1
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Rocha G, Ramírez-Cárdenas J, Padilla-Pérez MC, Walpole S, Nepravishta R, García-Moreno MI, Sánchez-Fernández EM, Ortiz Mellet C, Angulo J, Muñoz-García JC. Speeding-up the Determination of Protein-Ligand Affinities by STD NMR: The Reduced Data Set STD NMR Approach (rd-STD NMR). Anal Chem 2024; 96:615-619. [PMID: 38165272 PMCID: PMC10853903 DOI: 10.1021/acs.analchem.3c03980] [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: 09/04/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
STD NMR spectroscopy is a powerful ligand-observed NMR tool for screening and characterizing the interactions of small molecules and low molecular weight fragments with a given macromolecule, identifying the main intermolecular contacts in the bound state. It is also a powerful analytical technique for the accurate determination of protein-ligand dissociation constants (KD) of medium-to-weak affinity, of interest in the pharmaceutical industry. However, accurate KD determination and epitope mapping requires a long series of experiments at increasing saturation times to carry out a full analysis using the so-called STD NMR build-up curve approach and apply the "initial slopes approximation". Here, we have developed a new protocol to bypass this important limitation, which allows us to obtain initial slopes by using just two saturation times and, hence, to very quickly determine precise protein-ligand dissociation constants by STD NMR.
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Affiliation(s)
- Gabriel Rocha
- Institute
for Chemical Research (IIQ), CSIC—University
of Seville, 49 Américo Vespucio St, 41092 Seville, Spain
| | - Jonathan Ramírez-Cárdenas
- Institute
for Chemical Research (IIQ), CSIC—University
of Seville, 49 Américo Vespucio St, 41092 Seville, Spain
| | - M. Carmen Padilla-Pérez
- Department
of Organic Chemistry, Faculty of Chemistry, University of Seville, 1 Prof. García González St, 41012 Seville, Spain
| | - Samuel Walpole
- School
of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
| | - Ridvan Nepravishta
- School
of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
- Cancer
Research Horizons, The Beatson Institute, Garscube Estate, Switchback Road,
Bearsden, Glasgow G61 1BD, United Kingdom
| | - M. Isabel García-Moreno
- Department
of Organic Chemistry, Faculty of Chemistry, University of Seville, 1 Prof. García González St, 41012 Seville, Spain
| | - Elena M. Sánchez-Fernández
- Department
of Organic Chemistry, Faculty of Chemistry, University of Seville, 1 Prof. García González St, 41012 Seville, Spain
| | - Carmen Ortiz Mellet
- Department
of Organic Chemistry, Faculty of Chemistry, University of Seville, 1 Prof. García González St, 41012 Seville, Spain
| | - Jesús Angulo
- Institute
for Chemical Research (IIQ), CSIC—University
of Seville, 49 Américo Vespucio St, 41092 Seville, Spain
- School
of Pharmacy, University of East Anglia, Norwich Research Park, NR4 7TJ Norwich, United Kingdom
| | - Juan C. Muñoz-García
- Institute
for Chemical Research (IIQ), CSIC—University
of Seville, 49 Américo Vespucio St, 41092 Seville, Spain
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2
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Matteucci C, Nepravishta R, Argaw-Denboba A, Mandaliti W, Giovinazzo A, Petrone V, Balestrieri E, Sinibaldi-Vallebona P, Pica F, Paci M, Garaci E. Thymosin α1 interacts with Galectin-1 modulating the β-galactosides affinity and inducing alteration in the biological activity. Int Immunopharmacol 2023; 118:110113. [PMID: 37028279 DOI: 10.1016/j.intimp.2023.110113] [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: 01/31/2023] [Revised: 03/17/2023] [Accepted: 03/18/2023] [Indexed: 04/09/2023]
Abstract
The study of mechanism of action of Thymosin alpha 1 (Tα1) and the basis of the pleiotropic effect in health and disease, is one of the main focus of our ongoing research. Tα1 is a thymic peptide that demonstrates a peculiar ability to restore homeostasis in different physiological and pathological conditions (i.e., infections, cancer, immunodeficiency, vaccination, and aging) acting as multitasking protein depending on the host state of inflammation or immune dysfunction. However, few are the information about mechanisms of action mediated by specific Tα1-target protein interaction that could explain its pleiotropic effect. We investigated the interaction of Tα1 with Galectin-1 (Gal-1), a protein belonging to an oligosaccharide binding protein family involved in a variety of biological and pathological processes, including immunoregulation, infections, cancer progression and aggressiveness. Using molecular and cellular methodological approaches, we demonstrated the interaction between these two proteins. Tα1 specifically inhibited the hemagglutination activity of Gal-1, the Gal-1 dependent in vitro formation of endothelial cell tubular structures, and the migration of cancer cells in wound healing assay. Physico-chemical methods revealed the details of the molecular interaction of Tα1 with Gal-1. Hence, the study allowed the identification of the not known until now specific interaction between Tα1 and Gal-1, and unraveled a novel mechanism of action of Tα1 that could support understanding of its pleiotropic activity.
