1
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Catalano F, Santorelli D, Astegno A, Favaretto F, D'Abramo M, Del Giudice A, De Sciscio ML, Troilo F, Giardina G, Di Matteo A, Travaglini-Allocatelli C. Conformational and dynamic properties of the KH1 domain of FMRP and its fragile X syndrome linked G266E variant. Biochim Biophys Acta Proteins Proteom 2024:141019. [PMID: 38641086 DOI: 10.1016/j.bbapap.2024.141019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/26/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
The Fragile X messenger ribonucleoprotein (FMRP) is a complex, multi-domain protein involved in interactions with various macromolecules, including proteins and coding/non-coding RNAs. The three KH domains (KH0, KH1 and KH2) within FMRP are recognized for their roles in mRNA binding. In the context of Fragile X syndrome (FXS), over-and-above CGG triplet repeats expansion, three specific point mutations have been identified, each affecting one of the three KH domains (R138QKH0, G266EKH1, and I304NKH2) resulting in the expression of non-functional FMRP. This study aims to elucidate the molecular mechanism underlying the loss of function associated with the G266EKH1 pathological variant. We investigate the conformational and dynamical properties of the isolated KH1 domain and the two KH1 site-directed mutants G266EKH1 and G266AKH1. Employing a combined in vitro and in silico approach, we reveal that the G266EKH1 variant lacks the characteristic features of a folded domain. This observation provides an explanation for functional impairment observed in FMRP carrying the G266E mutation within the KH1 domain, as it renders the domain unable to fold properly. Molecular Dynamics simulations suggest a pivotal role for residue 266 in regulating the structural stability of the KH domains, primarily through stabilizing the α-helices of the domain. Overall, these findings enhance our comprehension of the molecular basis for the dysfunction associated with the G266EKH1 variant in FMRP.
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Affiliation(s)
- Flavia Catalano
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Daniele Santorelli
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Filippo Favaretto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, Verona 37134, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Alessandra Del Giudice
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Maria Laura De Sciscio
- Department of Chemistry, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Francesca Troilo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, Rome 00185, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, P.le Aldo Moro 5, Rome 00185, Italy
| | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, Rome 00185, Italy.
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2
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Caruso L, Mellini M, Catalano Gonzaga O, Astegno A, Forte E, Di Matteo A, Giuffrè A, Visca P, Imperi F, Leoni L, Rampioni G. Hydrogen sulfide production does not affect antibiotic resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2024; 68:e0007524. [PMID: 38445869 PMCID: PMC10989007 DOI: 10.1128/aac.00075-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/18/2024] [Indexed: 03/07/2024] Open
Abstract
Hydrogen sulfide (H2S) has been proposed to protect bacteria from antibiotics, pointing to H2S-producing enzymes as possible targets for the development of antibiotic adjuvants. Here, MIC assays performed with Pseudomonas aeruginosa mutants producing altered H2S levels demonstrate that H2S does not affect antibiotic resistance in this bacterium. Moreover, correlation analyses in a large collection of P. aeruginosa cystic fibrosis isolates argue against the protective role of H2S from antibiotic activity during chronic lung infection.
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Affiliation(s)
| | - Marta Mellini
- Department of Science, University Roma Tre, Rome, Italy
| | | | | | - Elena Forte
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, Rome, Italy
| | | | - Paolo Visca
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Francesco Imperi
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Giordano Rampioni
- Department of Science, University Roma Tre, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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3
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Scribani Rossi C, Eckartt K, Scarchilli E, Angeli S, Price-Whelan A, Di Matteo A, Chevreuil M, Raynal B, Arcovito A, Giacon N, Fiorentino F, Rotili D, Mai A, Espinosa-Urgel M, Cutruzzolà F, Dietrich LEP, Paone A, Paiardini A, Rinaldo S. Molecular insights into RmcA-mediated c-di-GMP consumption: Linking redox potential to biofilm morphogenesis in Pseudomonas aeruginosa. Microbiol Res 2023; 277:127498. [PMID: 37776579 DOI: 10.1016/j.micres.2023.127498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
The ability of many bacteria to form biofilms contributes to their resilience and makes infections more difficult to treat. Biofilm growth leads to the formation of internal oxygen gradients, creating hypoxic subzones where cellular reducing power accumulates, and metabolic activities can be limited. The pathogen Pseudomonas aeruginosa counteracts the redox imbalance in the hypoxic biofilm subzones by producing redox-active electron shuttles (phenazines) and by secreting extracellular matrix, leading to an increased surface area-to-volume ratio, which favors gas exchange. Matrix production is regulated by the second messenger bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP) in response to different environmental cues. RmcA (Redox modulator of c-di-GMP) from P. aeruginosa is a multidomain phosphodiesterase (PDE) that modulates c-di-GMP levels in response to phenazine availability. RmcA can also sense the fermentable carbon source arginine via a periplasmic domain, which is linked via a transmembrane domain to four cytoplasmic Per-Arnt-Sim (PAS) domains followed by a diguanylate cyclase (DGC) and a PDE domain. The biochemical characterization of the cytoplasmic portion of RmcA reported in this work shows that the PAS domain adjacent to the catalytic domain tunes RmcA PDE activity in a redox-dependent manner, by differentially controlling protein conformation in response to FAD or FADH2. This redox-dependent mechanism likely links the redox state of phenazines (via FAD/FADH2 ratio) to matrix production as indicated by a hyperwrinkling phenotype in a macrocolony biofilm assay. This study provides insights into the role of RmcA in transducing cellular redox information into a structural response of the biofilm at the population level. Conditions of resource (i.e. oxygen and nutrient) limitation arise during chronic infection, affecting the cellular redox state and promoting antibiotic tolerance. An understanding of the molecular linkages between condition sensing and biofilm structure is therefore of crucial importance from both biological and engineering standpoints.
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Affiliation(s)
- Chiara Scribani Rossi
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Kelly Eckartt
- Department of Biological Sciences, Columbia University, New York, USA
| | - Elisabetta Scarchilli
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Simone Angeli
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | | | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, I-00185 Rome, Italy
| | - Maelenn Chevreuil
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528 CNRS, Paris, France
| | - Bertrand Raynal
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528 CNRS, Paris, France
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche e Perioperatorie Università Cattolica Del Sacro Cuore, Roma, Italy; Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
| | - Noah Giacon
- Dipartimento di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche e Perioperatorie Università Cattolica Del Sacro Cuore, Roma, Italy
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection. Estación Experimental del Zaidin, CSIC, Granada, Spain
| | - Francesca Cutruzzolà
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, USA
| | - Alessio Paone
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Alessandro Paiardini
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
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Pedretti M, Favretto F, Troilo F, Giovannoni M, Conter C, Mattei B, Dominici P, Travaglini-Allocatelli C, Di Matteo A, Astegno A. Role of myristoylation in modulating PCaP1 interaction with calmodulin. Plant Physiol Biochem 2023; 203:108003. [PMID: 37717348 DOI: 10.1016/j.plaphy.2023.108003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/09/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023]
Abstract
Plasma membrane-associated Cation-binding Protein 1 (PCaP1) belongs to the plant-unique DREPP protein family with largely unknown biological functions but ascertained roles in plant development and calcium (Ca2+) signaling. PCaP1 is anchored to the plasma membrane via N-myristoylation and a polybasic cluster, and its N-terminal region can bind Ca2+/calmodulin (CaM). However, the molecular determinants of PCaP1-Ca2+-CaM interaction and the functional impact of myristoylation in the complex formation and Ca2+ sensitivity of CaM remained to be elucidated. Herein, we investigated the direct interaction between Arabidopsis PCaP1 (AtPCaP1) and CaM1 (AtCaM1) using both myristoylated and non-myristoylated peptides corresponding to the N-terminal region of AtPCaP1. ITC analysis showed that AtCaM1 forms a high affinity 1:1 complex with AtPCaP1 peptides and the interaction is strictly Ca2+-dependent. Spectroscopic and kinetic Ca2+ binding studies showed that the myristoylated peptide dramatically increased the Ca2+-binding affinity of AtCaM1 and slowed the Ca2+ dissociation rates from both the C- and N-lobes, thus suggesting that the myristoylation modulates the mechanism of AtPCaP1 recognition by AtCaM1. Furthermore, NMR and CD spectroscopy revealed that the structure of both the N- and C-lobes of Ca2+-AtCaM1 changes markedly in the presence of the myristoylated AtPCaP1 peptide, which assumes a helical structure in the final complex. Overall, our results indicate that AtPCaP1 biological function is strictly related to the presence of multiple ligands, i.e., the myristoyl moiety, Ca2+ ions and AtCaM1 and only a full characterization of their equilibria will allow for a complete molecular understanding of the putative role of PCaP1 as signal protein.
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Affiliation(s)
- Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Filippo Favretto
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Francesca Troilo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Moira Giovannoni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Carolina Conter
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | | | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy.
