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Sgueglia G, Vrettas MD, Chino M, De Simone A, Lombardi A. MetalHawk: Enhanced Classification of Metal Coordination Geometries by Artificial Neural Networks. J Chem Inf Model 2024; 64:2356-2367. [PMID: 37956388 PMCID: PMC11005052 DOI: 10.1021/acs.jcim.3c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 06/08/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
The chemical properties of metal complexes are strongly dependent on the number and geometrical arrangement of ligands coordinated to the metal center. Existing methods for determining either coordination number or geometry rely on a trade-off between accuracy and computational costs, which hinders their application to the study of large structure data sets. Here, we propose MetalHawk (https://github.com/vrettasm/MetalHawk), a machine learning-based approach to perform simultaneous classification of metal site coordination number and geometry through artificial neural networks (ANNs), which were trained using the Cambridge Structural Database (CSD) and Metal Protein Data Bank (MetalPDB). We demonstrate that the CSD-trained model can be used to classify sites belonging to the most common coordination numbers and geometry classes with balanced accuracy equal to 96.51% for CSD-deposited metal sites. The CSD-trained model was also found to be capable of classifying bioinorganic metal sites from the MetalPDB database, with balanced accuracy equal to 84.29% on the whole PDB data set and to 91.66% on manually reviewed sites in the PDB validation set. Moreover, we report evidence that the output vectors of the CSD-trained model can be considered as a proxy indicator of metal-site distortions, showing that these can be interpreted as a low-dimensional representation of subtle geometrical features present in metal site structures.
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Affiliation(s)
- Gianmattia Sgueglia
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cintia 21, 80126 Napoli, Italy
| | - Michail D. Vrettas
- Department
of Pharmacy, University of Naples Federico
II, Via Domenico Montesano
49, 80131 Napoli, Italy
| | - Marco Chino
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cintia 21, 80126 Napoli, Italy
| | - Alfonso De Simone
- Department
of Pharmacy, University of Naples Federico
II, Via Domenico Montesano
49, 80131 Napoli, Italy
| | - Angela Lombardi
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cintia 21, 80126 Napoli, Italy
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2
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Chino M, La Gatta S, Leone L, De Fenza M, Lombardi A, Pavone V, Maglio O. Dye Decolorization by a Miniaturized Peroxidase Fe-MimochromeVI*a. Int J Mol Sci 2023; 24:11070. [PMID: 37446248 DOI: 10.3390/ijms241311070] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/23/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
Oxidases and peroxidases have found application in the field of chlorine-free organic dye degradation in the paper, toothpaste, and detergent industries. Nevertheless, their widespread use is somehow hindered because of their cost, availability, and batch-to-batch reproducibility. Here, we report the catalytic proficiency of a miniaturized synthetic peroxidase, Fe-Mimochrome VI*a, in the decolorization of four organic dyes, as representatives of either the heterocyclic or triarylmethane class of dyes. Fe-Mimochrome VI*a performed over 130 turnovers in less than five minutes in an aqueous buffer at a neutral pH under mild conditions.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Maria De Fenza
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 80126 Napoli, Italy
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
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3
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Leone L, Sgueglia G, La Gatta S, Chino M, Nastri F, Lombardi A. Enzymatic and Bioinspired Systems for Hydrogen Production. Int J Mol Sci 2023; 24:ijms24108605. [PMID: 37239950 DOI: 10.3390/ijms24108605] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/30/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do not produce carbon-containing byproducts. Hydrogenases promote reversible proton reduction to hydrogen in a variety of anoxic bacteria and algae, displaying unparallel catalytic performances. Attempts to use these sophisticated enzymes in scalable hydrogen production have been hampered by limitations associated with their production and stability. Inspired by nature, significant efforts have been made in the development of artificial systems able to promote the hydrogen evolution reaction, via either electrochemical or light-driven catalysis. Starting from small-molecule coordination compounds, peptide- and protein-based architectures have been constructed around the catalytic center with the aim of reproducing hydrogenase function into robust, efficient, and cost-effective catalysts. In this review, we first provide an overview of the structural and functional properties of hydrogenases, along with their integration in devices for hydrogen and energy production. Then, we describe the most recent advances in the development of homogeneous hydrogen evolution catalysts envisioned to mimic hydrogenases.
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Affiliation(s)
- Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Gianmattia Sgueglia
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
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4
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Chino M, Di Costanzo LF, Leone L, La Gatta S, Famulari A, Chiesa M, Lombardi A, Pavone V. Designed Rubredoxin miniature in a fully artificial electron chain triggered by visible light. Nat Commun 2023; 14:2368. [PMID: 37185349 PMCID: PMC10130062 DOI: 10.1038/s41467-023-37941-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Designing metal sites into de novo proteins has significantly improved, recently. However, identifying the minimal coordination spheres, able to encompass the necessary information for metal binding and activity, still represents a great challenge, today. Here, we test our understanding with a benchmark, nevertheless difficult, case. We assemble into a miniature 28-residue protein, the quintessential elements required to fold properly around a FeCys4 redox center, and to function efficiently in electron-transfer. This study addresses a challenge in de novo protein design, as it reports the crystal structure of a designed tetra-thiolate metal-binding protein in sub-Å agreement with the intended design. This allows us to well correlate structure to spectroscopic and electrochemical properties. Given its high reduction potential compared to natural and designed FeCys4-containing proteins, we exploit it as terminal electron acceptor of a fully artificial chain triggered by visible light.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Napoli, Italy
| | - Luigi Franklin Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Napoli, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Napoli, Italy
| | - Antonino Famulari
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy
- Department of Condensed Matter Physics, University of Zaragoza, Calle Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Napoli, Italy.
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Napoli, Italy.
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Pirro F, La Gatta S, Arrigoni F, Famulari A, Maglio O, Del Vecchio P, Chiesa M, De Gioia L, Bertini L, Chino M, Nastri F, Lombardi A. A De Novo-Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity. Angew Chem Int Ed Engl 2023; 62:e202211552. [PMID: 36334012 DOI: 10.1002/anie.202211552] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Indexed: 11/07/2022]
Abstract
De novo metalloprotein design is a remarkable approach to shape protein scaffolds toward specific functions. Here, we report the design and characterization of Due Rame 1 (DR1), a de novo designed protein housing a di-copper site and mimicking the Type 3 (T3) copper-containing polyphenol oxidases (PPOs). To achieve this goal, we hierarchically designed the first and the second di-metal coordination spheres to engineer the di-copper site into a simple four-helix bundle scaffold. Spectroscopic, thermodynamic, and functional characterization revealed that DR1 recapitulates the T3 copper site, supporting different copper redox states, and being active in the O2 -dependent oxidation of catechols to o-quinones. Careful design of the residues lining the substrate access site endows DR1 with substrate recognition, as revealed by Hammet analysis and computational studies on substituted catechols. This study represents a premier example in the construction of a functional T3 copper site into a designed four-helix bundle protein.
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Affiliation(s)
- Fabio Pirro
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Salvatore La Gatta
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonino Famulari
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy.,Department of Condensed Matter Physics, University of of Zaragoza, Calle Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy.,Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Mario Chiesa
- Department of Chemistry, University of Torino, Via Giuria 9, 10125, Torino, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Luca Bertini
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy
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6
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Pirro F, La Gatta S, Arrigoni F, Famulari A, Maglio O, Del Vecchio P, Chiesa M, De Gioia L, Bertini L, Chino M, Nastri F, Lombardi A. A De Novo‐Designed Type 3 Copper Protein Tunes Catechol Substrate Recognition and Reactivity. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211552] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fabio Pirro
- University of Naples Federico II: Universita degli Studi di Napoli Federico II Department of Chemical Science ITALY
| | - Salvatore La Gatta
- University of Naples Federico II: Universita degli Studi di Napoli Federico II Department of Chemical Science ITALY
| | - Federica Arrigoni
- University of Milano–Bicocca: Universita degli Studi di Milano-Bicocca Department of Biotechnology and Biosciences ITALY
| | - Antonino Famulari
- University of Turin: Universita degli Studi di Torino Department of Chemistry ITALY
| | - Ornella Maglio
- University of Naples Federico II: Universita degli Studi di Napoli Federico II Department of Chemical Sciences ITALY
| | - Pompea Del Vecchio
- University of Naples Federico II: Universita degli Studi di Napoli Federico II Department of Chemical Sciences ITALY
| | - Mario Chiesa
- University of Turin: Universita degli Studi di Torino Department of Chemistry ITALY
| | - Luca De Gioia
- University of Milano–Bicocca: Universita degli Studi di Milano-Bicocca Department of Biotechnology and Biosciences ITALY
| | - Luca Bertini
- University of Milano–Bicocca: Universita degli Studi di Milano-Bicocca Department of Biotechnology and Biosciences ITALY
| | - Marco Chino
- University of Naples Federico II: Universita degli Studi di Napoli Federico II Department of Chemical Sciences ITALY
| | - Flavia Nastri
- University of Naples Federico II: Universita degli Studi di Napoli Federico II Department of Chemical Sciences ITALY
| | - Angela Lombardi
- University of Napoli “Federico II” Department of Chemical Sciences Via Cintia 80126 Napoli ITALY
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7
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Rodrigues ACM, Barbieri MV, Chino M, Manco G, Febbraio F. A 3D printable adapter for solid-state fluorescence measurements: the case of an immobilized enzymatic bioreceptor for organophosphate pesticides detection. Anal Bioanal Chem 2022; 414:1999-2008. [PMID: 35064794 PMCID: PMC8791905 DOI: 10.1007/s00216-021-03835-1] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/12/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022]
Abstract
The widespread use of pesticides in the last decades and their accumulation into the environment gave rise to major environmental and human health concerns. To address this topic, the scientific community pointed out the need to develop methodologies to detect and measure the presence of pesticides in different matrices. Biosensors have been recently explored as fast, easy, and sensitive methods for direct organophosphate pesticides monitoring. Thus, the present work aimed at designing and testing a 3D printed adapter useful on different equipment, and a membrane support to immobilize the esterase-2 from Alicyclobacillus acidocaldarius (EST2) bioreceptor. The latter is labelled with the IAEDANS, a bright fluorescent probe. EST2 was selected since it shows a high specificity toward paraoxon. Our results showed good stability and replicability, with an increasing linear fluorescent intensity recorded from 15 to 150 pmol of labelled EST2. Linearity of data was also observed when using the immobilized labelled EST2 to detect increasing amounts of paraoxon, with a limit of detection (LOD) of 0.09 pmol. This LOD value reveals the high sensitivity of our membrane support when mounted on the 3D adapter, comparable to modern methods using robotic workstations. Notably, the use of an independent support significantly simplified the manipulation of the membrane during experimental procedures and enabled it to match the specificities of different systems. In sum, this work emphasizes the advantages of using 3D printed accessories adapted to respond to the newest research needs.
