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Noro I, Bettin I, Fasoli S, Smania M, Lunardi L, Giannini M, Andreoni L, Montioli R, Gotte G. Human RNase 1 can extensively oligomerize through 3D domain swapping thanks to the crucial contribution of its C-terminus. Int J Biol Macromol 2023; 249:126110. [PMID: 37536419 DOI: 10.1016/j.ijbiomac.2023.126110] [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: 04/24/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]
Abstract
Human ribonuclease (RNase) 1 and bovine RNase A are the proto-types of the secretory "pancreatic-type" (pt)-RNase super-family. RNase A can oligomerize through the 3D domain swapping (DS) mechanism upon acetic acid (HAc) lyophilisation, producing enzymatically active oligomeric conformers by swapping both N- and C-termini. Also some RNase 1 mutants were found to self-associate through 3D-DS, however forming only N-swapped dimers. Notably, enzymatically active dimers and larger oligomers of wt-RNase 1 were collected here, in higher amount than RNase A, from HAc lyophilisation. In particular, RNase 1 self-associates through the 3D-DS of its N-terminus and, at a higher extent, of the C-terminus. Since RNase 1 is four-residues longer than RNase A, we further analyzed its oligomerization tendency in a mutant lacking the last four residues. The C-terminus role has been investigated also in amphibian onconase (ONC®), a pt-RNase that can form only a N-swapped dimer, since its C-terminus, that is three-residues longer than RNase A, is locked by a disulfide bond. While ONC mutants designed to unlock or cut this constraint were almost unable to dimerize, the RNase 1 mutant self-associated at a higher extent than the wt, suggesting a specific role of the C-terminus in the oligomerization of different RNases. Overall, RNase 1 reaches here the highest ability, among pt-RNases, to extensively self-associate through 3D-DS, paving the way for new investigations on the structural and biological properties of its oligomers.
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Affiliation(s)
- Irene Noro
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Ilaria Bettin
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Sabrina Fasoli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Marcello Smania
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Luca Lunardi
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Michele Giannini
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Leonardo Andreoni
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Riccardo Montioli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
| | - Giovanni Gotte
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
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Donnarumma F, Tucci V, Ambrosino C, Altucci L, Carafa V. NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family. Clin Epigenetics 2022; 14:182. [PMID: 36539894 PMCID: PMC9769039 DOI: 10.1186/s13148-022-01402-8] [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: 10/04/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Chromatin structural organization, gene expression and proteostasis are intricately regulated in a wide range of biological processes, both physiological and pathological. Protein acetylation, a major post-translational modification, is tightly involved in interconnected biological networks, modulating the activation of gene transcription and protein action in cells. A very large number of studies describe the pivotal role of the so-called acetylome (accounting for more than 80% of the human proteome) in orchestrating different pathways in response to stimuli and triggering severe diseases, including cancer. NAA60/NatF (N-terminal acetyltransferase F), also named HAT4 (histone acetyltransferase type B protein 4), is a newly discovered acetyltransferase in humans modifying N-termini of transmembrane proteins starting with M-K/M-A/M-V/M-M residues and is also thought to modify lysine residues of histone H4. Because of its enzymatic features and unusual cell localization on the Golgi membrane, NAA60 is an intriguing acetyltransferase that warrants biochemical and clinical investigation. Although it is still poorly studied, this review summarizes current findings concerning the structural hallmarks and biological role of this novel targetable epigenetic enzyme.
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Affiliation(s)
- Federica Donnarumma
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy
| | - Valeria Tucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Concetta Ambrosino
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.47422.370000 0001 0724 3038Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Lucia Altucci
- grid.428067.f0000 0004 4674 1402Biogem, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy ,grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
| | - Vincenzo Carafa
- grid.9841.40000 0001 2200 8888Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico De Crecchio7, 80138 Naples, Italy
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Fernández-Millán P, Vázquez-Monteagudo S, Boix E, Prats-Ejarque G. Exploring the RNase A scaffold to combine catalytic and antimicrobial activities. Structural characterization of RNase 3/1 chimeras. Front Mol Biosci 2022; 9:964717. [PMID: 36188223 PMCID: PMC9515509 DOI: 10.3389/fmolb.2022.964717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Design of novel antibiotics to fight antimicrobial resistance is one of the first global health priorities. Novel protein-based strategies come out as alternative therapies. Based on the structure-function knowledge of the RNase A superfamily we have engineered a chimera that combines RNase 1 highest catalytic activity with RNase 3 unique antipathogen properties. A first construct (RNase 3/1-v1) was successfully designed with a catalytic activity 40-fold higher than RNase 3, but alas in detriment of its anti-pathogenic activity. Next, two new versions of the original chimeric protein were created showing improvement in the antimicrobial activity. Both second generation versions (RNases 3/1-v2 and -v3) incorporated a loop characteristic of RNase 3 (L7), associated to antimicrobial activity. Last, removal of an RNase 1 flexible loop (L1) in the third version enhanced its antimicrobial properties and catalytic efficiency. Here we solved the 3D structures of the three chimeras at atomic resolution by X-ray crystallography. Structural analysis outlined the key functional regions. Prediction by molecular docking of the protein chimera in complex with dinucleotides highlighted the contribution of the C-terminal region to shape the substrate binding cavity and determine the base selectivity and catalytic efficiency. Nonetheless, the structures that incorporated the key features related to RNase 3 antimicrobial activity retained the overall RNase 1 active site conformation together with the essential structural elements for binding to the human ribonuclease inhibitor (RNHI), ensuring non-cytotoxicity. Results will guide us in the design of the best RNase pharmacophore for anti-infective therapies.