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
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5
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Scafati V, Troilo F, Ponziani S, Giovannoni M, Scortica A, Pontiggia D, Angelucci F, Di Matteo A, Mattei B, Benedetti M. Characterization of two 1,3-β-glucan-modifying enzymes from Penicillium sumatraense reveals new insights into 1,3-β-glucan metabolism of fungal saprotrophs. Biotechnol Biofuels Bioprod 2022; 15:138. [PMID: 36510318 PMCID: PMC9745967 DOI: 10.1186/s13068-022-02233-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND 1,3-β-glucan is a polysaccharide widely distributed in the cell wall of several phylogenetically distant organisms, such as bacteria, fungi, plants and microalgae. The presence of highly active 1,3-β-glucanases in fungi evokes the biological question on how these organisms can efficiently metabolize exogenous sources of 1,3-β-glucan without incurring in autolysis. RESULTS To elucidate the molecular mechanisms at the basis of 1,3-β-glucan metabolism in fungal saprotrophs, the putative exo-1,3-β-glucanase G9376 and a truncated form of the putative glucan endo-1,3-β-glucosidase (ΔG7048) from Penicillium sumatraense AQ67100 were heterologously expressed in Pichia pastoris and characterized both in terms of activity and structure. G9376 efficiently converted laminarin and 1,3-β-glucan oligomers into glucose by acting as an exo-glycosidase, whereas G7048 displayed a 1,3-β-transglucanase/branching activity toward 1,3-β-glucan oligomers with a degree of polymerization higher than 5, making these oligomers more recalcitrant to the hydrolysis acted by exo-1,3-β-glucanase G9376. The X-ray crystallographic structure of the catalytic domain of G7048, solved at 1.9 Å of resolution, consists of a (β/α)8 TIM-barrel fold characteristic of all the GH17 family members. The catalytic site is in a V-shaped cleft containing the two conserved catalytic glutamic residues. Molecular features compatible with the activity of G7048 as 1,3-β-transglucanase are discussed. CONCLUSIONS The antagonizing activity between ΔG7048 and G9376 indicates how opportunistic fungi belonging to Penicillium genus can feed on substrates similar for composition and structure to their own cell wall without incurring in a self-deleterious autohydrolysis.
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Affiliation(s)
- Valentina Scafati
- grid.158820.60000 0004 1757 2611Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Francesca Troilo
- grid.5326.20000 0001 1940 4177Institute of Molecular Biology and Pathology, CNR, P.Le Aldo Moro 5, 00185 Rome, Italy
| | - Sara Ponziani
- grid.158820.60000 0004 1757 2611Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Moira Giovannoni
- grid.158820.60000 0004 1757 2611Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Anna Scortica
- grid.158820.60000 0004 1757 2611Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Daniela Pontiggia
- grid.7841.aDepartment of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Angelucci
- grid.158820.60000 0004 1757 2611Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Adele Di Matteo
- grid.5326.20000 0001 1940 4177Institute of Molecular Biology and Pathology, CNR, P.Le Aldo Moro 5, 00185 Rome, Italy
| | - Benedetta Mattei
- grid.158820.60000 0004 1757 2611Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Manuel Benedetti
- grid.158820.60000 0004 1757 2611Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
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6
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Ardini M, Baiocco P, Di Matteo A, Giardina G, Miele AE. Editorial: Tailored Modulation of Interactions Between Biomolecules: Fundamentals and Applications. Front Mol Biosci 2022; 9:961452. [PMID: 35911973 PMCID: PMC9332331 DOI: 10.3389/fmolb.2022.961452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/24/2022] [Indexed: 12/05/2022] Open
Affiliation(s)
- Matteo Ardini
- Department of Public Health, Life and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- *Correspondence: Matteo Ardini,
| | - Paola Baiocco
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, Roma, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Adriana Erica Miele
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
- Institut des Sciences Analytiques, UMR 5280 CNRS UCBL, University of Lyon, Villeurbanne, France
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7
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Cela I, Cufaro MC, Fucito M, Pieragostino D, Lanuti P, Sallese M, Del Boccio P, Di Matteo A, Allocati N, De Laurenzi V, Federici L. Proteomic Investigation of the Role of Nucleostemin in Nucleophosmin-Mutated OCI-AML 3 Cell Line. Int J Mol Sci 2022; 23:ijms23147655. [PMID: 35886999 PMCID: PMC9317519 DOI: 10.3390/ijms23147655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 02/06/2023] Open
Abstract
Nucleostemin (NS; a product of the GNL3 gene) is a nucleolar–nucleoplasm shuttling GTPase whose levels are high in stem cells and rapidly decrease upon differentiation. NS levels are also high in several solid and hematological neoplasms, including acute myeloid leukaemia (AML). While a role in telomere maintenance, response to stress stimuli and favoring DNA repair has been proposed in solid cancers, little or no information is available as to the role of nucleostemin in AML. Here, we investigate this issue via a proteomics approach. We use as a model system the OCI-AML 3 cell line harboring a heterozygous mutation at the NPM1 gene, which is the most frequent driver mutation in AML (approximately 30% of total AML cases). We show that NS is highly expressed in this cell line, and, contrary to what has previously been shown in other cancers, that its presence is dispensable for cell growth and viability. However, proteomics analysis of the OCI-AML 3 cell line before and after nucleostemin (NS) silencing showed several effects on different biological functions, as highlighted by ingenuity pathway analysis (IPA). In particular, we report an effect of down-regulating DNA repair through homologous recombination, and we confirmed a higher DNA damage rate in OCI-AML 3 cells when NS is depleted, which considerably increases upon stress induced by the topoisomerase II inhibitor etoposide. The data used are available via ProteomeXchange with the identifier PXD034012.
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Affiliation(s)
- Ilaria Cela
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (I.C.); (M.F.); (D.P.); (M.S.); (N.A.); (V.D.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (M.C.C.); (P.L.); (P.D.B.)
| | - Maria Concetta Cufaro
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (M.C.C.); (P.L.); (P.D.B.)
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Maurine Fucito
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (I.C.); (M.F.); (D.P.); (M.S.); (N.A.); (V.D.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (M.C.C.); (P.L.); (P.D.B.)
| | - Damiana Pieragostino
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (I.C.); (M.F.); (D.P.); (M.S.); (N.A.); (V.D.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (M.C.C.); (P.L.); (P.D.B.)
| | - Paola Lanuti
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (M.C.C.); (P.L.); (P.D.B.)
- Department of Medicine and Aging Science, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Michele Sallese
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (I.C.); (M.F.); (D.P.); (M.S.); (N.A.); (V.D.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (M.C.C.); (P.L.); (P.D.B.)
| | - Piero Del Boccio
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (M.C.C.); (P.L.); (P.D.B.)
- Department of Pharmacy, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, National Research Council of Italy, P.le Aldo Moro 5, 00185 Rome, Italy;
| | - Nerino Allocati
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (I.C.); (M.F.); (D.P.); (M.S.); (N.A.); (V.D.L.)
| | - Vincenzo De Laurenzi
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (I.C.); (M.F.); (D.P.); (M.S.); (N.A.); (V.D.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (M.C.C.); (P.L.); (P.D.B.)
| | - Luca Federici
- Department of Innovative Technologies in Medicine & Dentistry, University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (I.C.); (M.F.); (D.P.); (M.S.); (N.A.); (V.D.L.)
- Center for Advanced Studies and Technology (CAST), University “G. d’Annunzio” of Chieti-Pescara, 66100 Chieti, Italy; (M.C.C.); (P.L.); (P.D.B.)
- Correspondence:
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8
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Troilo F, Pedretti M, Travaglini-Allocatelli C, Astegno A, Di Matteo A. Rapid kinetics of calcium dissociation from plant calmodulin and calmodulin-like proteins and effect of target peptides. Biochem Biophys Res Commun 2022; 590:103-108. [PMID: 34974297 DOI: 10.1016/j.bbrc.2021.12.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/02/2022]
Abstract
Calcium (Ca2+) signaling represents a universal information code in plants, playing crucial roles spanning developmental processes to stress responses. Ca2+ signals are decoded into defined plant adaptive responses by different Ca2+ sensing proteins, including calmodulin (CaM) and calmodulin-like (CML) proteins. Although major advances have been achieved in describing how these Ca2+ decoding proteins interact and regulate downstream target effectors, the molecular details of these processes remain largely unknown. Herein, the kinetics of Ca2+ dissociation from a conserved CaM and two CML isoforms from A. thaliana has been studied by fluorescence stopped-flow spectroscopy. Kinetic data were obtained for the isolated Ca2+-bound proteins as well as for the proteins complexed with different target peptides. Moreover, the lobe specific interactions between the Ca2+ sensing proteins and their targets were characterized by using a panel of protein mutants deficient in Ca2+ binding at the N-lobe or C-lobe. Results were analyzed and discussed in the context of the Ca2+-decoding and Ca2+-controlled target binding mechanisms in plants.
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Affiliation(s)
- Francesca Troilo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | | | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.
| | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, P.le Aldo Moro 5, 00185, Rome, Italy.
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9
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Fata F, Silvestri I, Ardini M, Ippoliti R, Di Leandro L, Demitri N, Polentarutti M, Di Matteo A, Lyu H, Thatcher GR, Petukhov PA, Williams DL, Angelucci F. Probing the Surface of a Parasite Drug Target Thioredoxin Glutathione Reductase Using Small Molecule Fragments. ACS Infect Dis 2021; 7:1932-1944. [PMID: 33950676 DOI: 10.1021/acsinfecdis.0c00909] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Fragment screening is a powerful drug discovery approach particularly useful for enzymes difficult to inhibit selectively, such as the thiol/selenol-dependent thioredoxin reductases (TrxRs), which are essential and druggable in several infectious diseases. Several known inhibitors are reactive electrophiles targeting the selenocysteine-containing C-terminus and thus often suffering from off-target reactivity in vivo. The lack of structural information on the interaction modalities of the C-terminus-targeting inhibitors, due to the high mobility of this domain and the lack of alternative druggable sites, prevents the development of selective inhibitors for TrxRs. In this work, fragments selected from actives identified in a large screen carried out against Thioredoxin Glutathione Reductase from Schistosoma mansoni (SmTGR) were probed by X-ray crystallography. SmTGR is one of the most promising drug targets for schistosomiasis, a devastating, neglected disease. Utilizing a multicrystal method to analyze electron density maps, structural analysis, and functional studies, three binding sites were characterized in SmTGR: two sites are close to or partially superposable with the NADPH binding site, while the third one is found between two symmetry related SmTGR subunits of the crystal lattice. Surprisingly, one compound bound to this latter site stabilizes, through allosteric effects mediated by the so-called guiding bar residues, the crucial redox active C-terminus of SmTGR, making it finally visible at high resolution. These results further promote fragments as small molecule probes for investigating functional aspects of the target protein, exemplified by the allosteric effect on the C-terminus, and providing fundamental chemical information exploitable in drug discovery.
