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Scheu AHA, Lim SYT, Metzner FJ, Mohammed S, Howarth M. NeissLock provides an inducible protein anhydride for covalent targeting of endogenous proteins. Nat Commun 2021; 12:717. [PMID: 33514717 PMCID: PMC7846742 DOI: 10.1038/s41467-021-20963-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/04/2021] [Indexed: 11/22/2022] Open
Abstract
The Neisseria meningitidis protein FrpC contains a self-processing module (SPM) undergoing autoproteolysis via an aspartic anhydride. Herein, we establish NeissLock, using a binding protein genetically fused to SPM. Upon calcium triggering of SPM, the anhydride at the C-terminus of the binding protein allows nucleophilic attack by its target protein, ligating the complex. We establish a computational tool to search the Protein Data Bank, assessing proximity of amines to C-termini. We optimize NeissLock using the Ornithine Decarboxylase/Antizyme complex. Various sites on the target (α-amine or ε-amines) react with the anhydride, but reaction is blocked if the partner does not dock. Ligation is efficient at pH 7.0, with half-time less than 2 min. We arm Transforming Growth Factor-α with SPM, enabling specific covalent coupling to Epidermal Growth Factor Receptor at the cell-surface. NeissLock harnesses distinctive protein chemistry for high-yield covalent targeting of endogenous proteins, advancing the possibilities for molecular engineering. Covalent conjugation of endogenous protein complexes offers many opportunities for fundamental and clinical research. Based on a bacterial protein domain that forms a reactive anhydride in the presence of Ca2+, the authors here develop a system that enables the covalent capture of endogenous binding partners.
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Affiliation(s)
- Arne H A Scheu
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Sheryl Y T Lim
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Felix J Metzner
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377, Munich, Germany
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Abstract
The Ca2+-dependent clip-and-link activity of large repeat-in-toxin (RTX) proteins is an exceptional posttranslational process in which an internal domain called a self-processing module (SPM) mediates Ca2+-dependent processing of a highly specific aspartate-proline (Asp-Pro) peptide bond and covalent linkage of the released aspartyl to an adjacent lysine residue through an isopeptide bond. Here, we report the solution structures of the Ca2+-loaded SPM (Ca-SPM) defining the mechanism of the autocatalytic cleavage of the Asp414-Pro415 peptide bond of the Neisseria meningitidis FrpC exoprotein. Moreover, deletion of the SPM domain in the ApxIVA protein, the FrpC homolog of Actinobacillus pleuropneumoniae, resulted in attenuation of virulence of the bacterium in a pig infection model, indicating that the Ca2+-dependent clip-and-link activity plays a role in the virulence of Gram-negative pathogens. The posttranslational Ca2+-dependent “clip-and-link” activity of large repeat-in-toxin (RTX) proteins starts by Ca2+-dependent structural rearrangement of a highly conserved self-processing module (SPM). Subsequently, an internal aspartate-proline (Asp-Pro) peptide bond at the N-terminal end of SPM breaks, and the liberated C-terminal aspartyl residue can react with a free ε-amino group of an adjacent lysine residue to form a new isopeptide bond. Here, we report a solution structure of the calcium-loaded SPM (Ca-SPM) derived from the FrpC protein of Neisseria meningitidis. The Ca-SPM structure defines a unique protein architecture and provides structural insight into the autocatalytic cleavage of the Asp-Pro peptide bond through a “twisted-amide” activation. Furthermore, in-frame deletion of the SPM domain from the ApxIVA protein of Actinobacillus pleuropneumoniae attenuated the virulence of this porcine pathogen in a pig respiratory challenge model. We hypothesize that the Ca2+-dependent clip-and-link activity represents an unconventional strategy for Gram-negative pathogens to adhere to the host target cell surface.
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Sviridova E, Rezacova P, Bondar A, Veverka V, Novak P, Schenk G, Svergun DI, Kuta Smatanova I, Bumba L. Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis. Sci Rep 2017; 7:40408. [PMID: 28084396 PMCID: PMC5233953 DOI: 10.1038/srep40408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/06/2016] [Indexed: 01/14/2023] Open
Abstract
The iron-regulated protein FrpD from Neisseria meningitidis is an outer membrane lipoprotein that interacts with very high affinity (Kd ~ 0.2 nM) with the N-terminal domain of FrpC, a Type I-secreted protein from the Repeat in ToXin (RTX) protein family. In the presence of Ca2+, FrpC undergoes Ca2+ -dependent protein trans-splicing that includes an autocatalytic cleavage of the Asp414-Pro415 peptide bond and formation of an Asp414-Lys isopeptide bond. Here, we report the high-resolution structure of FrpD and describe the structure-function relationships underlying the interaction between FrpD and FrpC1-414. We identified FrpD residues involved in FrpC1-414 binding, which enabled localization of FrpD within the low-resolution SAXS model of the FrpD-FrpC1-414 complex. Moreover, the trans-splicing activity of FrpC resulted in covalent linkage of the FrpC1-414 fragment to plasma membrane proteins of epithelial cells in vitro, suggesting that formation of the FrpD-FrpC1-414 complex may be involved in the interaction of meningococci with the host cell surface.