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Affiliation(s)
| | | | - Ester Boix
- *Correspondence: Ester Boix, ; Guillem Prats-Ejarque,
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Delfi M, Leone S, Emendato A, Ami D, Borriello M, Natalello A, Iannuzzi C, Picone D. Understanding the self-assembly pathways of a single chain variant of monellin: A first step towards the design of sweet nanomaterials. Int J Biol Macromol 2020; 152:21-29. [PMID: 32088237 DOI: 10.1016/j.ijbiomac.2020.02.229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 12/20/2022]
Abstract
Peptides and proteins possess an inherent tendency to self-assemble, prompting the formation of amyloid aggregates from their soluble and functional states. Amyloids are linked to many devastating diseases, but self-assembling proteins can also represent formidable tools to produce new and sustainable biomaterials for biomedical and biotechnological applications. The mechanism of fibrillar aggregation, which influences the morphology and the properties of the protein aggregates, depend on factors such as pH, ionic strength, temperature, agitation, and protein concentration. We have here used intensive mechanical agitation, with or without beads, to prompt the aggregation of the single-chain derivative of the plant protein monellin, named MNEI, which is a well characterized sweet protein. Transmission electron microscopy confirmed the formation of fibrils several micrometers long, morphologically different from the previously characterized fibers of MNEI. Changes in the protein secondary structures during the aggregation process were monitored by Fourier transform infrared spectroscopy, which detected differences in the conformation of the final aggregates obtained under mechanical agitation. Moreover, soluble oligomers could be detected in the early phases of aggregation by polyacrylamide gel-electrophoresis. These findings emphasize the existence of multiple pathways of fibrillar aggregation for MNEI, which could be exploited for the design of innovative protein-based biomaterials.
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Affiliation(s)
- Masoud Delfi
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Serena Leone
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Alessandro Emendato
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Margherita Borriello
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Clara Iannuzzi
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy.
| | - Delia Picone
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia, 80126 Napoli, Italy.
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Gotte G, Menegazzi M. Biological Activities of Secretory RNases: Focus on Their Oligomerization to Design Antitumor Drugs. Front Immunol 2019; 10:2626. [PMID: 31849926 PMCID: PMC6901985 DOI: 10.3389/fimmu.2019.02626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ribonucleases (RNases) are a large number of enzymes gathered into different bacterial or eukaryotic superfamilies. Bovine pancreatic RNase A, bovine seminal BS-RNase, human pancreatic RNase 1, angiogenin (RNase 5), and amphibian onconase belong to the pancreatic type superfamily, while binase and barnase are in the bacterial RNase N1/T1 family. In physiological conditions, most RNases secreted in the extracellular space counteract the undesired effects of extracellular RNAs and become protective against infections. Instead, if they enter the cell, RNases can digest intracellular RNAs, becoming cytotoxic and having advantageous effects against malignant cells. Their biological activities have been investigated either in vitro, toward a number of different cancer cell lines, or in some cases in vivo to test their potential therapeutic use. However, immunogenicity or other undesired effects have sometimes been associated with their action. Nevertheless, the use of RNases in therapy remains an appealing strategy against some still incurable tumors, such as mesothelioma, melanoma, or pancreatic cancer. The RNase inhibitor (RI) present inside almost all cells is the most efficacious sentry to counteract the ribonucleolytic action against intracellular RNAs because it forms a tight, irreversible and enzymatically inactive complex with many monomeric RNases. Therefore, dimerization or multimerization could represent a useful strategy for RNases to exert a remarkable cytotoxic activity by evading the interaction with RI by steric hindrance. Indeed, the majority of the mentioned RNases can hetero-dimerize with antibody derivatives, or even homo-dimerize or multimerize, spontaneously or artificially. This can occur through weak interactions or upon introducing covalent bonds. Immuno-RNases, in particular, are fusion proteins representing promising drugs by combining high target specificity with easy delivery in tumors. The results concerning the biological features of many RNases reported in the literature are described and discussed in this review. Furthermore, the activities displayed by some RNases forming oligomeric complexes, the mechanisms driving toward these supramolecular structures, and the biological rebounds connected are analyzed. These aspects are offered with the perspective to suggest possible efficacious therapeutic applications for RNases oligomeric derivatives that could contemporarily lack, or strongly reduce, immunogenicity and other undesired side-effects.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Marta Menegazzi
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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