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Affiliation(s)
- Francesca Fata
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Ilaria Silvestri
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Matteo Ardini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Luana Di Leandro
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Nicola Demitri
- Elettra − Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, 34149 Basovizza − Trieste, Italy
| | - Maurizio Polentarutti
- Elettra − Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, 34149 Basovizza − Trieste, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Department of Biochemical Sciences “A Rossi Fanelli” - Sapienza University of Rome, 00185 Rome, Italy
| | - Haining Lyu
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Gregory R.J. Thatcher
- Department of Pharmacology & Toxicology, College of Pharmacy, the University of Arizona, Tucson, Arizona 85721, United States
| | - Pavel A. Petukhov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - David L. Williams
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, Illinois 60612, United States
| | - Francesco Angelucci
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
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10
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Di Natale C, Florio D, Di Somma S, Di Matteo A, Federici L, Netti PA, Morelli G, Malfitano AM, Marasco D. Proteostasis unbalance of nucleophosmin 1 in Acute Myeloid Leukemia: An aggregomic perspective. Int J Biol Macromol 2020; 164:3501-3507. [PMID: 32890557 DOI: 10.1016/j.ijbiomac.2020.08.248] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/31/2020] [Accepted: 08/31/2020] [Indexed: 01/22/2023]
Abstract
The role exerted by the nucleus in the regulation of proteostasis in both health and disease is recognized of outmost importance, even though not fully understood. Many recent investigations are focused on its ability to modulate and coordinate protein quality control machineries in mammalian cells. Nucleophosmin 1 (NPM1) is one of the most abundant nucleolar proteins and its gene is mutated in ~30% of Acute Myeloid Leukemia (AML) patients. Mutations are localized in the C-terminal domain of the protein and cause cytoplasmatically delocalized and possibly aggregated forms of NPM1 (NPM1c+). Therapeutic interventions targeted on NPM1c+ are in demand and, to this end, deeper knowledge of NPM1c+ behavior in the blasts' cytosol is required. Here by means of complementary biophysical techniques we compared the conformational and aggregative behavior of the entire C-terminal domains of NPM1wt and type A NPM1c+ (bearing the most common mutation). Overall data show that only Cterm_mutA is able to form amyloid-like assemblies with fibrillar morphology and that the oligomers are toxic in human neuroblastoma SHSY cells. This study adds a novel piece of knowledge to the comprehension of the molecular roles exerted by cytoplasmatic NPM1c+ and suggests the exploitation of the amyloidogenic propensity of NPM1c+ as a new strategy for targeting AML with NPM1 mutations.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, University of Naples "Federico II", 80134, Italy; Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy; Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, P.le Tecchio 80, Naples 80125, Italy
| | - Daniele Florio
- Department of Pharmacy, University of Naples "Federico II", 80134, Italy
| | - Sarah Di Somma
- Department of Translational Medical Science, University of Naples Federico II, 80131 Napoli, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, National Research Council of Italy, c/o Department of Biochemical Sciences "A Rossi Fanelli" - Sapienza University of Rome, 00185 Rome, Italy
| | - Luca Federici
- Center of Advanced Studies and Technology (CAST) and Department of Clinical, Oral and Biotechnological Sciences, University of Chieti "G. d'Annunzio", 66100 Chieti, Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, Naples, Italy; Interdisciplinary Research Centre on Biomaterials (CRIB), University of Naples Federico II, P.le Tecchio 80, Naples 80125, Italy; Department of Chemical Materials and Industrial Production (DICMAPI), University of Naples Federico II, P.le Tecchio 80, Naples 80125, Italy
| | - Giancarlo Morelli
- Department of Pharmacy, University of Naples "Federico II", 80134, Italy
| | - Anna Maria Malfitano
- Department of Translational Medical Science, University of Naples Federico II, 80131 Napoli, Italy
| | - Daniela Marasco
- Department of Pharmacy, University of Naples "Federico II", 80134, Italy.
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11
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Abstract
Nucleophosmin (NPM1) is a mainly nucleolar protein that shuttles between nucleoli, nucleoplasm and cytoplasm to fulfill its many functions. It is a chaperone of both nucleic acids and proteins and plays a role in cell cycle control, centrosome duplication, ribosome maturation and export, as well as the cellular response to a variety of stress stimuli. NPM1 is a hub protein in nucleoli where it contributes to nucleolar organization through heterotypic and homotypic interactions. Furthermore, several alterations, including overexpression, chromosomal translocations and mutations are present in solid and hematological cancers. Recently, novel germline mutations that cause dyskeratosis congenita have also been described. This review focuses on NPM1 interactions and inhibition. Indeed, the list of NPM1 binding partners is ever-growing and, in recent years, many studies contributed to clarifying the structural basis for NPM1 recognition of both nucleic acids and several proteins. Intriguingly, a number of natural and synthetic ligands that interfere with NPM1 interactions have also been reported. The possible role of NPM1 inhibitors in the treatment of multiple cancers and other pathologies is emerging as a new therapeutic strategy.
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Affiliation(s)
- Ilaria Cela
- Center for Advanced Studies and Technology (CAST), University of Chieti “G. d’Annunzio”, Via Polacchi, 66100 Chieti, Italy;
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology (IBPM) of the CNR, c/o “Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy;
| | - Luca Federici
- Center for Advanced Studies and Technology (CAST), University of Chieti “G. d’Annunzio”, Via Polacchi, 66100 Chieti, Italy;
- Department of Medical, Oral and Biotechnological Sciences, University of Chieti “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
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12
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Scala R, Di Matteo A, Coluccia A, Lo Sciuto A, Federici L, Travaglini-Allocatelli C, Visca P, Silvestri R, Imperi F. Mutational analysis of the essential lipopolysaccharide-transport protein LptH of Pseudomonas aeruginosa to uncover critical oligomerization sites. Sci Rep 2020; 10:11276. [PMID: 32647254 PMCID: PMC7347655 DOI: 10.1038/s41598-020-68054-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/16/2020] [Indexed: 01/24/2023] Open
Abstract
Lipopolysaccharide (LPS) is a critical component of the outer membrane (OM) of many Gram-negative bacteria. LPS is translocated to the OM by the LPS transport (Lpt) system. In the human pathogen Pseudomonas aeruginosa, the periplasmic Lpt component, LptH, is essential for LPS transport, planktonic and biofilm growth, OM stability and infectivity. LptH has been proposed to oligomerize and form a protein bridge that accommodates LPS during transport. Based on the known LptH crystal structure, here we predicted by in silico modeling five different sites likely involved in LptH oligomerization. The relevance of these sites for LptH activity was verified through plasmid-mediated expression of site-specific mutant proteins in a P. aeruginosa lptH conditional mutant. Complementation and protein expression analyses provided evidence that all mutated sites are important for LptH activity in vivo. It was observed that the lptH conditional mutant overcomes the lethality of nonfunctional lptH variants through RecA-mediated homologous recombination between the wild-type lptH gene in the genome and mutated copies in the plasmid. Finally, biochemical assays on purified recombinant proteins showed that some LptH variants are indeed specifically impaired in oligomerization, while others appear to have defects in protein folding and/or stability.
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Affiliation(s)
- Romina Scala
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Rome, Italy
| | - Antonio Coluccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy.,Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
| | - Alessandra Lo Sciuto
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy.,Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Luca Federici
- Department of Medical, Oral and Biotechnological Science and C.A.S.T. Center for Advanced Studies and Technology, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | | | - Paolo Visca
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy.,Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesco Imperi
- Department of Science, Roma Tre University, Viale G. Marconi 446, 00146, Rome, Italy.
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13
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Trande M, Pedretti M, Bonza MC, Di Matteo A, D'Onofrio M, Dominici P, Astegno A. Cation and peptide binding properties of CML7, a calmodulin-like protein from Arabidopsis thaliana. J Inorg Biochem 2019; 199:110796. [PMID: 31419675 DOI: 10.1016/j.jinorgbio.2019.110796] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
Plants contain a large family of so-called calmodulin-like proteins (CMLs) which differ from canonical calmodulin in that they show greater variability in sequence, length, and number of EF-hand domains. The presence of this extended CML family has raised questions regarding the role of these proteins: are they functionally redundant or do they play specific functions in physiological plant processes? To answer these questions, comprehensive biochemical and structural information on CML proteins is fundamental. Among the 50 CMLs from Arabidopsis thaliana, herein we described the ability of CML7 to bind metal ions focusing on the Ca2+ and Mg2+ sensing properties, as well as on metal-induced conformational changes. Circular dichroism and nuclear magnetic resonance (NMR) studies indicated that both Ca2+ and Mg2+ stabilize CML7, as reflected in conformational rearrangements in secondary and tertiary structure and in increases in thermal stability of the protein. However, the conformational changes that binding induces differ between the two metal ions, and only Ca2+ binding controls a structural transition that leads to hydrophobic exposure, as suggested by 8-anilino-1-naphthalenesulfonic acid fluorescence. Isothermal titration calorimetry data coupled with NMR experiments revealed the presence of two high affinity Ca2+-binding sites in the C-lobe of CML7 and two weaker sites in the N-lobe. The paired nature of these CML7 EF-hands enables them to bind Ca2+ with positive cooperativity within each globular domain. Our results clearly place CML7 in the category of Ca2+ sensors. Along with this, the protein can bind to a model target peptide (melittin) in a Ca2+-dependent manner.