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Affiliation(s)
- Ekaterina Sviridova
- Faculty of Science, University of South Bohemia Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.,Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Pavlina Rezacova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Alexey Bondar
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, Zamek 136, 37333 Nove Hrady, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Vaclav Veverka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague, Czech Republic
| | - Petr Novak
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
| | - Gundolf Schenk
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Dmitri I Svergun
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Ivana Kuta Smatanova
- Faculty of Science, University of South Bohemia Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.,Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, Zamek 136, 37333 Nove Hrady, Czech Republic
| | - Ladislav Bumba
- Institute of Microbiology, Czech Academy of Sciences, Videnska 1083, 14220 Prague, Czech Republic
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Masin J, Osickova A, Sukova A, Fiser R, Halada P, Bumba L, Linhartova I, Osicka R, Sebo P. Negatively charged residues of the segment linking the enzyme and cytolysin moieties restrict the membrane-permeabilizing capacity of adenylate cyclase toxin. Sci Rep 2016; 6:29137. [PMID: 27581058 PMCID: PMC5007505 DOI: 10.1038/srep29137] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/15/2016] [Indexed: 11/10/2022] Open
Abstract
The whooping cough agent, Bordetella pertussis, secretes an adenylate cyclase toxin-hemolysin (CyaA) that plays a crucial role in host respiratory tract colonization. CyaA targets CR3-expressing cells and disrupts their bactericidal functions by delivering into their cytosol an adenylate cyclase enzyme that converts intracellular ATP to cAMP. In parallel, the hydrophobic domain of CyaA forms cation-selective pores that permeabilize cell membrane. The invasive AC and pore-forming domains of CyaA are linked by a segment that is unique in the RTX cytolysin family. We used mass spectrometry and circular dichroism to show that the linker segment forms α-helical structures that penetrate into lipid bilayer. Replacement of the positively charged arginine residues, proposed to be involved in target membrane destabilization by the linker segment, reduced the capacity of the toxin to translocate the AC domain across cell membrane. Substitutions of negatively charged residues then revealed that two clusters of negative charges within the linker segment control the size and the propensity of CyaA pore formation, thereby restricting the cell-permeabilizing capacity of CyaA. The ‘AC to Hly-linking segment’ thus appears to account for the smaller size and modest cell-permeabilizing capacity of CyaA pores, as compared to typical RTX hemolysins.
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Affiliation(s)
- Jiri Masin
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Adriana Osickova
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Anna Sukova
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Radovan Fiser
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Halada
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Ladislav Bumba
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Irena Linhartova
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Radim Osicka
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
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Matyska Liskova P, Fiser R, Macek P, Chmelik J, Sykora J, Bednarova L, Konopasek I, Bumba L. Probing the Ca(2+)-assisted π-π interaction during Ca(2+)-dependent protein folding. SOFT MATTER 2016; 12:531-541. [PMID: 26489523 DOI: 10.1039/c5sm01796c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein folding is governed by a balance of non-covalent interactions, of which cation-π and π-π play important roles. Theoretical calculations revealed a strong cooperativity between cation-π involving alkali and alkaline earth metal ions and π-π interactions, but however, no experimental evidence was provided in this regard. Here, we characterized a Ca(2+)-binding self-processing module (SPM), which mediates a highly-specific Ca(2+)-dependent autocatalytic processing of iron-regulated protein FrpC secreted by the pathogenic Gram-negative bacterium Neisseria meningitidis. The SPM undergoes a Ca(2+)-induced transition from an intrinsically unstructured conformation to the compact protein fold that is ultimately stabilized by the π-π interaction between two unique tryptophan residues arranged in the T-shaped orientation. Moreover, the pair of tryptophans is located in a close vicinity of a calcium-binding site, suggesting the involvement of a Ca(2+)-assisted π-π interaction in the stabilization of the tertiary structure of the SPM. This makes the SPM an excellent model for the investigation of the Ca(2+)-assisted π-π interaction during Ca(2+)-induced protein folding.
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Affiliation(s)
- Petra Matyska Liskova
- Laboratory of Molecular Biology of Bacterial Pathogens, Institute of Microbiology of the ASCR, v.v.i., Videnska 1083, 14200 Prague, Czech Republic.
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