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Affiliation(s)
- Andreia C M Rodrigues
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), 80131, Naples, Italy
| | - Maria Vittoria Barbieri
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), 80131, Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples "Federico II", 80126, Naples, Italy.
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), 80131, Naples, Italy
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), 80131, Naples, Italy.
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8
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Rodrigues ACM, Barbieri MV, Chino M, Manco G, Febbraio F. A FRET Approach to Detect Paraoxon among Organophosphate Pesticides Using a Fluorescent Biosensor. Sensors (Basel) 2022; 22:561. [PMID: 35062524 PMCID: PMC8778994 DOI: 10.3390/s22020561] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/04/2022] [Accepted: 01/09/2022] [Indexed: 02/01/2023]
Abstract
The development of faster, sensitive and real-time methods for detecting organophosphate (OP) pesticides is of utmost priority in the in situ monitoring of these widespread compounds. Research on enzyme-based biosensors is increasing, and a promising candidate as a bioreceptor is the thermostable enzyme esterase-2 from Alicyclobacillus acidocaldarius (EST2), with a lipase-like Ser-His-Asp catalytic triad with a high affinity for OPs. This study aimed to evaluate the applicability of Förster resonance energy transfer (FRET) as a sensitive and reliable method to quantify OPs at environmentally relevant concentrations. For this purpose, the previously developed IAEDANS-labelled EST2-S35C mutant was used, in which tryptophan and IAEDANS fluorophores are the donor and the acceptor, respectively. Fluorometric measurements showed linearity with increased EST2-S35C concentrations. No significant interference was observed in the FRET measurements due to changes in the pH of the medium or the addition of other organic components (glucose, ascorbic acid or yeast extract). Fluorescence quenching due to the presence of paraoxon was observed at concentrations as low as 2 nM, which are considered harmful for the ecosystem. These results pave the way for further experiments encompassing more complex matrices.
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Affiliation(s)
- Andreia C. M. Rodrigues
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (M.V.B.); (G.M.)
| | - Maria Vittoria Barbieri
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (M.V.B.); (G.M.)
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, 80126 Naples, Italy;
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (M.V.B.); (G.M.)
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, CNR, Via P. Castellino 111, 80131 Naples, Italy; (M.V.B.); (G.M.)
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9
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De Capua A, Palladino A, Chino M, Attanasio C, Lombardi A, Vecchione R, Netti PA. Active targeting of cancer cells by CD44 binding peptide-functionalized oil core-based nanocapsules. RSC Adv 2021; 11:24487-24499. [PMID: 35481036 PMCID: PMC9036919 DOI: 10.1039/d1ra03322k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/28/2021] [Accepted: 07/01/2021] [Indexed: 01/08/2023] Open
Abstract
Selectivity in tumor targeting is one of the major issues in cancer treatment. Therefore, surface functionalization of drug delivery systems with active moieties, able to selectively target tumors, has become a worldwide-recognized strategy. The CD44 receptor is largely used as a biomarker, being overexpressed in several tumors, and consequently as a target thanks to the identification of the CD44 binding peptide. Here we implemented the CD44 binding peptide logic onto an oil core–polymer multilayer shell, taking into account and optimizing all relevant features of drug delivery systems, such as small size (down to 100 nm), narrow size distribution, drug loading capability, antifouling and biodegradability. Besides promoting active targeting, the oil core-based system enables the delivery of natural and synthetic therapeutic compounds. Biological tests, using curcumin as a bioactive compound and fluorescent tag, demonstrated that CD44 binding peptide-functionalized nanocapsules selectively accumulate and internalize in cancer cells, compared to the control, thanks to ligand–receptor binding. CD44 binding peptide was implemented onto an oil core–polymer multilayer shell of 100 nm size and completely biodegradable. Biological tests, demonstrated that the proposed nanocarrier selectively accumulates and internalizes in cancer cells.![]()
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Affiliation(s)
- A De Capua
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia Largo Barsanti e Matteucci 53 Napoli 80125 Italy .,Department of Chemical, Materials & Industrial Production Engineering, University of Naples Federico II Naples 80125 Italy
| | - A Palladino
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II Via F. Delpino 1 80137 Naples Italy
| | - M Chino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo Via Cintia 45 80126 Naples Italy
| | - C Attanasio
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia Largo Barsanti e Matteucci 53 Napoli 80125 Italy .,Department of Veterinary Medicine and Animal Productions, University of Naples Federico II Via F. Delpino 1 80137 Naples Italy
| | - A Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo Via Cintia 45 80126 Naples Italy
| | - R Vecchione
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia Largo Barsanti e Matteucci 53 Napoli 80125 Italy
| | - P A Netti
- Center for Advanced Biomaterials for Health Care@CRIB, Istituto Italiano di Tecnologia Largo Barsanti e Matteucci 53 Napoli 80125 Italy .,Department of Chemical, Materials & Industrial Production Engineering, University of Naples Federico II Naples 80125 Italy.,Interdisciplinary Research Center of Biomaterials, CRIB, University Federico II P. le Tecchio 80 80125 Naples Italy
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10
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Maglio O, Chino M, Vicari C, Pavone V, Louro RO, Lombardi A. Histidine orientation in artificial peroxidase regioisomers as determined by paramagnetic NMR shifts. Chem Commun (Camb) 2021; 57:990-993. [PMID: 33399143 DOI: 10.1039/d0cc06676a] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Fe-Mimochrome VI*a is a synthetic peroxidase and peroxygenase, featuring two different peptides that are covalently-linked to deuteroheme. To perform a systematic structure/function correlation, we purposely shortened the distance between the distal peptide and the heme, allowing for the separation and characterization of two regioisomers. They differ in both His axial-ligand orientation, as determined by paramagnetic NMR shifts, and activity. These findings highlight that synthetic metalloenzymes may provide an efficient tool for disentangling the role of axial ligand orientation over peroxidase activity.
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Affiliation(s)
- Ornella Maglio
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy. and IBB-CNR, Via Mezzocannone 16, Naples, 80134, Italy
| | - Marco Chino
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
| | - Claudia Vicari
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
| | - Vincenzo Pavone
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
| | - Ricardo O Louro
- ITQB-UNL, Av. da Republica (EAN), Oeiras 2780-157, Portugal.
| | - Angela Lombardi
- Department of Chemical Sciences, University Federico II of Naples, Via Cintia 21, Naples, 80126, Italy.
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11
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Hussein HA, Hassan RYA, Chino M, Febbraio F. Point-of-Care Diagnostics of COVID-19: From Current Work to Future Perspectives. Sensors (Basel) 2020; 20:E4289. [PMID: 32752043 PMCID: PMC7435936 DOI: 10.3390/s20154289] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/22/2020] [Accepted: 07/30/2020] [Indexed: 01/08/2023]
Abstract
Coronaviruses have received global concern since 2003, when an outbreak caused by SARS-CoV emerged in China. Later on, in 2012, the Middle-East respiratory syndrome spread in Saudi Arabia, caused by MERS-CoV. Currently, the global crisis is caused by the pandemic SARS-CoV-2, which belongs to the same lineage of SARS-CoV. In response to the urgent need of diagnostic tools, several lab-based and biosensing techniques have been proposed so far. Five main areas have been individuated and discussed in terms of their strengths and weaknesses. The cell-culture detection and the microneutralization tests are still considered highly reliable methods. The genetic screening, featuring the well-established Real-time polymerase chain reaction (RT-PCR), represents the gold standard for virus detection in nasopharyngeal swabs. On the other side, immunoassays were developed, either by screening/antigen recognition of IgM/IgG or by detecting the whole virus, in blood and sera. Next, proteomic mass-spectrometry (MS)-based methodologies have also been proposed for the analysis of swab samples. Finally, virus-biosensing devices were efficiently designed. Both electrochemical immunosensors and eye-based technologies have been described, showing detection times lower than 10 min after swab introduction. Alternative to swab-based techniques, lateral flow point-of-care immunoassays are already commercially available for the analysis of blood samples. Such biosensing devices hold the advantage of being portable for on-site testing in hospitals, airports, and hotspots, virtually without any sample treatment or complicated lab precautions.