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Affiliation(s)
- Matteo Trande
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Maria Cristina Bonza
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
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14
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Rocchio S, Santorelli D, Rinaldo S, Franceschini M, Malatesta F, Imperi F, Federici L, Travaglini-Allocatelli C, Di Matteo A. Structural and functional investigation of the Small Ribosomal Subunit Biogenesis GTPase A (RsgA) from Pseudomonas aeruginosa. FEBS J 2019; 286:4245-4260. [PMID: 31199072 DOI: 10.1111/febs.14959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/03/2019] [Accepted: 06/11/2019] [Indexed: 01/16/2023]
Abstract
The Small Ribosomal Subunit Biogenesis GTPase A (RsgA) is a bacterial assembly factor involved in the late stages of the 30S subunit maturation. It is a multidomain GTPase in which the central circularly permutated GTPase domain is flanked by an OB domain and a Zn-binding domain. All three domains participate in the interaction with the 30S particle thus ensuring an efficient coupling between catalytic activity and biological function. In vivo studies suggested the relevance of rsgA in bacterial growth and cellular viability, but other pleiotropic roles of RsgA are also emerging. Here, we report the 3D structure of RsgA from Pseudomonas aeruginosa (PaRsgA) in the GDP-bound form. We also report a biophysical and biochemical characterization of the protein in both the GDP-bound and its nucleotide-free form. In particular, we report a kinetic analysis of the RsgA binding to GTP and GDP. We found that PaRsgA is able to bind both nucleotides with submicromolar affinity. The higher affinity towards GDP (KD = 0.011 μm) with respect to GTP (KD = 0.16 μm) is mainly ascribed to a smaller GDP dissociation rate. Our results confirm that PaRsgA, like most other GTPases, has a weak intrinsic enzymatic activity (kCAT = 0.058 min-1 ). Finally, the biological role of RsgA in P. aeruginosa was investigated, allowing us to conclude that rsgA is dispensable for P. aeruginosa growth but important for drug resistance and virulence in an animal infection model. DATABASES: Coordinates and structure factors for the protein structure described in this manuscript have been deposited in the Protein Data Bank (https://www.rcsb.org) with the accession code 6H4D.
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Affiliation(s)
- Serena Rocchio
- Dipartimento di Scienze Biochimiche, "A Rossi Fanelli"- Sapienza Università di Roma, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Daniele Santorelli
- Dipartimento di Scienze Biochimiche, "A Rossi Fanelli"- Sapienza Università di Roma, Italy
| | - Serena Rinaldo
- Dipartimento di Scienze Biochimiche, "A Rossi Fanelli"- Sapienza Università di Roma, Italy
| | - Mimma Franceschini
- Ce.S.I.-MeT Centro di Scienze dell'Invecchiamento e Medicina Traslazionale, Università "G. d'Annunzio" di Chieti, Italy.,Dipartimento di Scienze Mediche, Orali e Biotecnologiche - Università "G. d'Annunzio" di Chieti, Italy
| | - Francesco Malatesta
- Dipartimento di Scienze Biochimiche, "A Rossi Fanelli"- Sapienza Università di Roma, Italy
| | - Francesco Imperi
- Dipartimento di Scienze, Università Roma Tre, Italy.,Dipartimento di Biologia e Biotecnologie Charles Darwin, Laboratorio affiliato all'Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, Italy
| | - Luca Federici
- Ce.S.I.-MeT Centro di Scienze dell'Invecchiamento e Medicina Traslazionale, Università "G. d'Annunzio" di Chieti, Italy.,Dipartimento di Scienze Mediche, Orali e Biotecnologiche - Università "G. d'Annunzio" di Chieti, Italy
| | | | - Adele Di Matteo
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
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15
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Di Matteo A, Federici L, Masulli M, Carletti E, Santorelli D, Cassidy J, Paradisi F, Di Ilio C, Allocati N. Structural Characterization of the Xi Class Glutathione Transferase From the Haloalkaliphilic Archaeon Natrialba magadii. Front Microbiol 2019; 10:9. [PMID: 30713525 PMCID: PMC6345682 DOI: 10.3389/fmicb.2019.00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/07/2019] [Indexed: 12/30/2022] Open
Abstract
Xi class glutathione transferases (GSTs) are a recently identified group, within this large superfamily of enzymes, specifically endowed with glutathione-dependent reductase activity on glutathionyl-hydroquinone. Enzymes belonging to this group are widely distributed in bacteria, fungi, and plants but not in higher eukaryotes. Xi class GSTs are also frequently found in archaea and here we focus on the enzyme produced by the extreme haloalkaliphilic archaeon Natrialba magadii (NmGHR). We investigated its function and stability and determined its 3D structure in the apo form by X-ray crystallography. NmGHR displays the same fold of its mesophilic counterparts, is enriched in negatively charged residues, which are evenly distributed along the surface of the protein, and is characterized by a peculiar distribution of hydrophobic residues. A distinctive feature of haloalkaliphilic archaea is their preference for γ-glutamyl-cysteine over glutathione as a reducing thiol. Indeed we found that the N. magadii genome lacks a gene coding for glutathione synthase. Analysis of NmGHR structure suggests that the thiol binding site (G-site) of the enzyme is well suited for hosting γ-glutamyl-cysteine.
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Affiliation(s)
- Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Rome, Italy
| | - Luca Federici
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,CeSI-MeT, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Michele Masulli
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Erminia Carletti
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,CeSI-MeT, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Daniele Santorelli
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,CeSI-MeT, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Jennifer Cassidy
- Synthesis and Solid State Pharmaceutical Centre (SSPC), School of Chemistry, University College Dublin, Dublin, Ireland
| | - Francesca Paradisi
- Synthesis and Solid State Pharmaceutical Centre (SSPC), School of Chemistry, University College Dublin, Dublin, Ireland.,School of Chemistry, University of Nottingham, Nottingham, United Kingdom
| | - Carmine Di Ilio
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Nerino Allocati
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
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16
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Luchinat E, Chiarella S, Franceschini M, Di Matteo A, Brunori M, Banci L, Federici L. Identification of a novel nucleophosmin-interaction motif in the tumor suppressor p14arf. FEBS J 2018; 285:832-847. [PMID: 29283500 DOI: 10.1111/febs.14373] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/20/2017] [Accepted: 12/20/2017] [Indexed: 12/16/2022]
Abstract
The tumor suppressor p14arf interacts, in response to oncogenic signals, with the p53 E3-ubiquitin ligase HDM2, thereby resulting in p53 stabilization and activation. In addition, it also exerts tumor-suppressive functions in p53-independent contexts. The activities of p14arf are regulated by the nucleolar chaperone nucleophosmin (NPM1), which controls its levels and cellular localization. In acute myeloid leukemia with mutations in the NPM1 gene, mutated NPM1 aberrantly translocates in the cytosol carrying with itself p14arf that is subsequently degraded, thus impairing the p14arf-HDM2-p53 axis. In this work we investigated the complex between these two proteins by means of NMR and other techniques. We identified a novel NPM1-interacting motif in the C-terminal region of p14arf, which corresponds to its predicted nucleolar localization signal. This motif recognizes a specific region of the NPM1 N-terminal domain and, upon binding, the two proteins form soluble high molecular weight complexes. By NMR, we identified critical residues on both proteins involved in the interaction. Collectively, our data provide a structural framework to rationalize the overall assembly of the p14arf-NPM1 supramolecular complexes. A number of p14arf cancer-associated mutations cluster in this motif and their effect on the interaction with NPM1 was also analyzed.
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Affiliation(s)
- Enrico Luchinat
- CERM, Centro Risonanze Magnetiche, Università di Firenze, Italy.,Dipartimento di Scienze Biomediche, Sperimentali e Cliniche - Università di Firenze, Italy
| | - Sara Chiarella
- Ce.S.I.-MeT Centro di Scienze dell'Invecchiamento e Medicina Traslazionale, Università "G. d'Annunzio" di Chieti, Italy.,Dipartimento di Scienze Mediche, Orali e Biotecnologiche - Università "G. d'Annunzio" di Chieti, Italy
| | - Mimma Franceschini
- Ce.S.I.-MeT Centro di Scienze dell'Invecchiamento e Medicina Traslazionale, Università "G. d'Annunzio" di Chieti, Italy.,Dipartimento di Scienze Mediche, Orali e Biotecnologiche - Università "G. d'Annunzio" di Chieti, Italy
| | - Adele Di Matteo
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche, "A. Rossi Fanelli" - Sapienza Università di Roma, Italy
| | - Lucia Banci
- CERM, Centro Risonanze Magnetiche, Università di Firenze, Italy.,Dipartimento di Chimica, Università di Firenze, Italy
| | - Luca Federici
- Ce.S.I.-MeT Centro di Scienze dell'Invecchiamento e Medicina Traslazionale, Università "G. d'Annunzio" di Chieti, Italy.,Dipartimento di Scienze Mediche, Orali e Biotecnologiche - Università "G. d'Annunzio" di Chieti, Italy
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17
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De Santis A, La Manna S, Krauss IR, Malfitano AM, Novellino E, Federici L, De Cola A, Di Matteo A, D'Errico G, Marasco D. Nucleophosmin-1 regions associated with acute myeloid leukemia interact differently with lipid membranes. Biochim Biophys Acta Gen Subj 2018; 1862:967-978. [PMID: 29330024 DOI: 10.1016/j.bbagen.2018.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 12/04/2017] [Accepted: 01/08/2018] [Indexed: 01/25/2023]
Affiliation(s)
- Augusta De Santis
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Florence, Italy
| | - Sara La Manna
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Florence, Italy
| | - Anna Maria Malfitano
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy
| | - Luca Federici
- Department of Medical, Oral and Biotechnological Sciences and CeSI-MeT, University of Chieti "G. d'Annunzio", Via dei Vestini 31, 66100 Chieti, Italy
| | - Antonella De Cola
- Department of Medical, Oral and Biotechnological Sciences and CeSI-MeT, University of Chieti "G. d'Annunzio", Via dei Vestini 31, 66100 Chieti, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Gerardino D'Errico
- Department of Chemical Sciences, University of Naples "Federico II", Naples, Italy; CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase, Florence, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II", 80134, Naples, Italy.
