valentina Evic
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ruzica Soic
- Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marko Mocibob
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Mario Kekez
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Josef Houser
- Central European Institute of Technology (CEITEC), Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Wimmerová
- Central European Institute of Technology (CEITEC), Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Dubravka Matković-Čalogović
- Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ita Gruic-Sovulj
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivana Kekez
- Division of General and Inorganic Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jasmina Rokov-Plavec
- Division of Biochemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
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47
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Liu N, Xiao H, Zang Y, Zhou L, Mencius J, Yang Z, Quan S, Chen X. Simultaneous Improvement in the Thermostability and Catalytic Activity of Epoxidase Lsd18 for the Synthesis of Lasalocid A. Int J Mol Sci 2023; 24:16795. [PMID: 38069118 PMCID: PMC10706071 DOI: 10.3390/ijms242316795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Enzymes used in the synthesis of natural products are potent catalysts, capable of efficient and stereoselective chemical transformations. Lsd18 catalyzes two sequential epoxidations during the biosynthesis of lasalocid A, a polyether polyketide natural product. We performed protein engineering on Lsd18 to improve its thermostability and catalytic activity. Utilizing structure-guided methods of FoldX and Rosetta-ddG, we designed 15 mutants of Lsd18. Screening of these mutants using thermal shift assay identified stabilized variants Lsd18-T189M, Lsd18-S195M, and the double mutant Lsd18-T189M-S195M. Trypsin digestion, molecular dynamic simulation, circular dichroism (CD) spectroscopy, and X-ray crystallography provided insights into the molecular basis for the improved enzyme properties. Notably, enhanced hydrophobic interaction within the enzyme core and interaction of the protein with the FAD cofactor appear to be responsible for its better thermostability.
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Affiliation(s)
- Ning Liu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (N.L.); (H.X.)
| | - Hongli Xiao
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (N.L.); (H.X.)
| | - Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.Z.); (Z.Y.)
- Institute of Physics and Electronic Information, Yunnan Normal University, Kunming 650504, China
| | - Longji Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (L.Z.); (J.M.)
| | - Jun Mencius
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (L.Z.); (J.M.)
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Y.Z.); (Z.Y.)
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; (L.Z.); (J.M.)
| | - Xi Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, China; (N.L.); (H.X.)
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48
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De Rose SA, Isupov MN, Worthy HL, Stracke C, Harmer NJ, Siebers B, Littlechild JA. Structural characterization of a novel cyclic 2,3-diphosphoglycerate synthetase involved in extremolyte production in the archaeon Methanothermus fervidus. Front Microbiol 2023; 14:1267570. [PMID: 38045033 PMCID: PMC10690619 DOI: 10.3389/fmicb.2023.1267570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/28/2023] [Indexed: 12/05/2023] Open
Abstract
The enzyme cyclic di-phosphoglycerate synthetase that is involved in the production of the osmolyte cyclic 2,3-diphosphoglycerate has been studied both biochemically and structurally. Cyclic 2,3-diphosphoglycerate is found exclusively in the hyperthermophilic archaeal methanogens, such as Methanothermus fervidus, Methanopyrus kandleri, and Methanothermobacter thermoautotrophicus. Its presence increases the thermostability of archaeal proteins and protects the DNA against oxidative damage caused by hydroxyl radicals. The cyclic 2,3-diphosphoglycerate synthetase enzyme has been crystallized and its structure solved to 1.7 Å resolution by experimental phasing. It has also been crystallized in complex with its substrate 2,3 diphosphoglycerate and the co-factor ADP and this structure has been solved to 2.2 Å resolution. The enzyme structure has two domains, the core domain shares some structural similarity with other NTP-dependent enzymes. A significant proportion of the structure, including a 127 amino acid N-terminal domain, has no structural similarity to other known enzyme structures. The structure of the complex shows a large conformational change that occurs in the enzyme during catalytic turnover. The reaction involves the transfer of the γ-phosphate group from ATP to the substrate 2,3 -diphosphoglycerate and the subsequent SN2 attack to form a phosphoanhydride. This results in the production of the unusual extremolyte cyclic 2,3 -diphosphoglycerate which has important industrial applications.