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Affiliation(s)
- Heba A. Hussein
- Virology Department, Animal Health Research Institute (AHRI), Agricultural Research Center (ARC), Dokki, Giza 12619, Egypt;
| | - Rabeay Y. A. Hassan
- Nanoscience Program, University of Science and Technology (UST), Zewail City of Science and Technology, 6th October City, Giza 12578, Egypt;
- Applied Organic Chemistry Department, National Research Centre (NRC), Dokki, Giza 12622, Egypt
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”. Via Cintia 21, 80126 Napoli, Italy;
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy
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12
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Leone L, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mimochrome, a metalloporphyrin‐based catalytic Swiss knife†. Biotechnol Appl Biochem 2020; 67:495-515. [DOI: 10.1002/bab.1985] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Leone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Marco Chino
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
- IBB ‐ National Research Council Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences University of Napoli “Federico II” Napoli Italy
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13
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Zambrano G, Nastri F, Pavone V, Lombardi A, Chino M. Use of an Artificial Miniaturized Enzyme in Hydrogen Peroxide Detection by Chemiluminescence. Sensors (Basel) 2020; 20:E3793. [PMID: 32640736 PMCID: PMC7374304 DOI: 10.3390/s20133793] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/25/2020] [Accepted: 07/03/2020] [Indexed: 11/16/2022]
Abstract
Advanced oxidation processes represent a viable alternative in water reclamation for potable reuse. Sensing methods of hydrogen peroxide are, therefore, needed to test both process progress and final quality of the produced water. Several bio-based assays have been developed so far, mainly relying on peroxidase enzymes, which have the advantage of being fast, efficient, reusable, and environmentally safe. However, their production/purification and, most of all, batch-to-batch consistency may inherently prevent their standardization. Here, we provide evidence that a synthetic de novo miniaturized designed heme-enzyme, namely Mimochrome VI*a, can be proficiently used in hydrogen peroxide assays. Furthermore, a fast and automated assay has been developed by using a lab-bench microplate reader. Under the best working conditions, the assay showed a linear response in the 10.0-120 μM range, together with a second linearity range between 120 and 500 μM for higher hydrogen peroxide concentrations. The detection limit was 4.6 μM and quantitation limits for the two datasets were 15.5 and 186 μM, respectively. In perspective, Mimochrome VI*a could be used as an active biological sensing unit in different sensor configurations.
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Affiliation(s)
| | | | | | | | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”. Via Cintia, 80126 Napoli, Italy; (G.Z.); (F.N.); (V.P.); (A.L.)
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14
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Zambrano G, Chino M, Renzi E, Di Girolamo R, Maglio O, Pavone V, Lombardi A, Nastri F. Clickable artificial heme-peroxidases for the development of functional nanomaterials. Biotechnol Appl Biochem 2020; 67:549-562. [PMID: 33463759 DOI: 10.1002/bab.1969] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/06/2020] [Indexed: 11/08/2022]
Abstract
Artificial metalloenzymes as catalysts are promising candidates for their use in different technologies, such as bioremediation, biomass transformation, or biosensing. Despite this, their practical exploitation is still at an early stage. Immobilized natural enzymes have been proposed to enhance their applicability. Immobilization may offer several advantages: (i) catalyst reuse; (ii) easy separation of the enzyme from the reaction medium; (iii) better tolerance to harsh temperature and pH conditions. Here, we report an easy immobilization procedure of an artificial peroxidase on different surfaces, by means of click chemistry. FeMC6*a, a recently developed peroxidase mimic, has been functionalized with a pegylated aza-dibenzocyclooctyne to afford a "clickable" biocatalyst, namely FeMC6*a-PEG4@DBCO, which easily reacts with azide-functionalized molecules and/or nanomaterials to afford functional bioconjugates. The clicked biocatalyst retains its structural and, to some extent, its functional behaviors, thus housing high potential for biotechnological applications.
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Affiliation(s)
- Gerardo Zambrano
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Emilia Renzi
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Rocco Di Girolamo
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy.,Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, Italy
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15
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Oliva R, Chino M, Lombardi A, Nastri F, Notomista E, Petraccone L, Del Vecchio P. Similarities and differences for membranotropic action of three unnatural antimicrobial peptides. J Pept Sci 2020; 26:e3270. [PMID: 32558092 DOI: 10.1002/psc.3270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 04/15/2020] [Revised: 05/23/2020] [Accepted: 06/02/2020] [Indexed: 02/06/2023]
Abstract
Previously, we described the design and synthesis of three nine-residue AMPs, P9Nal(SS), P9Trp(SS), and P9Nal(SR), showing high stability in serum and broad spectrum antimicrobial activity. The peptides P9Trp(SS) and P9Nal(SR) differ from P9Nal(SS) for the replacement of the two 2Nal residues with Trp residues and for the replacement of the two Cys (StBu) with Cys (tBu) residues, respectively. These changes led to peptides with a lower hydrophobicity respect to the P9Nal(SS). Interestingly, the three peptides have very similar activity against Gram-negative bacteria. Instead, they exhibit a significant difference towards Gram-positive bacteria, being P9Nal(SS) the most active. In order to evaluate the impact of amino acids substitution on membranotropic activity and rationalize the observed effects in vivo, here, we report the detailed biophysical characterization of the interaction between P9Nal(SR) and P9Trp(SS) and liposomes by combining differential scanning calorimetry, circular dichroism, and fluorescence spectroscopy. The comparison with the results for the previously characterized P9Nal(SS) peptide reveals similarities and differences on the interaction process and perturbation activities. It was found that the three peptides can penetrate at different extent inside the bilayer upon changing their conformation and inducing lipid domains formation, revealing that the formation of lipid domains is fundamental for the activity against Gram-negative bacteria. On the contrary, the dissimilar activity against Gram-positive bacteria well correlate with the different affinity of peptides for the lipoteichoic acid, a component selectively present in the cell wall of Gram-positive bacteria.
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Affiliation(s)
- Rosario Oliva
- Physical Chemistry I, Technical University of Dortmund, Dortmund, Germany.,Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Angelina Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
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16
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Le JM, Alachouzos G, Chino M, Frontier AJ, Lombardi A, Bren KL. Tuning Mechanism through Buffer Dependence of Hydrogen Evolution Catalyzed by a Cobalt Mini-enzyme. Biochemistry 2020; 59:1289-1297. [DOI: 10.1021/acs.biochem.0c00060] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jennifer M. Le
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Georgios Alachouzos
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cintia 45, 80126 Naples, Italy
| | - Alison J. Frontier
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario Monte S. Angelo, via Cintia 45, 80126 Naples, Italy
| | - Kara L. Bren
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
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Cetrangolo GP, Rusko J, Gori C, Carullo P, Manco G, Chino M, Febbraio F. Highly Sensitive Detection of Chemically Modified Thio-Organophosphates by an Enzymatic Biosensing Device: An Automated Robotic Approach. Sensors (Basel) 2020; 20:s20051365. [PMID: 32131482 PMCID: PMC7085774 DOI: 10.3390/s20051365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 01/28/2020] [Accepted: 02/28/2020] [Indexed: 12/28/2022]
Abstract
Pesticides represent some of the most common man-made chemicals in the world. Despite their unquestionable utility in the agricultural field and in the prevention of pest infestation in public areas of cities, pesticides and their biotransformation products are toxic to the environment and hazardous to human health. Esterase-based biosensors represent a viable alternative to the expensive and time-consuming systems currently used for their detection. In this work, we used the esterase-2 from Alicyclobacillus acidocaldarius as bioreceptor for a biosensing device based on an automated robotic approach. Coupling the robotic system with a fluorescence inhibition assay, in only 30 s of enzymatic assay, we accomplished the detection limit of 10 pmol for 11 chemically oxidized thio-organophosphates in solution. In addition, we observed differences in the shape of the inhibition curves determined measuring the decrease of esterase-2 residual activity over time. These differences could be used for the characterization and identification of thio-organophosphate pesticides, leading to a pseudo fingerprinting for each of these compounds. This research represents a starting point to develop technologies for automated screening of toxic compounds in samples from industrial sectors, such as the food industry, and for environmental monitoring.
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Affiliation(s)
- Giovanni Paolo Cetrangolo
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
| | - Janis Rusko
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
- Institute of Food Safety, Animal Health and Environment “BIOR”, Lejupes Street 3, LV-1076 Riga, Latvia
| | - Carla Gori
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
| | - Paola Carullo
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
| | - Giuseppe Manco
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
- Correspondence: (G.M.); (F.F.); Tel.: +39-081-6132-296 (G.M.); +39-081-6132-611 (F.F.)
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”. Via Cintia, 80126 Napoli, Italy;
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, National Research Council (CNR), Via P. Castellino 111, 80131 Naples, Italy; (G.P.C.); (J.R.); (C.G.); (P.C.)
- Correspondence: (G.M.); (F.F.); Tel.: +39-081-6132-296 (G.M.); +39-081-6132-611 (F.F.)
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Esposito A, di Giovanni C, De Fenza M, Talarico G, Chino M, Palumbo G, Guaragna A, D'Alonzo D. A Stereoconvergent Tsuji-Trost Reaction in the Synthesis of Cyclohexenyl Nucleosides. Chemistry 2020; 26:2597-2601. [PMID: 31860145 DOI: 10.1002/chem.201905367] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/18/2019] [Indexed: 12/14/2022]
Abstract
A highly regio- and stereoselective route to d- and l-cyclohexenyl nucleosides has been devised, using the Tsuji-Trost reaction as the key step. Contrarily to the widely accepted mechanism (involving a net retention of configuration), the reaction proceeded in a highly stereoconvergent manner, providing cis nucleosides regardless of the relative configuration of the starting materials. DFT calculations confirmed the experimental data while suggesting the origin of the stereochemical reaction outcome.