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18
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Di Natale C, Scognamiglio PL, Cascella R, Cecchi C, Russo A, Leone M, Penco A, Relini A, Federici L, Di Matteo A, Chiti F, Vitagliano L, Marasco D. Nucleophosmin contains amyloidogenic regions that are able to form toxic aggregates under physiological conditions. FASEB J 2015; 29:3689-701. [PMID: 25977257 DOI: 10.1096/fj.14-269522] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/04/2015] [Indexed: 01/08/2023]
Abstract
Nucleophosmin (NPM)-1 is a multifunctional protein involved in a variety of biologic processes and has been implicated in the pathogenesis of several human malignancies. To gain insight into the role of isolated fragments in NPM1 activities, we dissected the C-terminal domain (CTD) into its helical fragments. In this study, we observed the unexpected structural behavior of the peptide fragment corresponding to helix (H)2 (residues 264-277). This peptide has a strong tendency to form amyloidlike assemblies endowed with fibrillar morphology and β-sheet structure, under physiologic conditions, as shown by circular dichroism, thioflavin T, and Congo red binding assays; dynamic light scattering; and atomic force microscopy. The aggregates are also toxic to neuroblastoma cells, as determined using 3-(4;5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide reduction and Ca(2+) influx assays. We also found that the extension of the H2 sequence beyond its N terminus, comprising the connecting loop with H1, delayed aggregation and its associated cytotoxicity, suggesting that contiguous regions of H2 have a protective role in preventing aggregation. Our findings and those in the literature suggest that the helical structures present in the CTD are important in preventing harmful aggregation. These findings could elucidate the pathogenesis of acute myeloid leukemia (AML) caused by NPM1 mutants. Because the CTD is not properly folded in these mutants, we hypothesize that the aggregation propensity of this NPM1 region is involved in the pathogenesis of AML. Preliminary assays on NPM1-Cter-MutA, the most frequent AML-CTD mutation, revealed its significant propensity for aggregation. Thus, the aggregation phenomena should be seriously considered in studies aimed at unveiling the molecular mechanisms of this pathology.
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Affiliation(s)
- Concetta Di Natale
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Pasqualina Liana Scognamiglio
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Cascella
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Cristina Cecchi
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Anna Russo
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Marilisa Leone
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Amanda Penco
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Annalisa Relini
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Luca Federici
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Adele Di Matteo
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Fabrizio Chiti
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Luigi Vitagliano
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Daniela Marasco
- *Department of Pharmacy, Diagnostica e Farmaceutica Molecolari-Società Cooperativa a Responsabilità Limitata, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, University of Naples "Federico II," Naples, Italy; Section of Biochemistry, Department of Biomedical Experimental and Clinical Sciences "Mario Serio," University of Florence, Florence, Italy; Institute of Biostructures and Bioimaging, Consiglio Nazionale delle Ricerche, Naples, Italy; Department of Physics, University of Genoa, Genoa, Italy; Department of Medical, Oral, and Biotechnological Sciences, University of Chieti "G. d'Annunzio," Chieti, Italy; and Institute of Molecular Biology and Pathology, Consiglio Nazionale delle Ricerche, Rome, Italy
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19
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Arcovito A, Chiarella S, Della Longa S, Di Matteo A, Lo Sterzo C, Scaglione GL, Federici L. Synergic role of nucleophosmin three-helix bundle and a flanking unstructured tail in the interaction with G-quadruplex DNA. J Biol Chem 2014; 289:21230-41. [PMID: 24952945 DOI: 10.1074/jbc.m114.565010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, mainly localized at nucleoli, that plays a number of functions in ribosome biogenesis and export, cell cycle control, and response to stress stimuli. NPM1 is the most frequently mutated gene in acute myeloid leukemia; mutations map to the C-terminal domain of the protein and cause its denaturation and aberrant cytoplasmic translocation. NPM1 C-terminal domain binds G-quadruplex regions at ribosomal DNA and at gene promoters, including the well characterized sequence from the nuclease-hypersensitive element III region of the c-MYC promoter. These activities are lost by the leukemic variant. Here we analyze the NPM1/G-quadruplex interaction, focusing on residues belonging to both the NPM1 terminal three-helix bundle and a lysine-rich unstructured tail, which has been shown to be necessary for high affinity recognition. We performed extended site-directed mutagenesis and measured binding rate constants through surface plasmon resonance analysis. These data, supported by molecular dynamics simulations, suggest that the unstructured tail plays a double role in the reaction mechanism. On the one hand, it facilitates the formation of an encounter complex through long range electrostatic interactions; on the other hand, it directly contacts the G-quadruplex scaffold through multiple and transient electrostatic interactions, significantly enlarging the contact surface.
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Affiliation(s)
- Alessandro Arcovito
- From the Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Sara Chiarella
- Ce.S.I. Centro Scienze dell'Invecchiamento, "Fondazione Università D'Annunzio," 66013 Chieti, Italy, Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Della Longa
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'Ambiente, Università dell'Aquila, 67100 Coppito (L'Aquila), Italy
| | - Adele Di Matteo
- Istituto di Biologia, Medicina Molecolare e NanoBiotecnologie, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy, and
| | - Carlo Lo Sterzo
- Dipartimento di Scienze Biochimiche, Sapienza Università di Roma, 00185 Rome, Italy
| | - Giovanni Luca Scaglione
- From the Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Luca Federici
- Ce.S.I. Centro Scienze dell'Invecchiamento, "Fondazione Università D'Annunzio," 66013 Chieti, Italy, Dipartimento di Scienze Sperimentali e Cliniche, Università di Chieti "G. D'Annunzio," 66013 Chieti, Italy
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20
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Benedetti M, Andreani F, Leggio C, Galantini L, Di Matteo A, Pavel NV, De Lorenzo G, Cervone F, Federici L, Sicilia F. A single amino-acid substitution allows endo-polygalacturonase of Fusarium verticillioides to acquire recognition by PGIP2 from Phaseolus vulgaris. PLoS One 2013; 8:e80610. [PMID: 24260434 DOI: 10.1371/10.1371/journal.pone.0080610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/12/2013] [Indexed: 05/25/2023] Open
Abstract
Polygalacturonases (PGs) are secreted by phytopathogenic fungi to degrade the plant cell wall homogalacturonan during plant infection. To counteract Pgs, plants have evolved polygalacturonase-inhibiting proteins (PGIPs) that slow down fungal infection and defend cell wall integrity. PGIPs favour the accumulation of oligogalacturonides, which are homogalacturonan fragments that act as endogenous elicitors of plant defence responses. We have previously shown that PGIP2 from Phaseolus vulgaris (PvPGIP2) forms a complex with PG from Fusarium phyllophilum (FpPG), hindering the enzyme active site cleft from substrate. Here we analyse by small angle X-ray scattering (SAXS) the interaction between PvPGIP2 and a PG from Colletotrichum lupini (CluPG1). We show a different shape of the PG-PGIP complex, which allows substrate entry and provides a structural explanation for the different inhibition kinetics exhibited by PvPGIP2 towards the two isoenzymes. The analysis of SAXS structures allowed us to investigate the basis of the inability of PG from Fusarium verticilloides (FvPG) to be inhibited by PvPGIP2 or by any other known PGIP. FvPG is 92.5% identical to FpPG, and we show here, by both loss- and gain-of-function mutations, that a single amino acid site acts as a switch for FvPG recognition by PvPGIP2.
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Affiliation(s)
- Manuel Benedetti
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Roma, Italy
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21
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Benedetti M, Andreani F, Leggio C, Galantini L, Di Matteo A, Pavel NV, De Lorenzo G, Cervone F, Federici L, Sicilia F. A single amino-acid substitution allows endo-polygalacturonase of Fusarium verticillioides to acquire recognition by PGIP2 from Phaseolus vulgaris. PLoS One 2013; 8:e80610. [PMID: 24260434 PMCID: PMC3834070 DOI: 10.1371/journal.pone.0080610] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/12/2013] [Indexed: 12/04/2022] Open
Abstract
Polygalacturonases (PGs) are secreted by phytopathogenic fungi to degrade the plant cell wall homogalacturonan during plant infection. To counteract Pgs, plants have evolved polygalacturonase-inhibiting proteins (PGIPs) that slow down fungal infection and defend cell wall integrity. PGIPs favour the accumulation of oligogalacturonides, which are homogalacturonan fragments that act as endogenous elicitors of plant defence responses. We have previously shown that PGIP2 from Phaseolus vulgaris (PvPGIP2) forms a complex with PG from Fusarium phyllophilum (FpPG), hindering the enzyme active site cleft from substrate. Here we analyse by small angle X-ray scattering (SAXS) the interaction between PvPGIP2 and a PG from Colletotrichum lupini (CluPG1). We show a different shape of the PG-PGIP complex, which allows substrate entry and provides a structural explanation for the different inhibition kinetics exhibited by PvPGIP2 towards the two isoenzymes. The analysis of SAXS structures allowed us to investigate the basis of the inability of PG from Fusarium verticilloides (FvPG) to be inhibited by PvPGIP2 or by any other known PGIP. FvPG is 92.5% identical to FpPG, and we show here, by both loss- and gain-of-function mutations, that a single amino acid site acts as a switch for FvPG recognition by PvPGIP2.
