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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: 29] [Impact Index Per Article: 4.8] [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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De Laet M, Gilis D, Rooman M. Stability strengths and weaknesses in protein structures detected by statistical potentials: Application to bovine seminal ribonuclease. Proteins 2015; 84:143-58. [DOI: 10.1002/prot.24962] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 10/27/2015] [Accepted: 11/09/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Marie De Laet
- 3BIO-BioInfo Department; Université Libre De Bruxelles; Avenue F. Roosevelt 50 CP 165/61 Brussels 1050 Belgium
| | - Dimitri Gilis
- 3BIO-BioInfo Department; Université Libre De Bruxelles; Avenue F. Roosevelt 50 CP 165/61 Brussels 1050 Belgium
| | - Marianne Rooman
- 3BIO-BioInfo Department; Université Libre De Bruxelles; Avenue F. Roosevelt 50 CP 165/61 Brussels 1050 Belgium
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Spadaccini R, Ercole C, Graziano G, Wechselberger R, Boelens R, Picone D. Mechanism of 3D domain swapping in bovine seminal ribonuclease. FEBS J 2014; 281:842-50. [PMID: 24616921 PMCID: PMC7164040 DOI: 10.1111/febs.12651] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
3D domain swapping (3D‐DS) is a complex protein aggregation process for which no unique mechanism exists. We report an analysis of 3D‐DS in bovine seminal ribonuclease, a homodimeric protein whose subunits are linked by two disulfide bridges, based on NMR and biochemical studies. The presence of the covalent bonds between the subunits stabilizes the unswapped dimer, and allows distinct evaluation of the structural and dynamic effects of the swapping with respect to the dimerization process. In comparison with the monomeric subunit, which, in solution has a compact structure without any propensity for local unfolding, both swapped and unswapped dimers show increased flexibility. NMR analysis, together with urea denaturation and hydrogen–deuterium exchange data, indicates that the two dimers have increased conformational fluctuations. Furthermore, we found that the rate‐limiting step of both the swapping and unswapping pathways is the detachment of the N‐terminal helices from the monomers. These results suggest a new general mechanism in which a dimeric intermediate could facilitate 3D‐DS in globular proteins. Structured digital abstract http://www.uniprot.org/uniprot/P00669 and http://www.uniprot.org/uniprot/P00669 http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0407 by http://www.ebi.ac.uk/ontology-lookup/?termId=MI:0077 (http://www.ebi.ac.uk/intact/interaction/EBI-8870415)
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The multiple forms of bovine seminal ribonuclease: structure and stability of a C-terminal swapped dimer. FEBS Lett 2013; 587:3755-62. [PMID: 24140346 DOI: 10.1016/j.febslet.2013.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/07/2013] [Indexed: 11/20/2022]
Abstract
Bovine seminal ribonuclease (BS-RNase) acquires an interesting anti-tumor activity associated with the swapping on the N-terminal. The first direct experimental evidence on the formation of a C-terminal swapped dimer (C-dimer) obtained from the monomeric derivative of BS-RNase, although under non-native conditions, is here reported. The X-ray model of this dimer reveals a quaternary structure different from that of the C-dimer of RNase A, due to the presence of three mutations in the hinge peptide 111-116. The mutations increase the hinge peptide flexibility and decrease the stability of the C-dimer against dissociation. The biological implications of the structural data are also discussed.
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Double domain swapping in bovine seminal RNase: formation of distinct N- and C-swapped tetramers and multimers with increasing biological activities. PLoS One 2012; 7:e46804. [PMID: 23071641 PMCID: PMC3469567 DOI: 10.1371/journal.pone.0046804] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 09/10/2012] [Indexed: 12/24/2022] Open
Abstract
Bovine seminal (BS) RNase, the unique natively dimeric member of the RNase super-family, represents a special case not only for its additional biological actions but also for the singular features of 3D domain swapping. The native enzyme is indeed a mixture of two isoforms: M = M, a dimer held together by two inter-subunit disulfide bonds, and MxM, 70% of the total, which, besides the two mentioned disulfides, is additionally stabilized by the swapping of its N-termini. When lyophilized from 40% acetic acid, BS-RNase oligomerizes as the super-family proto-type RNase A does. In this paper, we induced BS-RNase self-association and analyzed the multimers by size-exclusion chromatography, cross-linking, electrophoresis, mutagenesis, dynamic light scattering, molecular modelling. Finally, we evaluated their enzymatic and cytotoxic activities. Several BS-RNase domain-swapped oligomers were detected, including two tetramers, one exchanging only the N-termini, the other being either N- or C-swapped. The C-swapping event, confirmed by results on a BS-K113N mutant, has been firstly seen in BS-RNase here, and probably stabilizes also multimers larger than tetramers. Interestingly, all BS-RNase oligomers are more enzymatically active than the native dimer and, above all, they display a cytotoxic activity that definitely increases with the molecular weight of the multimers. This latter feature, to date unknown for BS-RNase, suggests again that the self-association of RNases strongly modulates their biological and potentially therapeutic properties.