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Affiliation(s)
- Anna Esposito
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Concetta di Giovanni
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Maria De Fenza
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Giovanni Talarico
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Marco Chino
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Giovanni Palumbo
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Annalisa Guaragna
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences, Università degli Studi di Napoli Federico II, via Cintia, 80126, Napoli, Italy
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Lombardi A, Pirro F, Maglio O, Chino M, DeGrado WF. De Novo Design of Four-Helix Bundle Metalloproteins: One Scaffold, Diverse Reactivities. Acc Chem Res 2019; 52:1148-1159. [PMID: 30973707 DOI: 10.1021/acs.accounts.8b00674] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
De novo protein design represents an attractive approach for testing and extending our understanding of metalloprotein structure and function. Here, we describe our work on the design of DF (Due Ferri or two-iron in Italian), a minimalist model for the active sites of much larger and more complex natural diiron and dimanganese proteins. In nature, diiron and dimanganese proteins protypically bind their ions in 4-Glu, 2-His environments, and they catalyze diverse reactions, ranging from hydrolysis, to O2-dependent chemistry, to decarbonylation of aldehydes. In the design of DF, the position of each atom-including the backbone, the first-shell ligands, the second-shell hydrogen-bonded groups, and the well-packed hydrophobic core-was bespoke using precise mathematical equations and chemical principles. The first member of the DF family was designed to be of minimal size and complexity and yet to display the quintessential elements required for binding the dimetal cofactor. After thoroughly characterizing its structural, dynamic, spectroscopic, and functional properties, we added additional complexity in a rational stepwise manner to achieve increasingly sophisticated catalytic functions, ultimately demonstrating substrate-gated four-electron reduction of O2 to water. We also briefly describe the extension of these studies to the design of proteins that bind nonbiological metal cofactors (a synthetic porphyrin and a tetranuclear cluster), and a Zn2+/proton antiporting membrane protein. Together these studies demonstrate a successful and generally applicable strategy for de novo metalloprotein design, which might indeed mimic the process by which primordial metalloproteins evolved. We began the design process with a highly symmetrical backbone and binding site, by using point-group symmetry to assemble the secondary structures that position the amino acid side chains required for binding. The resulting models provided a rough starting point and initial parameters for the subsequent precise design of the final protein using modern methods of computational protein design. Unless the desired site is itself symmetrical, this process requires reduction of the symmetry or lifting it altogether. Nevertheless, the initial symmetrical structure can be helpful to restrain the search space during assembly of the backbone. Finally, the methods described here should be generally applicable to the design of highly stable and robust catalysts and sensors. There is considerable potential in combining the efficiency and knowledge base associated with homogeneous metal catalysis with the programmability, biocompatibility, and versatility of proteins. While the work reported here focuses on testing and learning the principles of natural metalloproteins by designing and studying proteins one at a time, there is also considerable potential for using designed proteins that incorporate both biological and nonbiological metal ion cofactors for the evolution of novel catalysts.
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Affiliation(s)
- Angela Lombardi
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
- IBB, National Research Council, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli Federico II, Via Cintia, 26, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California 94158-9001, United States
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Leone L, D'Alonzo D, Balland V, Zambrano G, Chino M, Nastri F, Maglio O, Pavone V, Lombardi A. Mn-Mimochrome VI *a: An Artificial Metalloenzyme With Peroxygenase Activity. Front Chem 2018; 6:590. [PMID: 30564568 PMCID: PMC6288486 DOI: 10.3389/fchem.2018.00590] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 10/05/2018] [Accepted: 11/13/2018] [Indexed: 12/27/2022] Open
Abstract
Manganese-porphyrins are important tools in catalysis, due to their capability to promote a wide variety of synthetically valuable transformations. Despite their great reactivity, the difficulties to control the reaction selectivity and to protect the catalyst from self-degradation hamper their practical application. Compared to small-molecule porphyrin complexes, metalloenzymes display remarkable features, because the reactivity of the metal center is finely modulated by a complex interplay of interactions within the protein matrix. In the effort to combine the catalytic potential of manganese porphyrins with the unique properties of biological catalysts, artificial metalloenzymes have been reported, mainly by incorporation of manganese-porphyrins into native protein scaffolds. Here we describe the spectroscopic and catalytic properties of Mn-Mimochrome VI*a (Mn-MC6*a), a mini-protein with a manganese deuteroporphyrin active site within a scaffold of two synthetic peptides covalently bound to the porphyrin. Mn-MC6*a is an efficient catalyst endowed with peroxygenase activity. The UV-vis absorption spectrum of Mn-MC6*a resembles that of Mn-reconstituted horseradish peroxidase (Mn-HRP), both in the resting and high-valent oxidized states. Remarkably, Mn-MC6*a shows a higher reactivity compared to Mn-HRP, because higher yields and chemoselectivity were observed in thioether oxidation. Experimental evidences also provided indications on the nature of the high-valent reactive intermediate and on the sulfoxidation mechanism.
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Affiliation(s)
- Linda Leone
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Véronique Balland
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Gerardo Zambrano
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
- Institute of Biostructures and Bioimages, National Research Council, Naples, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Naples, Italy
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21
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Zambrano G, Ruggiero E, Malafronte A, Chino M, Maglio O, Pavone V, Nastri F, Lombardi A. Artificial Heme Enzymes for the Construction of Gold-Based Biomaterials. Int J Mol Sci 2018; 19:E2896. [PMID: 30250002 PMCID: PMC6213134 DOI: 10.3390/ijms19102896] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/11/2018] [Accepted: 09/19/2018] [Indexed: 12/14/2022] Open
Abstract
Many efforts are continuously devoted to the construction of hybrid biomaterials for specific applications, by immobilizing enzymes on different types of surfaces and/or nanomaterials. In addition, advances in computational, molecular and structural biology have led to a variety of strategies for designing and engineering artificial enzymes with defined catalytic properties. Here, we report the conjugation of an artificial heme enzyme (MIMO) with lipoic acid (LA) as a building block for the development of gold-based biomaterials. We show that the artificial MIMO@LA can be successfully conjugated to gold nanoparticles or immobilized onto gold electrode surfaces, displaying quasi-reversible redox properties and peroxidase activity. The results of this work open interesting perspectives toward the development of new totally-synthetic catalytic biomaterials for application in biotechnology and biomedicine, expanding the range of the biomolecular component aside from traditional native enzymes.
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Affiliation(s)
- Gerardo Zambrano
- Department of Chemical Sciences, University of Napoli "Federico II" Via Cintia, 80126 Napoli, Italy.
| | - Emmanuel Ruggiero
- Department of Chemical Sciences, University of Napoli "Federico II" Via Cintia, 80126 Napoli, Italy.
| | - Anna Malafronte
- Department of Chemical Sciences, University of Napoli "Federico II" Via Cintia, 80126 Napoli, Italy.
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli "Federico II" Via Cintia, 80126 Napoli, Italy.
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli "Federico II" Via Cintia, 80126 Napoli, Italy.
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy.
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Napoli "Federico II" Via Cintia, 80126 Napoli, Italy.
| | - Flavia Nastri
- Department of Chemical Sciences, University of Napoli "Federico II" Via Cintia, 80126 Napoli, Italy.
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli "Federico II" Via Cintia, 80126 Napoli, Italy.