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Affiliation(s)
- Manuel Benedetti
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Federico Andreani
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Claudia Leggio
- Dipartimento di Chimica, Sapienza Università di Roma, Roma, Italy
| | | | - Adele Di Matteo
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Roma, Italy
| | | | - Giulia De Lorenzo
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Felice Cervone
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
| | - Luca Federici
- Dipartimento di Scienze Sperimentali e Cliniche and Centro Scienze dell’Invecchiamento, Università di Chieti-Pescara “G. d’ Annunzio”, Chieti, Italy
| | - Francesca Sicilia
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Roma, Italy
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22
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Di Silvio E, Di Matteo A, Malatesta F, Travaglini-Allocatelli C. Recognition and binding of apocytochrome c to P. aeruginosa CcmI, a component of cytochrome c maturation machinery. Biochim Biophys Acta 2013; 1834:1554-61. [PMID: 23648553 DOI: 10.1016/j.bbapap.2013.04.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 01/13/2023]
Abstract
The biogenesis of c-type cytochromes (Cytc) is a process that in Gram-negative bacteria demands the coordinated action of different periplasmic proteins (CcmA-I), whose specific roles are still being investigated. Activities of Ccm proteins span from the chaperoning of heme b in the periplasm to the specific reduction of oxidized apocytochrome (apoCyt) cysteine residues and to chaperoning and recognition of the unfolded apoCyt before covalent attachment of the heme to the cysteine thiols can occur. We present here the functional characterization of the periplasmic domain of CcmI from the pathogen Pseudomonas aeruginosa (Pa-CcmI*). Pa-CcmI* is composed of a TPR domain and a peculiar C-terminal domain. Pa-CcmI* fulfills both the ability to recognize and bind to P. aeruginosa apo-cytochrome c551 (Pa-apoCyt) and a chaperoning activity towards unfolded proteins, as it prevents citrate synthase aggregation in a concentration-dependent manner. Equilibrium and kinetic experiments with Pa-CcmI*, or its isolated domains, with peptides mimicking portions of Pa-apoCyt sequence allow us to quantify the molecular details of the interaction between Pa-apoCyt and Pa-CcmI*. Binding experiments show that the interaction occurs at the level of the TPR domain and that the recognition is mediated mainly by the C-terminal sequence of Pa-apoCyt. The affinity of Pa-CcmI* to full-length Pa-apoCyt or to its C-terminal sequence is in the range expected for a component of a multi-protein complex, whose task is to receive the apoCyt and to deliver it to other components of the apoCyt:heme b ligation protein machinery.
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Affiliation(s)
- Eva Di Silvio
- Department of Biochemical Sciences, Università di Roma La Sapienza, Roma, Italy
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23
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Chiarella S, De Cola A, Scaglione GL, Carletti E, Graziano V, Barcaroli D, Lo Sterzo C, Di Matteo A, Di Ilio C, Falini B, Arcovito A, De Laurenzi V, Federici L. Nucleophosmin mutations alter its nucleolar localization by impairing G-quadruplex binding at ribosomal DNA. Nucleic Acids Res 2013; 41:3228-39. [PMID: 23328624 PMCID: PMC3597674 DOI: 10.1093/nar/gkt001] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Nucleophosmin (NPM1) is an abundant nucleolar protein implicated in ribosome maturation and export, centrosome duplication and response to stress stimuli. NPM1 is the most frequently mutated gene in acute myeloid leukemia. Mutations at the C-terminal domain led to variant proteins that aberrantly and stably translocate to the cytoplasm. We have previously shown that NPM1 C-terminal domain binds with high affinity G-quadruplex DNA. Here, we investigate the structural determinants of NPM1 nucleolar localization. We show that NPM1 interacts with several G-quadruplex regions found in ribosomal DNA, both in vitro and in vivo. Furthermore, the most common leukemic NPM1 variant completely loses this activity. This is the consequence of G-quadruplex–binding domain destabilization, as mutations aimed at refolding the leukemic variant also result in rescuing the G-quadruplex–binding activity and nucleolar localization. Finally, we show that treatment of cells with a G-quadruplex selective ligand results in wild-type NPM1 dislocation from nucleoli into nucleoplasm. In conclusion, this work establishes a direct correlation between NPM1 G-quadruplex binding at rDNA and its nucleolar localization, which is impaired in the acute myeloid leukemia-associated protein variants.
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Affiliation(s)
- Sara Chiarella
- Department of Biochemical Sciences, 'Sapienza' University of Rome, 00185 Rome, Italy
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24
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Gallo A, Lo Sterzo C, Mori M, Di Matteo A, Bertini I, Banci L, Brunori M, Federici L. Structure of nucleophosmin DNA-binding domain and analysis of its complex with a G-quadruplex sequence from the c-MYC promoter. J Biol Chem 2012; 287:26539-48. [PMID: 22707729 DOI: 10.1074/jbc.m112.371013] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling protein, mainly localized at nucleoli, that plays a key role in several cellular functions, including ribosome maturation and export, centrosome duplication, and response to stress stimuli. More than 50 mutations at the terminal exon of the NPM1 gene have been identified so far in acute myeloid leukemia; the mutated proteins are aberrantly and stably localized in the cytoplasm due to high destabilization of the NPM1 C-terminal domain and the appearance of a new nuclear export signal. We have shown previously that the 70-residue NPM1 C-terminal domain (NPM1-C70) is able to bind with high affinity a specific region at the c-MYC gene promoter characterized by parallel G-quadruplex structure. Here we present the solution structure of the NPM1-C70 domain and NMR analysis of its interaction with a c-MYC-derived G-quadruplex. These data were used to calculate an experimentally restrained molecular docking model for the complex. The NPM1-C70 terminal three-helix bundle binds the G-quadruplex DNA at the interface between helices H1 and H2 through electrostatic interactions with the G-quadruplex phosphate backbone. Furthermore, we show that the 17-residue lysine-rich sequence at the N terminus of the three-helix bundle is disordered and, although necessary, does not participate directly in the contact surface in the complex.
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Affiliation(s)
- Angelo Gallo
- Magnetic Resonance Center, Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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Di Matteo A, Calosci N, Gianni S, Jemth P, Brunori M, Travaglini-Allocatelli C. Structural and functional characterization of CcmG from Pseudomonas aeruginosa, a key component of the bacterial cytochrome c maturation apparatus. Proteins 2010; 78:2213-21. [PMID: 20544959 DOI: 10.1002/prot.22733] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The cytochrome c maturation process is carried out in the bacterial periplasm, where some specialized thiol-disulfide oxidoreductases work in close synergy for the correct reduction of oxidized apocytochrome before covalent heme attachment. We present a structural and functional characterization of the soluble periplasmic domain of CcmG from the opportunistic pathogen P. aeruginosa (Pa-CcmG), a component of the protein machinery involved in cyt c maturation in gram-negative bacteria. X-ray crystallography reveals that Pa-CcmG is a TRX-like protein; high-resolution crystal structures show that the oxidized and the reduced forms of the enzyme are identical except for the active-site disulfide. The standard redox potential was calculated to be E(0') = -0.213 V at pH 7.0; the pK(a) of the active site thiols were pK(a) = 6.13 +/- 0.05 for the N-terminal Cys74 and pK(a) = 10.5 +/- 0.17 for the C-terminal Cys77. Experiments were carried out to characterize and isolate the mixed disulfide complex between Pa-CcmG and Pa-CcmH (the other redox active component of System I in P. aeruginosa). Our data indicate that the target disulfide of this TRX-like protein is not the intramolecular disulfide of oxidized Pa-CcmH, but the intermolecular disulfide formed between Cys28 of Pa-CcmH and DTNB used for the in vitro experiments. This observation suggests that, in vivo, the physiological substrate of Pa-CcmG may be the mixed-disulfide complex between Pa-CcmH and apo-cyt.
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Affiliation(s)
- Adele Di Matteo
- Dipartimento di Scienze Biochimiche, Istituto di Biologia e Patologia Molecolari del CNR, Sapienza-Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
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Federici L, Arcovito A, Scaglione GL, Scaloni F, Lo Sterzo C, Di Matteo A, Falini B, Giardina B, Brunori M. Nucleophosmin C-terminal leukemia-associated domain interacts with G-rich quadruplex forming DNA. J Biol Chem 2010; 285:37138-49. [PMID: 20858903 DOI: 10.1074/jbc.m110.166736] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nucleophosmin (NPM1) is a nucleocytoplasmic shuttling phosphoprotein, mainly localized at nucleoli, that plays a key role in ribogenesis, centrosome duplication, and response to stress stimuli. Mutations at the C-terminal domain of NPM1 are the most frequent genetic lesion in acute myeloid leukemia and cause the aberrant and stable translocation of the protein in the cytoplasm. The NPM1 C-terminal domain was previously shown to bind nucleic acids. Here we further investigate the DNA binding properties of the NPM1 C-terminal domain both at the protein and nucleic acid levels; we investigate the domain boundaries and identify key residues for high affinity recognition. Furthermore, we demonstrate that the NPM1 C-terminal domain has a preference for G-quadruplex forming DNA regions and induces the formation of G-quadruplex structures in vitro. Finally we show that a specific sequence found at the SOD2 gene promoter, which was previously shown to be a target of NPM1 in vivo, is indeed folded as a G-quadruplex in vitro under physiological conditions. Our data extend considerably present knowledge on the DNA binding properties of NPM1 and suggest a general role in the transcription of genes characterized by the presence of G-quadruplex forming regions at their promoters.
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Affiliation(s)
- Luca Federici
- Department of Biomedical Sciences, University of Chieti G D'Annunzio, CeSI Center of Excellence on Aging, 66013 Chieti, Italy.