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Affiliation(s)
- Simone A. De Rose
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Harley L. Worthy
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Christina Stracke
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Nicholas J. Harmer
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Bettina Siebers
- Department of Molecular Enzyme Technology and Biochemistry, Environmental Microbiology and Biotechnology, and Centre for Water and Environmental Research, University of Duisburg-Essen, Essen, Germany
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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49
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Becker P, Naughton F, Brotherton D, Pacheco-Gomez R, Beckstein O, Cameron AD. Mechanism of substrate binding and transport in BASS transporters. eLife 2023; 12:RP89167. [PMID: 37963091 PMCID: PMC10645422 DOI: 10.7554/elife.89167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
The bile acid sodium symporter (BASS) family transports a wide array of molecules across membranes, including bile acids in humans, and small metabolites in plants. These transporters, many of which are sodium-coupled, have been shown to use an elevator mechanism of transport, but exactly how substrate binding is coupled to sodium ion binding and transport is not clear. Here, we solve the crystal structure at 2.3 Å of a transporter from Neisseria meningitidis (ASBTNM) in complex with pantoate, a potential substrate of ASBTNM. The BASS family is characterised by two helices that cross-over in the centre of the protein in an arrangement that is intricately held together by two sodium ions. We observe that the pantoate binds, specifically, between the N-termini of two of the opposing helices in this cross-over region. During molecular dynamics simulations the pantoate remains in this position when sodium ions are present but is more mobile in their absence. Comparison of structures in the presence and absence of pantoate demonstrates that pantoate elicits a conformational change in one of the cross-over helices. This modifies the interface between the two domains that move relative to one another to elicit the elevator mechanism. These results have implications, not only for ASBTNM but for the BASS family as a whole and indeed other transporters that work through the elevator mechanism.
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Affiliation(s)
- Patrick Becker
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Fiona Naughton
- Department of Physics, Arizona State UniversityTempeUnited States
| | | | | | - Oliver Beckstein
- Department of Physics, Arizona State UniversityTempeUnited States
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50
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Russell C, Carter JL, Borgia JM, Bush J, Calderón F, Gabarró R, Conway SJ, Mottram JC, Wilkinson AJ, Jones NG. Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery. ACS Infect Dis 2023; 9:2340-2357. [PMID: 37906637 PMCID: PMC10644352 DOI: 10.1021/acsinfecdis.3c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023]
Abstract
Leishmaniases are a collection of neglected tropical diseases caused by kinetoplastid parasites in the genus Leishmania. Current chemotherapies are severely limited, and the need for new antileishmanials is of pressing international importance. Bromodomains are epigenetic reader domains that have shown promising therapeutic potential for cancer therapy and may also present an attractive target to treat parasitic diseases. Here, we investigate Leishmania donovani bromodomain factor 5 (LdBDF5) as a target for antileishmanial drug discovery. LdBDF5 contains a pair of bromodomains (BD5.1 and BD5.2) in an N-terminal tandem repeat. We purified recombinant bromodomains of L. donovani BDF5 and determined the structure of BD5.2 by X-ray crystallography. Using a histone peptide microarray and fluorescence polarization assay, we identified binding interactions of LdBDF5 bromodomains with acetylated peptides derived from histones H2B and H4. In orthogonal biophysical assays including thermal shift assays, fluorescence polarization, and NMR, we showed that BDF5 bromodomains bind to human bromodomain inhibitors SGC-CBP30, bromosporine, and I-BRD9; moreover, SGC-CBP30 exhibited activity against Leishmania promastigotes in cell viability assays. These findings exemplify the potential BDF5 holds as a possible drug target in Leishmania and provide a foundation for the future development of optimized antileishmanial compounds targeting this epigenetic reader protein.
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Affiliation(s)
- Catherine
N. Russell
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Jennifer L. Carter
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Juliet M. Borgia
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Jacob Bush
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
| | | | | | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Jeremy C. Mottram
- York
Biomedical Research Institute, Department of Biology, University of York, York YO10 5NG, U.K.
| | - Anthony J. Wilkinson
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Nathaniel G. Jones
- York
Biomedical Research Institute, Department of Biology, University of York, York YO10 5NG, U.K.
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