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Caserta G, Chino M, Firpo V, Zambrano G, Leone L, D'Alonzo D, Nastri F, Maglio O, Pavone V, Lombardi A. Cover Feature: Enhancement of Peroxidase Activity in Artificial Mimochrome VI Catalysts through Rational Design (ChemBioChem 17/2018). Chembiochem 2018. [DOI: 10.1002/cbic.201800453] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Giorgio Caserta
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
- Present address: Department of ChemistryTechnische Universität Berlin Strasse des 17 Juni 135 10623 Berlin Germany
| | - Marco Chino
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
| | - Vincenzo Firpo
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
| | - Gerardo Zambrano
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
| | - Linda Leone
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
| | - Daniele D'Alonzo
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
| | - Flavia Nastri
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
| | - Ornella Maglio
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
- IBBNational Research Council via Mezzocannone 16, 80134 Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
| | - Angela Lombardi
- Department of Chemical SciencesUniversity of Naples “Federico II” Via Cintia 80126 Napoli Italy
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23
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Perrella F, Raucci U, Chiariello MG, Chino M, Maglio O, Lombardi A, Rega N. Unveiling the structure of a novel artificial heme-enzyme with peroxidase-like activity: A theoretical investigation. Biopolymers 2018; 109:e23225. [DOI: 10.1002/bip.23225] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/11/2018] [Accepted: 04/25/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Fulvio Perrella
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II, Complesso Universitario di M.S.Angelo, via Cintia; Napoli 80126 Italy
| | - Umberto Raucci
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II, Complesso Universitario di M.S.Angelo, via Cintia; Napoli 80126 Italy
| | - Maria Gabriella Chiariello
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II, Complesso Universitario di M.S.Angelo, via Cintia; Napoli 80126 Italy
| | - Marco Chino
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II, Complesso Universitario di M.S.Angelo, via Cintia; Napoli 80126 Italy
| | - Ornella Maglio
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II, Complesso Universitario di M.S.Angelo, via Cintia; Napoli 80126 Italy
- IBB-CNR, Via Mezzocannone 16; Napoli 80134 Italy
| | - Angela Lombardi
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II, Complesso Universitario di M.S.Angelo, via Cintia; Napoli 80126 Italy
| | - Nadia Rega
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II, Complesso Universitario di M.S.Angelo, via Cintia; Napoli 80126 Italy
- CRIB Center for Advanced Biomaterials for Healthcare, Piazzale Tecchio; Napoli 80125 Italy
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24
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Chino M, Zhang SQ, Pirro F, Leone L, Maglio O, Lombardi A, DeGrado WF. Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster. Biopolymers 2018; 109:e23339. [PMID: 30203532 PMCID: PMC6218314 DOI: 10.1002/bip.23229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 03/19/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/27/2022]
Abstract
De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn2+ clusters. The crystal structures of the helical proteins were in good agreement with the overall design, and the metal-binding and conformational properties of the helical bundles in solution were consistent with the crystal structures. However, the corresponding apo-proteins were not fully folded in solution. In this work, we design three peptides, based on the crystal structure of the original bundles. One of the peptides forms tetramers in aqueous solution in the absence of metal ions as assessed by CD and NMR. It also binds Zn2+ in the intended stoichiometry. These studies strongly suggest that the desired structure has been achieved in the apo state, providing evidence that the peptide is able to actively impart the designed geometry to the metal cluster.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Shao-Qing Zhang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104-6396, United States
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
- Institute of Biostructure and Bioimaging, National Research Council, via Mezzocannone, 16, 80134, Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
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25
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Caserta G, Chino M, Firpo V, Zambrano G, Leone L, D'Alonzo D, Nastri F, Maglio O, Pavone V, Lombardi A. Enhancement of Peroxidase Activity in Artificial Mimochrome VI Catalysts through Rational Design. Chembiochem 2018; 19:1823-1826. [PMID: 29898243 DOI: 10.1002/cbic.201800200] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 04/18/2018] [Indexed: 11/09/2022]
Abstract
Rational design provides an attractive strategy to tune and control the reactivity of bioinspired catalysts. Although there has been considerable progress in the design of heme oxidase mimetics with active-site environments of ever-growing complexity and catalytic efficiency, their stability during turnover is still an open challenge. Herein, we show that the simple incorporation of two 2-aminoisobutyric acids into an artificial peptide-based peroxidase results in a new catalyst (FeIII -MC6*a) with higher resistance against oxidative damage and higher catalytic efficiency. The turnover number of this catalyst is twice as high as that of its predecessor. These results point out the protective role exerted by the peptide matrix and pave the way to the synthesis of robust bioinspired catalysts.
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Affiliation(s)
- Giorgio Caserta
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy.,Present address: Department of Chemistry, Technische Universität Berlin, Strasse des 17 Juni 135, 10623, Berlin, Germany
| | - Marco Chino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Vincenzo Firpo
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Gerardo Zambrano
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy.,IBB, National Research Council, via Mezzocannone, 16, 80134, Napoli, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples "Federico II", Via Cintia, 80126, Napoli, Italy
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26
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Oliva R, Chino M, Pane K, Pistorio V, De Santis A, Pizzo E, D'Errico G, Pavone V, Lombardi A, Del Vecchio P, Notomista E, Nastri F, Petraccone L. Exploring the role of unnatural amino acids in antimicrobial peptides. Sci Rep 2018; 8:8888. [PMID: 29892005 PMCID: PMC5995839 DOI: 10.1038/s41598-018-27231-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [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] [Received: 02/19/2018] [Accepted: 05/23/2018] [Indexed: 12/14/2022] Open
Abstract
Cationic antimicrobial peptides (CAMPs) are a promising alternative to treat multidrug-resistant bacteria, which have developed resistance to all the commonly used antimicrobial, and therefore represent a serious threat to human health. One of the major drawbacks of CAMPs is their sensitivity to proteases, which drastically limits their half-life. Here we describe the design and synthesis of three nine-residue CAMPs, which showed high stability in serum and broad spectrum antimicrobial activity. As for all peptides a very low selectivity between bacterial and eukaryotic cells was observed, we performed a detailed biophysical characterization of the interaction of one of these peptides with liposomes mimicking bacterial and eukaryotic membranes. Our results show a surface binding on the DPPC/DPPG vesicles, coupled with lipid domain formation, and, above a threshold concentration, a deep insertion into the bilayer hydrophobic core. On the contrary, mainly surface binding of the peptide on the DPPC bilayer was observed. These observed differences in the peptide interaction with the two model membranes suggest a divergence in the mechanisms responsible for the antimicrobial activity and for the observed high toxicity toward mammalian cell lines. These results could represent an important contribution to unravel some open and unresolved issues in the development of synthetic CAMPs.
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Affiliation(s)
- Rosario Oliva
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, I-80126, Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, I-80126, Naples, Italy
| | - Katia Pane
- Department of Biology, University of Naples "Federico II", Via Cintia, I-80126, Naples, Italy
| | - Valeria Pistorio
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via Pansini, 5, I-80131, Naples, Italy
| | - Augusta De Santis
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, I-80126, Naples, Italy
| | - Elio Pizzo
- Department of Biology, University of Naples "Federico II", Via Cintia, I-80126, Naples, Italy
| | - Gerardino D'Errico
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, I-80126, Naples, Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, I-80126, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, I-80126, Naples, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, I-80126, Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples "Federico II", Via Cintia, I-80126, Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, I-80126, Naples, Italy
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples "Federico II", via Cintia, I-80126, Naples, Italy.
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27
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Chino M, Leone L, Zambrano G, Pirro F, D'Alonzo D, Firpo V, Aref D, Lista L, Maglio O, Nastri F, Lombardi A. Oxidation catalysis by iron and manganese porphyrins within enzyme-like cages. Biopolymers 2018; 109:e23107. [DOI: 10.1002/bip.23107] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/31/2018] [Accepted: 02/05/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Gerardo Zambrano
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Vincenzo Firpo
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Diaa Aref
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Liliana Lista
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
- Institute of Biostructures and Bioimages-National Research Council, Via Mezzocannone 16; Napoli 80134 Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II,” Via Cintia; Napoli 80126 Italy
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28
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Zhang SQ, Chino M, Liu L, Tang Y, Hu X, DeGrado WF, Lombardi A. De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles. J Am Chem Soc 2018; 140:1294-1304. [PMID: 29249157 PMCID: PMC5860638 DOI: 10.1021/jacs.7b08261] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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] [Indexed: 01/09/2023]
Abstract
De novo design provides an attractive approach to test the mechanism by which metalloproteins define the geometry and reactivity of their metal ion cofactors. While there has been considerable progress in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments has not been accomplished. Here, we describe the design of tetranuclear clusters, consisting of four Zn2+ and four carboxylate oxygens situated at the vertices of a distorted cube-like structure. The tetra-Zn2+ clusters are bound at a buried site within a four-helix bundle, with each helix donating a single carboxylate (Glu or Asp) and imidazole (His) ligand, as well as second- and third-shell ligands. Overall, the designed site consists of four Zn2+ and 16 polar side chains in a fully connected hydrogen-bonded network. The designed proteins have apolar cores at the top and bottom of the bundle, which drive the assembly of the liganding residues near the center of the bundle. The steric bulk of the apolar residues surrounding the binding site was varied to determine how subtle changes in helix-helix packing affect the binding site. The crystal structures of two of four proteins synthesized were in good agreement with the overall design; both formed a distorted cuboidal site stabilized by flanking second- and third-shell interactions that stabilize the primary ligands. A third structure bound a single Zn2+ in an unanticipated geometry, and the fourth bound multiple Zn2+ at multiple sites at partial occupancy. The metal-binding and conformational properties of the helical bundles in solution, probed by circular dichroism spectroscopy, analytical ultracentrifugation, and NMR, were consistent with the crystal structures.
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Affiliation(s)
- Shao-Qing Zhang
- Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104-6396, United States
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - Marco Chino
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, I-80126 Napoli, Italy
| | - Lijun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- DLX Scientific, Lawrence, KS 66049, United States
| | - Youzhi Tang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- College of Veterinary Medicine, South China Agricultural University, Guangdong 510642, China
| | - Xiaozhen Hu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, I-80126 Napoli, Italy
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Chino M, Leone L, Maglio O, D'Alonzo D, Pirro F, Pavone V, Nastri F, Lombardi A. A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-Dependent Oxidation. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
- IBB-National Research Council; Via Mezzocannone 16 80134 Napoli Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
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30
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Chino M, Leone L, Maglio O, D'Alonzo D, Pirro F, Pavone V, Nastri F, Lombardi A. A De Novo Heterodimeric Due Ferri Protein Minimizes the Release of Reactive Intermediates in Dioxygen-Dependent Oxidation. Angew Chem Int Ed Engl 2017; 56:15580-15583. [DOI: 10.1002/anie.201707637] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Linda Leone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Ornella Maglio
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
- IBB-National Research Council; Via Mezzocannone 16 80134 Napoli Italy
| | - Daniele D'Alonzo
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Fabio Pirro
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Flavia Nastri
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
| | - Angela Lombardi
- Department of Chemical Sciences; University of Napoli “Federico II”; Via Cintia 80126 Napoli Italy
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31
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Itri F, Monti DM, Chino M, Vinciguerra R, Altucci C, Lombardi A, Piccoli R, Birolo L, Arciello A. Identification of novel direct protein-protein interactions by irradiating living cells with femtosecond UV laser pulses. Biochem Biophys Res Commun 2017; 492:67-73. [PMID: 28807828 DOI: 10.1016/j.bbrc.2017.08.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 07/31/2017] [Accepted: 08/10/2017] [Indexed: 12/13/2022]
Abstract
The identification of protein-protein interaction networks in living cells is becoming increasingly fundamental to elucidate main biological processes and to understand disease molecular bases on a system-wide level. We recently described a method (LUCK, Laser UV Cross-linKing) to cross-link interacting protein surfaces in living cells by UV laser irradiation. By using this innovative methodology, that does not require any protein modification or cell engineering, here we demonstrate that, upon UV laser irradiation of HeLa cells, a direct interaction between GAPDH and alpha-enolase was "frozen" by a cross-linking event. We validated the occurrence of this direct interaction by co-immunoprecipitation and Immuno-FRET analyses. This represents a proof of principle of the LUCK capability to reveal direct protein interactions in their physiological environment.