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Federici L, Lo Sterzo C, Pezzola S, Di Matteo A, Scaloni F, Federici G, Caccuri AM. Structural basis for the binding of the anticancer compound 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol to human glutathione s-transferases. Cancer Res 2009; 69:8025-34. [PMID: 19808963 DOI: 10.1158/0008-5472.can-09-1314] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Glutathione S-transferases (GST) constitute a superfamily of enzymes with diversified functions including detoxification from xenobiotics. In many human cancers, Pi class GST (GSTP1-1) is overexpressed and contributes to multidrug resistance by conjugating chemotherapeutics. In addition, GSTP1-1 displays antiapoptotic activity by interacting with c-Jun NH(2)-terminal kinase, a key regulator of apoptosis. Therefore, GSTP1-1 is considered a promising target for pharmaceutical treatment. Recently, a potent inhibitor of GSTs, 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX), was identified and tested on several tumor cell lines demonstrating high antiproliferative activity. To establish the structural basis of NBDHEX activity, we determined the crystal structure of NBDHEX bound to either GSTP1-1 or GSTM2-2 (mu class). NBDHEX in both cases binds to the H-site but occupies different positions. Furthermore, the compound is covalently attached to the GSH sulfur in the GSTM2-2 crystal, forming a sigma-complex, although it is bound but not conjugated in the GSTP1-1 crystal. Several differences in the H-sites of the two isozymes determine the higher affinity of NBDHEX for GSTM2-2 with respect to GSTP1-1. One such difference is the presence of Ile(104) in GSTP1-1 close to the bound NBDHEX, whereas the corresponding position is occupied by an alanine in GSTM2-2. Mutation of Ile(104) into valine is a frequent GSTP1-1 polymorphism and we show here that the Ile(104)Val and Ile(104)Ala variants display a 4-fold higher affinity for the compound. Remarkably, the GSTP1-1/Ile(104)Ala structure in complex with NBDHEX shows a considerable shift of the compound inside the H-site. These data might be useful for the development of new anticancer compounds.
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Affiliation(s)
- Luca Federici
- Department of Biomedical Sciences, University of Chieti, CeSI Center of Excellence on Aging, G D'Annunzio University Foundation, Chieti, Italy.
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Giardina G, Rinaldo S, Johnson KA, Di Matteo A, Brunori M, Cutruzzolà F. NO sensing in Pseudomonas aeruginosa: Structure of the Transcriptional Regulator DNR. J Mol Biol 2008; 378:1002-15. [DOI: 10.1016/j.jmb.2008.03.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 03/04/2008] [Accepted: 03/06/2008] [Indexed: 11/17/2022]
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Bonivento D, Pontiggia D, Matteo AD, Fernandez-Recio J, Salvi G, Tsernoglou D, Cervone F, Lorenzo GD, Federici L. Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins. Proteins 2008; 70:294-9. [PMID: 17876815 DOI: 10.1002/prot.21610] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Daniele Bonivento
- Dipartimento di Scienze Biochimiche, Dipartimento di Biologia Vegetale, Università di Roma "La Sapienza," Piazzale Aldo Moro 5, 00185 Roma, Italy
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30
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Di Matteo A, Scandurra FM, Testa F, Forte E, Sarti P, Brunori M, Giuffrè A. The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis. J Biol Chem 2007; 283:4061-8. [PMID: 18077462 DOI: 10.1074/jbc.m705605200] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The flavodiiron proteins (FDP) are widespread among strict or facultative anaerobic prokaryotes, where they are involved in the response to nitrosative and/or oxidative stress. Unexpectedly, FDPs were fairly recently identified in a restricted group of microaerobic protozoa, including Giardia intestinalis, the causative agent of the human infectious disease giardiasis. The FDP from Giardia was expressed, purified, and extensively characterized by x-ray crystallography, stopped-flow spectroscopy, respirometry, and NO amperometry. Contrary to flavorubredoxin, the FDP from Escherichia coli, the enzyme from Giardia has high O(2)-reductase activity (>40 s(-1)), but very low NO-reductase activity (approximately 0.2 s(-1)); O(2) reacts with the reduced protein quite rapidly (milliseconds) and with high affinity (K(m) < or = 2 microM), producing H(2)O. The three-dimensional structure of the oxidized protein determined at 1.9A resolution shows remarkable similarities with prokaryotic FDPs. Consistent with HPLC analysis, the enzyme is a dimer of dimers with FMN and the non-heme di-iron site topologically close at the monomer-monomer interface. Unlike the FDP from Desulfovibrio gigas, the residue His-90 is a ligand of the di-iron site, in contrast with the proposal that ligation of this histidine is crucial for a preferential specificity for NO. We propose that in G. intestinalis the primary function of FDP is to efficiently scavenge O(2), allowing this microaerobic parasite to survive in the human small intestine, thus promoting its pathogenicity.
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Affiliation(s)
- Adele Di Matteo
- Department of Biochemical Sciences, CNR Institute of Molecular Biology and Pathology and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, University of Rome, Rome I-00185, Italy
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31
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Di Matteo A, Gianni S, Schininà ME, Giorgi A, Altieri F, Calosci N, Brunori M, Travaglini-Allocatelli C. A Strategic Protein in Cytochrome c Maturation. J Biol Chem 2007; 282:27012-27019. [PMID: 17623665 DOI: 10.1074/jbc.m702702200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CcmH (cytochromes c maturation protein H) is an essential component of the assembly line necessary for the maturation of c-type cytochromes in the periplasm of Gram-negative bacteria. The protein is a membrane-anchored thiol-oxidoreductase that has been hypothesized to be involved in the recognition and reduction of apocytochrome c, a prerequisite for covalent heme attachment. Here, we present the 1.7A crystal structure of the soluble periplasmic domain of CcmH from the opportunistic pathogen Pseudomonas aeruginosa (Pa-CcmH*). The protein contains a three-helix bundle, i.e. a fold that is different from that of all other thiol-oxidoreductases reported so far. The catalytic Cys residues of the conserved LRCXXC motif (Cys(25) and Cys(28)), located in a long loop connecting the first two helices, form a disulfide bond in the oxidized enzyme. We have determined the pK(a) values of these 2 Cys residues of Pa-CcmH* (both >8) and propose a possible mechanistic role for a conserved Ser(36) and a water molecule in the active site. The interaction between Pa-CcmH* and Pa-apocyt c(551) (where cyt c(551) represents cytochrome c(551)) was characterized in vitro following the binding kinetics by stopped-flow using a Trp-containing fluorescent variant of Pa-CcmH* and a dansylated peptide, mimicking the apocytochrome c(551) heme binding motif. The kinetic results show that the protein has a moderate affinity to its apocyt substrate, consistent with the role of Pa-CcmH as an intermediate component of the assembly line for c-type cytochrome biogenesis.
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Affiliation(s)
- Adele Di Matteo
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche (CNR), La Sapienza, Università di Roma, Piazzale A. Moro 5, 00185 Roma Italy
| | - Stefano Gianni
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche (CNR), La Sapienza, Università di Roma, Piazzale A. Moro 5, 00185 Roma Italy
| | - M Eugenia Schininà
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche (CNR), La Sapienza, Università di Roma, Piazzale A. Moro 5, 00185 Roma Italy
| | - Alessandra Giorgi
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche (CNR), La Sapienza, Università di Roma, Piazzale A. Moro 5, 00185 Roma Italy
| | - Fabio Altieri
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche (CNR), La Sapienza, Università di Roma, Piazzale A. Moro 5, 00185 Roma Italy
| | - Nicoletta Calosci
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche (CNR), La Sapienza, Università di Roma, Piazzale A. Moro 5, 00185 Roma Italy
| | - Maurizio Brunori
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche (CNR), La Sapienza, Università di Roma, Piazzale A. Moro 5, 00185 Roma Italy.
| | - Carlo Travaglini-Allocatelli
- Dipartimento di Scienze Biochimiche and Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche (CNR), La Sapienza, Università di Roma, Piazzale A. Moro 5, 00185 Roma Italy
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Federici L, Masulli M, Bonivento D, Di Matteo A, Gianni S, Favaloro B, Di Ilio C, Allocati N. Role of Ser11 in the stabilization of the structure of Ochrobactrum anthropi glutathione transferase. Biochem J 2007; 403:267-74. [PMID: 17223798 PMCID: PMC1874244 DOI: 10.1042/bj20061707] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
GSTs (glutathione transferases) are a multifunctional group of enzymes, widely distributed and involved in cellular detoxification processes. In the xenobiotic-degrading bacterium Ochrobactrum anthropi, GST is overexpressed in the presence of toxic concentrations of aromatic compounds such as 4-chlorophenol and atrazine. We have determined the crystal structure of the GST from O. anthropi (OaGST) in complex with GSH. Like other bacterial GSTs, OaGST belongs to the Beta class and shows a similar binding pocket for GSH. However, in contrast with the structure of Proteus mirabilis GST, GSH is not covalently bound to Cys10, but is present in the thiolate form. In our investigation of the structural basis for GSH stabilization, we have identified a conserved network of hydrogen-bond interactions, mediated by the presence of a structural water molecule that links Ser11 to Glu198. Partial disruption of this network, by mutagenesis of Ser11 to alanine, increases the K(m) for GSH 15-fold and decreases the catalytic efficiency 4-fold, even though Ser11 is not involved in GSH binding. Thermal- and chemical-induced unfolding studies point to a global effect of the mutation on the stability of the protein and to a central role of these residues in zippering the terminal helix of the C-terminal domain to the starting helix of the N-terminal domain.