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Merlino A, Picone D, Ercole C, Balsamo A, Sica F. Chain termini cross-talk in the swapping process of bovine pancreatic ribonuclease. Biochimie 2012; 94:1108-18. [PMID: 22273774 DOI: 10.1016/j.biochi.2012.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 01/11/2012] [Indexed: 10/14/2022]
Abstract
3D domain swapping is the process by which two or more protein molecules exchange part of their structure to form intertwined dimers or higher oligomers. Bovine pancreatic ribonuclease (RNase A) is able to swap the N-terminal α-helix (residues 1-13) and/or the C-terminal β-strand (residues 116-124), thus forming a variety of oligomers, including two different dimers. Cis-trans isomerization of the Asn113-Pro114 peptide group was observed when the protein formed the C-terminal swapped dimer. To study the effect of the substitution of Pro114 on the swapping process of RNase A, we have prepared and characterized the P114A monomeric and dimeric variants of the enzyme. In contrast with previous reports, the crystal structure and NMR data on the monomer reveals a mixed cis-trans conformation for the Asn113-Ala114 peptide group, whereas the X-ray structure of the C-terminal swapped dimer of the variant is very close to that of the corresponding dimer of RNase A. The mutation at the C-terminus affects the capability of the N-terminal α-helix to swap and the stability of both dimeric forms. The present results underscore the importance of the hydration shell in determining the cross-talk between the chain termini in the swapping process of RNase A.
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Affiliation(s)
- Antonello Merlino
- Department of Chemistry, University of Naples Federico II, Complesso Universitario Monte S. Angelo, Via Cinthia, I-80126 Naples, Italy
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Spadaccini R, Ercole C, Gentile MA, Sanfelice D, Boelens R, Wechselberger R, Batta G, Bernini A, Niccolai N, Picone D. NMR studies on structure and dynamics of the monomeric derivative of BS-RNase: new insights for 3D domain swapping. PLoS One 2012; 7:e29076. [PMID: 22253705 PMCID: PMC3257227 DOI: 10.1371/journal.pone.0029076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/20/2011] [Indexed: 11/18/2022] Open
Abstract
Three-dimensional domain swapping is a common phenomenon in pancreatic-like ribonucleases. In the aggregated state, these proteins acquire new biological functions, including selective cytotoxicity against tumour cells. RNase A is able to dislocate both N- and C-termini, but usually this process requires denaturing conditions. In contrast, bovine seminal ribonuclease (BS-RNase), which is a homo-dimeric protein sharing 80% of sequence identity with RNase A, occurs natively as a mixture of swapped and unswapped isoforms. The presence of two disulfides bridging the subunits, indeed, ensures a dimeric structure also to the unswapped molecule. In vitro, the two BS-RNase isoforms interconvert under physiological conditions. Since the tendency to swap is often related to the instability of the monomeric proteins, in these paper we have analysed in detail the stability in solution of the monomeric derivative of BS-RNase (mBS) by a combination of NMR studies and Molecular Dynamics Simulations. The refinement of NMR structure and relaxation data indicate a close similarity with RNase A, without any evidence of aggregation or partial opening. The high compactness of mBS structure is confirmed also by H/D exchange, urea denaturation, and TEMPOL mapping of the protein surface. The present extensive structural and dynamic investigation of (monomeric) mBS did not show any experimental evidence that could explain the known differences in swapping between BS-RNase and RNase A. Hence, we conclude that the swapping in BS-RNase must be influenced by the distinct features of the dimers, suggesting a prominent role for the interchain disulfide bridges.