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Affiliation(s)
- Francesco Itri
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Daria Maria Monti
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy; Istituto Nazionale di Biostrutture e Biosistemi (INBB), Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Roberto Vinciguerra
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Carlo Altucci
- Department of Physics "Ettore Pancini", University of Naples Federico II, Naples 80126, Italy; Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR, Naples, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Renata Piccoli
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy; Istituto Nazionale di Biostrutture e Biosistemi (INBB), Italy
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy; Istituto Nazionale di Biostrutture e Biosistemi (INBB), Italy.
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32
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Gaglione R, Dell'Olmo E, Bosso A, Chino M, Pane K, Ascione F, Itri F, Caserta S, Amoresano A, Lombardi A, Haagsman HP, Piccoli R, Pizzo E, Veldhuizen EJA, Notomista E, Arciello A. Novel human bioactive peptides identified in Apolipoprotein B: Evaluation of their therapeutic potential. Biochem Pharmacol 2017; 130:34-50. [PMID: 28131846 DOI: 10.1016/j.bcp.2017.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [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: 12/02/2016] [Accepted: 01/23/2017] [Indexed: 10/20/2022]
Abstract
Host defence peptides (HDPs) are short, cationic amphipathic peptides that play a key role in the response to infection and inflammation in all complex life forms. It is increasingly emerging that HDPs generally have a modest direct activity against a broad range of microorganisms, and that their anti-infective properties are mainly due to their ability to modulate the immune response. Here, we report the recombinant production and characterization of two novel HDPs identified in human Apolipoprotein B (residues 887-922) by using a bioinformatics method recently developed by our group. We focused our attention on two variants of the identified HDP, here named r(P)ApoBL and r(P)ApoBS, 38- and 26-residue long, respectively. Both HDPs were found to be endowed with a broad-spectrum antimicrobial activity while they show neither toxic nor haemolytic effects towards eukaryotic cells. Interestingly, both HDPs were found to display a significant anti-biofilm activity, and to act in synergy with either commonly used antibiotics or EDTA. The latter was selected for its ability to affect bacterial outer membrane permeability, and to sensitize bacteria to several antibiotics. Circular dichroism analyses showed that SDS, TFE, and LPS significantly alter r(P)ApoBL conformation, whereas slighter or no significant effects were detected in the case of r(P)ApoBS peptide. Interestingly, both ApoB derived peptides were found to elicit anti-inflammatory effects, being able to mitigate the production of pro-inflammatory interleukin-6 and nitric oxide in LPS induced murine macrophages. It should also be emphasized that r(P)ApoBL peptide was found to play a role in human keratinocytes wound closure in vitro. Altogether, these findings open interesting perspectives on the therapeutic use of the herein identified HDPs.
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Affiliation(s)
- Rosa Gaglione
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; Department of Infectious Diseases and Immunology, Division Molecular Host Defence, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Eliana Dell'Olmo
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Andrea Bosso
- Department of Infectious Diseases and Immunology, Division Molecular Host Defence, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands; Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Katia Pane
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Flora Ascione
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, 80125 Naples, Italy
| | - Francesco Itri
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Sergio Caserta
- Department of Chemical, Materials and Production Engineering, University of Naples Federico II, 80125 Naples, Italy; CEINGE Biotecnologie Avanzate, Via Sergio Pansini, 5, 80131 Naples, Italy; Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), UdR INSTM Napoli Federico II, P.le Tecchio, 80, 80125 Naples, Italy
| | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Angelina Lombardi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy
| | - Henk P Haagsman
- Department of Infectious Diseases and Immunology, Division Molecular Host Defence, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Renata Piccoli
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; Istituto Nazionale di Biostrutture e Biosistemi (INBB), Italy
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Edwin J A Veldhuizen
- Department of Infectious Diseases and Immunology, Division Molecular Host Defence, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; Istituto Nazionale di Biostrutture e Biosistemi (INBB), Italy.
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33
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Cimini D, Corte KD, Finamore R, Andreozzi L, Stellavato A, Pirozzi AVA, Ferrara F, Formisano R, De Rosa M, Chino M, Lista L, Lombardi A, Pavone V, Schiraldi C. Production of human pro-relaxin H2 in the yeast Pichia pastoris. BMC Biotechnol 2017; 17:4. [PMID: 28088197 PMCID: PMC5237503 DOI: 10.1186/s12896-016-0319-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 05/06/2016] [Accepted: 12/07/2016] [Indexed: 12/16/2022] Open
Abstract
Background Initially known as the reproductive hormone, relaxin was shown to possess other therapeutically useful properties that include extracellular matrix remodeling, anti-inflammatory, anti-ischemic and angiogenic effects. All these findings make relaxin a potential drug for diverse medical applications. Its precursor, pro-relaxin, is an 18 kDa protein, that shows activity in in vitro assays. Since extraction of relaxin from animal tissues raises several issues, prokaryotes and eukaryotes were both used as expression systems for recombinant relaxin production. Most productive results were obtained when using Escherichia coli as a host for human relaxin expression. However, in such host, relaxin precipitated in the form of inclusion bodies and, therefore, required several expensive recovery steps as cell lysis, refolding and reduction. Results To overcome the issues related to prokaryotic expression here we report the production and purification of secreted human pro-relaxin H2 by using the methylotrophic yeast Pichia pastoris as expression host. The methanol inducible promoter AOX1 was used to drive expression of the native and histidine tagged forms of pro-relaxin H2 in dual phase fed-batch experiments on the 22 L scale. Both protein forms presented the correct structure, as determined by mass spectrometry and western blotting analyses, and demonstrated to be biologically active in immune enzymatic assays. The presence of the tag allowed to simplify pro-relaxin purification obtaining higher purity. Conclusions This work presents a strategy for microbial production of recombinant human pro-relaxin H2 in Pichia pastoris that allowed the obtainment of biologically active pro-hormone, with a final concentration in the fermentation broth ranging between 10 and 14 mg/L of product, as determined by densitometric analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0319-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- D Cimini
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy.
| | - K Della Corte
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy
| | - R Finamore
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy
| | - L Andreozzi
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy
| | - A Stellavato
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy
| | - A V A Pirozzi
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy
| | - F Ferrara
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy
| | - R Formisano
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy
| | - M De Rosa
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy
| | - M Chino
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia I, 80126, Naples, Italy
| | - L Lista
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia I, 80126, Naples, Italy
| | - A Lombardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia I, 80126, Naples, Italy
| | - V Pavone
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia I, 80126, Naples, Italy
| | - C Schiraldi
- Department of Experimental Medicine, Section of Biotechnology and Molecular Biology, Second University of Naples and University of Campania Luigi Vanvitelli, via de Crecchio 7, 80138, Naples, Italy.
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Abstract
Many efforts are being made in the design and engineering of metalloenzymes with catalytic properties fulfilling the needs of practical applications. Progress in this field has recently been accelerated by advances in computational, molecular and structural biology. This review article focuses on the recent examples of oxygen-activating metalloenzymes, developed through the strategies of de novo design, miniaturization processes and protein redesign. Considerable progress in these diverse design approaches has produced many metal-containing biocatalysts able to adopt the functions of native enzymes or even novel functions beyond those found in Nature.
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Affiliation(s)
- Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, A322 CLSL, 600 South Mathews Avenue, Urbana, IL 61801
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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Abstract
De novo design has proven a powerful methodology for understanding protein folding and function, and for mimicking or even bettering the properties of natural proteins. Extensive progress has been made in the design of helical bundles, simple structural motifs that can be nowadays designed with a high degree of precision. Among helical bundles, the four-helix bundle is widespread in nature, and is involved in numerous and fundamental processes. Representative examples are the carboxylate bridged diiron proteins, which perform a variety of different functions, ranging from reversible dioxygen binding to catalysis of dioxygen-dependent reactions, including epoxidation, desaturation, monohydroxylation, and radical formation. The "Due Ferri" (two-irons; DF) family of proteins is the result of a de novo design approach, aimed to reproduce in minimal four-helix bundle models the properties of the more complex natural diiron proteins, and to address how the amino acid sequence modulates their functions. The results so far obtained point out that asymmetric metal environments are essential to reprogram functions, and to achieve the specificity and selectivity of the natural enzymes. Here, we describe a design method that allows constructing asymmetric four-helix bundles through the covalent heterodimerization of two different α-helical harpins. In particular, starting from the homodimeric DF3 structure, we developed a protocol for covalently linking the two α2 monomers by using the Cu(I) catalyzed azide-alkyne cycloaddition. The protocol was then generalized, in order to include the construction of several linkers, in different protein positions. Our method is fast, low cost, and in principle can be applied to any couple of peptides/proteins we desire to link.