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Affiliation(s)
- Luca Federici
- *Ce.S.I. (Centro Studi sull'Invecchiamento), Fondazione Università di Chieti “G. d'Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy
- †Dipartimento di Scienze Biomediche, Università di Chieti “G. d'Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy
| | - Michele Masulli
- †Dipartimento di Scienze Biomediche, Università di Chieti “G. d'Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy
| | - Daniele Bonivento
- ‡Dipartimento di Scienze Biochimiche, Università di Roma “La Sapienza”, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Adele Di Matteo
- ‡Dipartimento di Scienze Biochimiche, Università di Roma “La Sapienza”, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Stefano Gianni
- §Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Università di Roma “La Sapienza”, Piazzale A. Moro 5, 00185 Rome, Italy
| | - Bartolo Favaloro
- *Ce.S.I. (Centro Studi sull'Invecchiamento), Fondazione Università di Chieti “G. d'Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy
- †Dipartimento di Scienze Biomediche, Università di Chieti “G. d'Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy
| | - Carmine Di Ilio
- *Ce.S.I. (Centro Studi sull'Invecchiamento), Fondazione Università di Chieti “G. d'Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy
- †Dipartimento di Scienze Biomediche, Università di Chieti “G. d'Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy
| | - Nerino Allocati
- †Dipartimento di Scienze Biomediche, Università di Chieti “G. d'Annunzio”, Via dei Vestini 31, 66013 Chieti, Italy
- To whom correspondence should be addressed (email )
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Spadoni S, Zabotina O, Di Matteo A, Mikkelsen JD, Cervone F, De Lorenzo G, Mattei B, Bellincampi D. Polygalacturonase-inhibiting protein interacts with pectin through a binding site formed by four clustered residues of arginine and lysine. Plant Physiol 2006; 141:557-64. [PMID: 16648220 PMCID: PMC1475430 DOI: 10.1104/pp.106.076950] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2006] [Revised: 04/13/2006] [Accepted: 04/19/2006] [Indexed: 05/08/2023]
Abstract
Polygalacturonase-inhibiting protein (PGIP) is a cell wall protein that inhibits fungal polygalacturonases (PGs) and retards the invasion of plant tissues by phytopathogenic fungi. Here, we report the interaction of two PGIP isoforms from Phaseolus vulgaris (PvPGIP1 and PvPGIP2) with both polygalacturonic acid and cell wall fractions containing uronic acids. We identify in the three-dimensional structure of PvPGIP2 a motif of four clustered arginine and lysine residues (R183, R206, K230, and R252) responsible for this binding. The four residues were mutated and the protein variants were expressed in Pichia pastoris. The ability of both wild-type and mutated proteins to bind pectins was investigated by affinity chromatography. Single mutations impaired the binding and double mutations abolished the interaction, thus indicating that the four clustered residues form the pectin-binding site. Remarkably, the binding of PGIP to pectin is displaced in vitro by PGs, suggesting that PGIP interacts with pectin and PGs through overlapping although not identical regions. The specific interaction of PGIP with polygalacturonic acid may be strategic to protect pectins from the degrading activity of fungal PGs.
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Affiliation(s)
- Sara Spadoni
- Dipartimento di Biologia Vegetale, Università di Roma La Sapienza, 00185 Rome, Italy
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34
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Di Matteo A, Bonivento D, Tsernoglou D, Federici L, Cervone F. Polygalacturonase-inhibiting protein (PGIP) in plant defence: a structural view. Phytochemistry 2006; 67:528-33. [PMID: 16458942 DOI: 10.1016/j.phytochem.2005.12.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Accepted: 12/16/2005] [Indexed: 05/06/2023]
Abstract
Polygalacturonase-inhibiting proteins are plant extracellular leucine-rich repeat proteins that specifically bind and inhibit fungal polygalacturonases. The interaction with PGIP limits the destructive potential of polygalacturonases and might trigger the plant defence responses induced by oligogalacturonides. A high degree of polymorphism is found both in PGs and PGIPs, accounting for the specificity of different plant inhibitors for PGs from different fungi. Here, we review the structural features and our current understanding of the PG-PGIP interaction.
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Affiliation(s)
- Adele Di Matteo
- Dipartimento di Biologia Vegetale, Universita' di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Roma, Italy
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Borgia A, Bonivento D, Travaglini-Allocatelli C, Di Matteo A, Brunori M. Unveiling a hidden folding intermediate in c-type cytochromes by protein engineering. J Biol Chem 2006; 281:9331-6. [PMID: 16452476 DOI: 10.1074/jbc.m512127200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Several investigators have highlighted a correlation between the basic features of the folding process of a protein and its topology, which dictates the folding pathway. Within this conceptual framework we proposed that different members of the cytochrome c (cyt c) family share the same folding mechanism, involving a consensus partially structured state. Pseudomonas aeruginosa cyt c(551) (Pa cyt c(551)) folds via an apparent two-state mechanism through a high energy intermediate. Here we present kinetic evidence demonstrating that it is possible to switch its folding mechanism from two to three state, stabilizing the high energy intermediate by rational mutagenesis. Characterization of the folding kinetics of one single-site mutant of the Pa cyt c(551) (Phe(7) to Ala) indeed reveals an additional refolding phase and a fast unfolding process which are explained by the accumulation of a partially folded species. Further kinetic analysis highlights the presence of two parallel processes both leading to the native state, suggesting that the above mentioned species is a non obligatory on-pathway intermediate. Determination of the crystallographic structure of F7A shows the presence of an extended internal cavity, which hosts three "bound" water molecules and a H-bond in the N-terminal helix, which is shorter than in the wild type protein. These two features allow us to propose a detailed structural interpretation for the stabilization of the native and especially the intermediate states induced by a single crucial mutation. These results show how protein engineering, x-ray crystallography and state-of-the-art kinetics concur to unveil a folding intermediate and the structural determinants of its stability.
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Affiliation(s)
- Alessandro Borgia
- Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche, Università di Roma "La Sapienza," P.le A. Moro 5, 00185 Rome, Italy
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36
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Federici L, Di Matteo A, Fernandez-Recio J, Tsernoglou D, Cervone F. Polygalacturonase inhibiting proteins: players in plant innate immunity? Trends Plant Sci 2006; 11:65-70. [PMID: 16406303 DOI: 10.1016/j.tplants.2005.12.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Revised: 11/16/2005] [Accepted: 12/21/2005] [Indexed: 05/06/2023]
Abstract
Polygalacturonase-inhibiting proteins (PGIPs) are extracellular leucine-rich repeat (LRR) proteins that recognize and inhibit fungal polygalacturonases (PGs). The PG-PGIP interaction favours the accumulation of elicitor-active oligogalacturonides and causes the activation of defence responses. Small gene families encode PGIP isoforms that differ in affinity and specificity for PGs secreted by different pathogens. The consensus motif within the LRR structure of PGIPs is the same as that of the extracellular receptors of the plant innate immune system. Structural and functional evidence suggest that PGIPs are versatile proteins involved in innate immunity and that they are capable of recognizing different surface motifs of functionally related but structurally variable PGs.
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Affiliation(s)
- Luca Federici
- Ce.S.I. Centro Studi sull'Invecchiamento and Dipartimento di Scienze Biomediche. Universita' di Chieti "G. D'Annunzio". Via dei Vestini 31, 66013 Chieti, Italy.
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37
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Travaglini-Allocatelli C, Gianni S, Dubey VK, Borgia A, Di Matteo A, Bonivento D, Cutruzzolà F, Bren KL, Brunori M. An obligatory intermediate in the folding pathway of cytochrome c552 from Hydrogenobacter thermophilus. J Biol Chem 2005; 280:25729-34. [PMID: 15883159 DOI: 10.1074/jbc.m502628200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The folding mechanism of many proteins involves the population of partially organized structures en route to the native state. Identification and characterization of these intermediates is particularly difficult, as they are often only transiently populated and may play different mechanistic roles, being either on-pathway productive species or off-pathway kinetic traps. Following different spectroscopic probes, and employing state-of-the-art kinetic analysis, we present evidence that the folding mechanism of the thermostable cytochrome c552 from Hydrogenobacter thermophilus does involve the presence of an elusive, yet compact, on-pathway intermediate. Characterization of the folding mechanism of this cytochrome c is particularly interesting for the purpose of comparative folding studies, because H. thermophilus cytochrome c552 shares high sequence identity and structural homology with its homologue from the mesophilic bacterium Pseudomonas aeruginosa cytochrome c551, which refolds through a broad energy barrier without the accumulation of intermediates. Analysis of the folding kinetics and correlation with the three-dimensional structure add new evidence for the validity of a consensus folding mechanism in the cytochrome c family.
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Affiliation(s)
- Carlo Travaglini-Allocatelli
- Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche, Università di Roma La Sapienza, P. le A. Moro 5, 00185, Roma Italy
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38
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Abstract
The CASP experiment has been run every other year since 1994. Its objective is to subject the available structure prediction methods to a blind test. This is a short report of the highlights of its last edition. 'Men who wish to know about the world must learn about it in its particular details' (Heraclitus of Ephesus, 535-475 bc).
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Affiliation(s)
- Domenico Cozzetto
- Department of Biochemical Sciences, University of Rome La Sapienza, Italy
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39
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Di Matteo A, Giovane A, Raiola A, Camardella L, Bonivento D, De Lorenzo G, Cervone F, Bellincampi D, Tsernoglou D. Structural basis for the interaction between pectin methylesterase and a specific inhibitor protein. Plant Cell 2005; 17:849-58. [PMID: 15722470 PMCID: PMC1069703 DOI: 10.1105/tpc.104.028886] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Accepted: 12/28/2004] [Indexed: 05/18/2023]
Abstract
Pectin, one of the main components of the plant cell wall, is secreted in a highly methyl-esterified form and subsequently deesterified in muro by pectin methylesterases (PMEs). In many developmental processes, PMEs are regulated by either differential expression or posttranslational control by protein inhibitors (PMEIs). PMEIs are typically active against plant PMEs and ineffective against microbial enzymes. Here, we describe the three-dimensional structure of the complex between the most abundant PME isoform from tomato fruit (Lycopersicon esculentum) and PMEI from kiwi (Actinidia deliciosa) at 1.9-A resolution. The enzyme folds into a right-handed parallel beta-helical structure typical of pectic enzymes. The inhibitor is almost all helical, with four long alpha-helices aligned in an antiparallel manner in a classical up-and-down four-helical bundle. The two proteins form a stoichiometric 1:1 complex in which the inhibitor covers the shallow cleft of the enzyme where the putative active site is located. The four-helix bundle of the inhibitor packs roughly perpendicular to the main axis of the parallel beta-helix of PME, and three helices of the bundle interact with the enzyme. The interaction interface displays a polar character, typical of nonobligate complexes formed by soluble proteins. The structure of the complex gives an insight into the specificity of the inhibitor toward plant PMEs and the mechanism of regulation of these enzymes.
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Affiliation(s)
- Adele Di Matteo
- Department of Biochemical Sciences, University of Rome, 00185 Rome, Italy
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