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Affiliation(s)
- Roberta Spadaccini
- Dipartimento di Scienze Biologiche ed Ambientali, Università del Sannio, Benevento, Italy
| | - Carmine Ercole
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Maria A. Gentile
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Domenico Sanfelice
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - Rolf Boelens
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Rainer Wechselberger
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Gyula Batta
- Institute of Chemistry, University of Debrecen, Debrecen, Hungary
| | - Andrea Bernini
- Dipartimento di Biotecnologie, Università degli Studi di Siena, Siena, Italy
| | - Neri Niccolai
- Dipartimento di Biotecnologie, Università degli Studi di Siena, Siena, Italy
| | - Delia Picone
- Dipartimento di Chimica, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- * E-mail:
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D'Errico G, Ercole C, Lista M, Pizzo E, Falanga A, Galdiero S, Spadaccini R, Picone D. Enforcing the positive charge of N-termini enhances membrane interaction and antitumor activity of bovine seminal ribonuclease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:3007-15. [DOI: 10.1016/j.bbamem.2011.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/29/2011] [Accepted: 08/04/2011] [Indexed: 11/29/2022]
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Vottariello F, Giacomelli E, Frasson R, Pozzi N, De Filippis V, Gotte G. RNase A oligomerization through 3D domain swapping is favoured by a residue located far from the swapping domains. Biochimie 2011; 93:1846-57. [PMID: 21771635 DOI: 10.1016/j.biochi.2011.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Accepted: 07/04/2011] [Indexed: 11/27/2022]
Abstract
Bovine pancreatic ribonuclease A forms 3D domain-swapped oligomers by lyophilization from 40% acetic acid solutions or if subjected to various thermally-induced denaturation procedures. Considering that the intrinsic swapping propensity of bovine seminal RNase, the only member of the pancreatic-type RNase super-family that is dimeric in nature, is decreased from 70 to 30% if Arg80 is substituted by Ser (the corresponding residue in native RNase A), we introduced the opposite mutation in position 80 of the pancreatic enzyme. Our aim was to detect if the RNase A tendency to aggregate through domain swapping could increase. Aggregation of the S80R-RNase A mutant was induced either through the 'classic' acetic acid lyophilization, or through a thermally-induced method. The results indicate that the S80R mutant aggregates to a higher extent than the native protein, and that the increase occurs especially through N-terminal swapping. Additional investigations on the dimeric and multimeric species formed indicate that the S80R mutation increases their stability against regression to monomer, and does not significantly change their structural and functional features.
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Affiliation(s)
- Francesca Vottariello
- Dipartimento di Scienze della Vita e della Riproduzione, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
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Giancola C, Ercole C, Fotticchia I, Spadaccini R, Pizzo E, D’Alessio G, Picone D. Structure-cytotoxicity relationships in bovine seminal ribonuclease: new insights from heat and chemical denaturation studies on variants. FEBS J 2010; 278:111-22. [DOI: 10.1111/j.1742-4658.2010.07937.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ercole C, Colamarino RA, Pizzo E, Fogolari F, Spadaccini R, Picone D. Comparison of the structural and functional properties of RNase A and BS-RNase: A stepwise mutagenesis approach. Biopolymers 2009; 91:1009-17. [DOI: 10.1002/bip.21176] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Merlino A, Ercole C, Picone D, Pizzo E, Mazzarella L, Sica F. The Buried Diversity of Bovine Seminal Ribonuclease: Shape and Cytotoxicity of the Swapped Non-covalent Form of the Enzyme. J Mol Biol 2008; 376:427-37. [DOI: 10.1016/j.jmb.2007.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2007] [Revised: 11/02/2007] [Accepted: 11/02/2007] [Indexed: 11/17/2022]
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Picone D, Di Fiore A, Ercole C, Franzese M, Sica F, Tomaselli S, Mazzarella L. The role of the hinge loop in domain swapping. The special case of bovine seminal ribonuclease. J Biol Chem 2005; 280:13771-8. [PMID: 15647261 DOI: 10.1074/jbc.m413157200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bovine seminal ribonuclease (BS-RNase) is a covalent homodimeric enzyme homologous to pancreatic ribonuclease (RNase A), endowed with a number of special biological functions. It is isolated as an equilibrium mixture of swapped (MxM) and unswapped (M=M) dimers. The interchanged N termini are hinged on the main bodies through the peptide 16-22, which changes conformation in the two isomers. At variance with other proteins, domain swapping in BS-RNase involves two dimers having a similar and highly constrained quaternary association, mainly dictated by two interchain disulfide bonds. This provides the opportunity to study the intrinsic ability to swap as a function of the hinge sequence, without additional effects arising from dissociation or quaternary structure modifications. Two variants, having Pro19 or the whole sequence of the hinge replaced by the corresponding residues of RNase A, show equilibrium and kinetic parameters of the swapping similar to those of the parent protein. In comparison, the x-ray structures of MxM indicate, within a substantial constancy of the quaternary association, a greater mobility of the hinge residues. The relative insensitivity of the swapping tendency to the substitutions in the hinge region, and in particular to the replacement of Pro19 by Ala, contrasts with the results obtained for other swapped proteins and can be rationalized in terms of the unique features of the seminal enzyme. Moreover, the results indirectly lend credit to the hypothesis that the major role of Pro19 resides in directing the assembly of the non-covalent dimer, the species produced by selective reduction of the interchain disulfides and considered responsible for the special biological functions of BS-RNase.
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Affiliation(s)
- Delia Picone
- Dipartimento di Chimica, Università Federico II di Napoli, Via Cynthia, 80126, Napoli, Italy
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