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Affiliation(s)
- M Chino
- University of Napoli Federico II, Napoli, Italy
| | - L Leone
- University of Napoli Federico II, Napoli, Italy
| | - O Maglio
- University of Napoli Federico II, Napoli, Italy; Institute of Biostructures and Bioimages-IBB, CNR, Napoli, Italy
| | - A Lombardi
- University of Napoli Federico II, Napoli, Italy.
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36
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Itri F, Monti DM, Della Ventura B, Vinciguerra R, Chino M, Gesuele F, Lombardi A, Velotta R, Altucci C, Birolo L, Piccoli R, Arciello A. Femtosecond UV-laser pulses to unveil protein-protein interactions in living cells. Cell Mol Life Sci 2015; 73:637-48. [PMID: 26265182 DOI: 10.1007/s00018-015-2015-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [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: 05/06/2015] [Revised: 07/30/2015] [Accepted: 08/06/2015] [Indexed: 12/30/2022]
Abstract
A hallmark to decipher bioprocesses is to characterize protein-protein interactions in living cells. To do this, the development of innovative methodologies, which do not alter proteins and their natural environment, is particularly needed. Here, we report a method (LUCK, Laser UV Cross-linKing) to in vivo cross-link proteins by UV-laser irradiation of living cells. Upon irradiation of HeLa cells under controlled conditions, cross-linked products of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were detected, whose yield was found to be a linear function of the total irradiation energy. We demonstrated that stable dimers of GAPDH were formed through intersubunit cross-linking, as also observed when the pure protein was irradiated by UV-laser in vitro. We proposed a defined patch of aromatic residues located at the enzyme subunit interface as the cross-linking sites involved in dimer formation. Hence, by this technique, UV-laser is able to photofix protein surfaces that come in direct contact. Due to the ultra-short time scale of UV-laser-induced cross-linking, this technique could be extended to weld even transient protein interactions in their native context.
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Affiliation(s)
- Francesco Itri
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Daria M Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.,Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | | | - Roberto Vinciguerra
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Felice Gesuele
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy
| | - Angelina Lombardi
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Raffaele Velotta
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy.,Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR, Naples, Italy
| | - Carlo Altucci
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy. .,Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR, Naples, Italy.
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.
| | - Renata Piccoli
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.,Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy. .,Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy.
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Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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38
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Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Cover Picture: Artificial Diiron Enzymes with a De Novo Designed Four‐Helix Bundle Structure (Eur. J. Inorg. Chem. 21/2015). Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201590084] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy, http://chemicalsciences.unina.it/documents/research‐groups
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy, http://chemicalsciences.unina.it/documents/research‐groups
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy, http://chemicalsciences.unina.it/documents/research‐groups
| | - Vincenzo Pavone
- Department of Structural and Functional Biology, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco San Francisco, CA 94158, USA
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy, http://chemicalsciences.unina.it/documents/research‐groups
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39
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Chino M, Maglio O, Nastri F, Pavone V, DeGrado WF, Lombardi A. Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure. Eur J Inorg Chem 2015; 2015:3371-3390. [PMID: 27630532 PMCID: PMC5019575 DOI: 10.1002/ejic.201500470] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Indexed: 12/26/2022]
Abstract
A single polypeptide chain may provide an astronomical number of conformers. Nature selected only a trivial number of them through evolution, composing an alphabet of scaffolds, that can afford the complete set of chemical reactions needed to support life. These structural templates are so stable that they allow several mutations without disruption of the global folding, even having the ability to bind several exogenous cofactors. With this perspective, metal cofactors play a crucial role in the regulation and catalysis of several processes. Nature is able to modulate the chemistry of metals, adopting only a few ligands and slightly different geometries. Several scaffolds and metal-binding motifs are representing the focus of intense interest in the literature. This review discusses the widespread four-helix bundle fold, adopted as a scaffold for metal binding sites in the context of de novo protein design to obtain basic biochemical components for biosensing or catalysis. In particular, we describe the rational refinement of structure/function in diiron-oxo protein models from the due ferri (DF) family. The DF proteins were developed by us through an iterative process of design and rigorous characterization, which has allowed a shift from structural to functional models. The examples reported herein demonstrate the importance of the synergic application of de novo design methods as well as spectroscopic and structural characterization to optimize the catalytic performance of artificial enzymes.
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Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
- IBB, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Nastri
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - Vincenzo Pavone
- Department of Structural and Functional Biology, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco San Francisco, CA 94158, USA
| | - Angela Lombardi
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia, 80126 Naples, Italy
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40
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Vitale R, Lista L, Cerrone C, Caserta G, Chino M, Maglio O, Nastri F, Pavone V, Lombardi A. An artificial heme-enzyme with enhanced catalytic activity: evolution, functional screening and structural characterization. Org Biomol Chem 2015; 13:4859-68. [DOI: 10.1039/c5ob00257e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The rational refinement of function into the heme-protein model Mimochrome VI (MC6) resulted in a new analogue, FeIII-E2L(TD)-MC6, with an improved peroxidase activity.
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Affiliation(s)
- Rosa Vitale
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | - Liliana Lista
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | - Corinne Cerrone
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | | | - Marco Chino
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | - Ornella Maglio
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
- IBB
| | - Flavia Nastri
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
| | - Vincenzo Pavone
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
- IMAST Scarl
| | - Angela Lombardi
- Department of Chemical Sciences
- University of Naples “Federico II”
- 80126 Naples
- Italy
- IMAST Scarl
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Sato S, Kitamura H, Chino M, Takei Y, Hiruma M, Nomura M. A 13-week oral dose subchronic toxicity study of gardenia yellow containing geniposide in rats. Food Chem Toxicol 2007; 45:1537-44. [PMID: 17524542 DOI: 10.1016/j.fct.2007.02.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Revised: 01/30/2007] [Accepted: 02/13/2007] [Indexed: 12/24/2022]
Abstract
Gardenia yellow powders A, B and C, containing geniposide at 0.284%, 0.938% and 2.783%, respectively, were administered orally to male and female SD rats as 3% feed admixtures for 13-weeks to evaluate any potential toxicity. Mean geniposide intake values were 5.72, 18.9 and 56.3mg/kg/day in groups receiving these feed admixtures, respectively. All animals survived the duration of the study. The following findings were evident in the gardenia yellow C group: chromatouria, slightly increased plasma total bilirubin, blackish brown discoloration of the kidneys and liver, brown pigments in the proximal tubular epithelium of the kidneys. Slightly increased plasma total bilirubin was considered to be due to interference of metabolite of geniposide with the system of measurement and not to be a toxic effect since there were no related changes in histopathology of the liver or in any blood chemistry parameters. Other findings were limited to pigmentations or discolorations attributable to metabolites of geniposide. No treatment-related effects were evident on body weight, food consumption, ophthalmology, hematology or organ weights in any group. Therefore, it was concluded that 3-month ingestion of the gardenia yellow powder containing geniposide at 2.783% (approximately 60 mg/kg/day as geniposide intake) does not cause any severe toxic effects.
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Affiliation(s)
- S Sato
- Ina Research Inc., 2148-188, Nishiminowa, Ina, Nagano 399-4501, Japan.
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42
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Ngang E, Matsufuji H, Chino M, Goda Y, Toyoda M, Takeda M. Structural determination of subsidiary colors in commercial Food Green No. 3 (fast green FCF, FD & C Green No. 3). Shokuhin Eiseigaku Zasshi 2001; 42:298-303. [PMID: 11775354 DOI: 10.3358/shokueishi.42.298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
HPLC analysis revealed that eight subsidiary colors existed in commercial Food Green No. 3 (fast green FCF, FD & C Green No. 3). Among them, four subsidiary colors C, F, G, and H were isolated by using preparative HPLC and their structures were determined by MS and NMR. They were the disodium salt of 2-[[4-[N-ethyl-N-(3- sulfophenylmethyl)amino]phenyl][4-[N-ethyl-N-(4- sulfophenylmethyl)amino]phenyl]methylio]-4-hydroxybenzenesulfonic acid (abbreviated as m,p-G-3), the sodium salt of 2-[[(4-N-ethylamino)phenyl][4-[N-ethyl-N-(3- sulfophenylmethyl)amino]-phenyl]methylio]-4-hydroxybenzenesulfonic acid [abbreviated as HSBA-(EA) (m-EBASA)], the sodium salt of 2-[[(4-N-diethylamino)phenyl][4-[N-ethyl-N-(3- sulfophenylmethyl)amino]phenyl]-methylio]-4-hydroxybenzenesulfonic acid [abbreviated as HSBA-(di-EA) (m-EBASA)], and the sodium salt of 2-[[4-[N-ethyl-N-(phenylmethyl)amino]phenyl][4-[N-ethyl-N-(3- sulfophenylmethyl)-amino]phenyl]methylio]-4-hydroxybenzenesulfonic acid [abbreviated as HSBA-(EBA)(m-EBASA)], respectively. HSBA-(di-EA) (m-EBASA) was a subsidiary color newly found in commercial Food Green No. 3.
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Affiliation(s)
- E Ngang
- College of Bioresource Sciences, Nihon University: 1866, Kameino, Fujisawa, Kanagawa, 252-8510, Japan
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Baba A, Yoshikawa T, Chino M, Murayama A, Mitani K, Nakagawa S, Fujii I, Shimada M, Akaishi M, Iwanaga S, Asakura Y, Fukuda K, Mitamura H, Ogawa S. Characterization of anti-myocardial autoantibodies in Japanese patients with dilated cardiomyopathy. Jpn Circ J 2001; 65:867-73. [PMID: 11665790 DOI: 10.1253/jcj.65.867] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Few previous reports have comprehensively screened all the anti-myocardial autoantibodies (AMCA) in relation to other clinical profiles in patients with idiopathic dilated cardiomyopathy (IDC), so the present study used both immunohistochemistry (FITC) and immunoblotting (IB) for screening patients with IDC in order to characterize the clinical significance of AMCA. Sera were collected from 100 patients with IDC and age-matched 100 healthy control subjects (CTL). For FITC, an unfixed frozen section of human myocardium was used for the standard indirect immunofluorescence; for IB, total cardiac homogenates of the same myocardium were blotted to serum at 2 sets of dilution (1:200 and 1:10,000). The positive rates of AMCA detection for each method were as follows (IDC vs CTL); 39% vs 6% for FITC, 38% vs 4% for IB (1:200), and 10% vs 0% for IB (1:10,000). Fifty-nine patients with IDC and 8 CTL were positive for AMCA by either method, and 18 patients with IDC and 2 CTL were positive for AMCA by both methods. IB-positivity at 1:200 was an independent predictor by multiple logistic regression analysis of non-sustained ventricular tachycardias as well as left ventricular end-diastolic diameter and plasma norepinephrine concentration.
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Affiliation(s)
- A Baba
- Department of Medicine, Kitasato Institute Hospital, Tokyo, Japan.
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Oikawa T, Tsukagawa Y, Chino M, Soda K. Increased transglycosylation activity of Rhodotorula glutinis endo-beta-glucanase in media containing organic solvent. Biosci Biotechnol Biochem 2001; 65:1889-92. [PMID: 11577737 DOI: 10.1271/bbb.65.1889] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [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: 11/08/2022]
Abstract
The transglycosylation of p-nitrophenyl-beta-D-cellotrioside to cellotetraose catalyzed by endo-1,4-beta-glucanase (cellulase, EC 3.2.1.4) from a psychrotrophic yeast, Rhodotorula glutinis KUJ 2731, was increased by addition of a miscible organic solvent in the reaction mixture. Among various organic solvents tested, acetone was most effective. The transglycosylation activity increased with an increase in acetone concentrations, while hydrolysis activity was suppressed. The transglycosylation preferably occurred at acidic pH with the optimum pH at 2 in 10 mM Gly-HCl buffer. The optimum temperature of transglycosylation was found to be 50 degrees C in the presence of 40% acetone.
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Affiliation(s)
- T Oikawa
- Department of Biotechnology, Faculty of Engineering, Kansai University, Osaka, Japan
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DeBruyn L, Chino M, Serna P, Fullerton-Gleason L. Child maltreatment in American Indian and Alaska Native communities: integrating culture, history, and public health for intervention and prevention. Child Maltreat 2001; 6:89-102. [PMID: 16705785 DOI: 10.1177/1077559501006002002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
This article addresses child maltreatment intervention and prevention among American Indians and Alaska Natives. The authors argue that history and culture must be included as context and variables for developing and implementing prevention programs in Indian Country. They propose that the public health violence prevention model would benefit from incorporating tenets of the history and culture(s) of diverse groups, in this instance American Indians and Alaska Natives. The authors offer an approach that focuses on population- and individual-level risk and protective factors for child maltreatment intervention and prevention in American Indian/Alaska Native communities. They include suggestions and examples for doing the work in Indian Country.
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Affiliation(s)
- L DeBruyn
- Division of Violence Prevention, National Center for Injury Prevention and Control, Centers for Disease Control and Prevention, USA
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46
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Chino M. [Cost analysis of procedural fee for percutaneous transluminal coronary angioplasty at six Japanese hospitals]. J Cardiol 2001; 37:83-90. [PMID: 11255699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
BACKGROUND Disease-specific cost analysis is rarely performed in Japan, but is essential for reform of the healthcare reimbursement system and assessment of procedural fees. METHODS The actual cost associated with the procedural fee of the percutaneous transluminal coronary angioplasty (PTCA) procedure was estimated by dividing into four categories: labor, disposable materials, expenses, and equipment costs. The special cost associated with PTCA devices such as angioplasty balloon and stent was responsible for the majority of PTCA-related hospitalization costs, but was not included in our survey. The six institutions that participated in the survey belong to the national, Red Cross, and Saiseikai organizations. Time study for labor was omitted, and procedural time was predetermined at 3 hours. RESULTS The labor cost amounted to yen 65,000 to yen 98,000/procedure. To calculate the cost of disposable materials across all six hospitals, a universal amount of yen 60,000 from a model hospital was used. The expenses ranged from yen 1,000 to yen 39,000, and the expenditure plus capital cost from yen 95,000 to yen 224,000, showing significant differences between the hospitals. The total mean cost was yen 294,000 +/- 55,000, which indicated that every hospital was in deficit. CONCLUSIONS Compared to Medicare in the United States of America, the procedural fee for Japanese physicians is extremely low, in contrast to the bloated special cost for devices, which causes significant pricing gaps between Japan and USA. The differences in total cost among the hospitals were mainly derived from the cost for angiographic equipment. Our survey did not include any private hospitals, but the PTCA-related procedural fee is less than the actual cost under the current health insurance reimbursement scheme at all hospitals.
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Affiliation(s)
- M Chino
- Department of Cardiology, National Tokyo Medical Center, Tokyo
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Mares P, Chino M, Kubová H, Mathern P, Veliký M. Convulsant action of systemically administered glutamate and bicuculline methiodide in immature rats. Epilepsy Res 2000. [PMID: 11074190 DOI: 10.1016/s0920-121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
Developmental changes of transport of drugs into the brain play an important role in ontogenetic neuropharmacology. Two convulsant drugs with different mechanisms of action (glutamate and bicuculline methiodide) were chosen to demonstrate these changes in developing rats. High dose of glutamate (4 g/kg i.p.) induced both minimal (predominantly clonic) and generalized tonic-clonic seizures in rat pups 7, 12, and 18 days old. In contrast, seizures were only exceptionally observed in 25 and 90 days old animals. Bicuculline methiodide was administered in a dose of 2 or 20 mg/kg i.p. The first sign of bicuculline methiodide action in all age groups was represented by automatisms, a symptomatology never seen after bicuculline hydrochloride administration. Minimal seizures were induced in 12-day-old and in a few 18-day-old and adult rats. Generalized seizures were common after the higher dose of bicuculline methiodide in 7- and 12-day-old rat pups, seldom in 18-day-old ones and never seen in 25-day-old and adult animals. Both glutamate and bicuculline methiodide enter the brain in immature rats but the mechanisms are probably different - glutamate is transported actively through the blood-brain barrier whereas no similar system is known for bicuculline methiodide.
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Affiliation(s)
- P Mares
- Institute of Physiology, Academy of Sciences of the Czech Republic, Vídenská 1083, CZ 142 20 4, Prague, Czech Republic.
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Abstract
Developmental changes of transport of drugs into the brain play an important role in ontogenetic neuropharmacology. Two convulsant drugs with different mechanisms of action (glutamate and bicuculline methiodide) were chosen to demonstrate these changes in developing rats. High dose of glutamate (4 g/kg i.p.) induced both minimal (predominantly clonic) and generalized tonic-clonic seizures in rat pups 7, 12, and 18 days old. In contrast, seizures were only exceptionally observed in 25 and 90 days old animals. Bicuculline methiodide was administered in a dose of 2 or 20 mg/kg i.p. The first sign of bicuculline methiodide action in all age groups was represented by automatisms, a symptomatology never seen after bicuculline hydrochloride administration. Minimal seizures were induced in 12-day-old and in a few 18-day-old and adult rats. Generalized seizures were common after the higher dose of bicuculline methiodide in 7- and 12-day-old rat pups, seldom in 18-day-old ones and never seen in 25-day-old and adult animals. Both glutamate and bicuculline methiodide enter the brain in immature rats but the mechanisms are probably different - glutamate is transported actively through the blood-brain barrier whereas no similar system is known for bicuculline methiodide.
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Affiliation(s)
- P Mares
- Institute of Physiology, Academy of Sciences of the Czech Republic, Vídenská 1083, CZ 142 20 4, Prague, Czech Republic.
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Affiliation(s)
- K Okubo
- National Tokyo Medical Center, Department of Cardiology, Japan
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Awazuhara M, Nakagawa A, Yamaguchi J, Fujiwara T, Hayashi H, Hatae K, Chino M, Shimada A. Distribution and characterization of enzymes causing starch degradation in rice (Oryza sativa cv. koshihikari). J Agric Food Chem 2000; 48:245-252. [PMID: 10691623 DOI: 10.1021/jf990408j] [Citation(s) in RCA: 24] [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] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The thermal dependency and stability of enzymes producing reducing sugar (RS) were examined in bran, the exterior 13% part (outer endosperm), and the remaining inner endosperm of rice grains. RS-producing enzymes in the inner endosperm showed a higher optimum temperature than those in other parts of the rice grain. Diethylaminoethyl-Sephacel chromatography of crude extracts revealed two peaks of RS-producing activity with different optimum temperatures (60 and 37 degrees C) in all three parts. alpha-Glucosidase (EC 3.2.1.20) and alpha-amylase (EC 3.2.1.1) isoform G were thought to be major components of the RS-producing activities with high and low optimum temperatures, respectively. The peak with a high optimum temperature was a more abundant component in the inner endosperm, compared with other parts of the rice grain. Thus, different parts of rice were found to have distinct enzyme sets having different thermal dependency and to be involved in starch degradation to various sugars.
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Affiliation(s)
- M Awazuhara
- Laboratory of Plant Nutrition and Fertilizer, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 113-8657, Japan.
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