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Affiliation(s)
- Claudia Matteucci
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy.
| | - Ridvan Nepravishta
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", Rome 00133, Italy
| | - Ayele Argaw-Denboba
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy; European Molecular Biology Laboratory, EMBL, Monterotondo, Rome 00015, Italy
| | - Walter Mandaliti
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", Rome 00133, Italy
| | - Alessandro Giovinazzo
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy; Institute of Biochemistry and Cell Biology, IBBC-CNR, Monterotondo, Rome 00015, Italy
| | - Vita Petrone
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy; Institute of Translational Pharmacology, National Research Council, Rome 00133, Italy
| | - Francesca Pica
- Department of Experimental Medicine, University of Tor Vergata, Rome 00133, Italy
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", Rome 00133, Italy
| | - Enrico Garaci
- IRCCS San Raffaele and IRCCS San Raffaele, Rome 00163, Italy; Medical and Experimental BioImaging Center, MEBIC Consortium, Rome 00166, Italy
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3
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Nepravishta R, Monaco S, Distefano M, Rizzo R, Cescutti P, Angulo J. Multifrequency STD NMR Unveils the Interactions of Antibiotics With Burkholderia multivorans Biofilm Exopolysaccharide. Front Mol Biosci 2021; 8:727980. [PMID: 34604306 PMCID: PMC8481691 DOI: 10.3389/fmolb.2021.727980] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
Biofilms confine bacterial cells within self-produced matrices, offering advantages such as protection from antibiotics and entrapment of nutrients. Polysaccharides are major components in these macromolecular assemblies, and their interactions with other chemicals are of high relevance for the benefits provided by the biofilm 3D molecular matrix. NMR is a powerful technique for the study and characterization of the interactions between molecules of biological relevance. In this study, we have applied multifrequency saturation transfer difference (STD) NMR and DOSY NMR approaches to elucidate the interactions between the exopolysaccharide produced by Burkholderia multivorans C1576 (EpolC1576) and the antibiotics kanamycin and ceftadizime. The NMR strategies presented here allowed for an extensive characterization at an atomic level of the mechanisms behind the implication of the EpolC1576 in the recalcitrance phenomena, which is the ability of bacteria in biofilms to survive in the presence of antibiotics. Our results suggest an active role for EpolC1576 in the recalcitrance mechanisms toward kanamycin and ceftadizime, though through two different mechanisms.
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Affiliation(s)
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich, United Kingdom
| | - Marco Distefano
- Department Life Sciences, University of Trieste, Trieste, Italy
| | - Roberto Rizzo
- Department Life Sciences, University of Trieste, Trieste, Italy
| | - Paola Cescutti
- Department Life Sciences, University of Trieste, Trieste, Italy
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich, United Kingdom.,Department of Organic Chemistry, Faculty of Chemistry, University of Seville, Seville, Spain.,Instituto de Investigaciones Químicas (CSIC-US), Seville, Spain
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4
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Gabrielli V, Kuraite A, da Silva MA, Edler KJ, Angulo J, Nepravishta R, Muñoz-García JC, Khimyak YZ. Spin diffusion transfer difference (SDTD) NMR: An advanced method for the characterisation of water structuration within particle networks. J Colloid Interface Sci 2021; 594:217-227. [PMID: 33756365 DOI: 10.1016/j.jcis.2021.02.094] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/13/2021] [Accepted: 02/23/2021] [Indexed: 11/26/2022]
Abstract
HYPOTHESIS The classical STD NMR protocol to monitor solvent interactions in gels is strongly dependent on gelator and solvent concentrations and does not report on the degree of structuration of the solvent at the particle/solvent interface. We hypothesised that, for suspensions of large gelator particles, solvent structuration could be characterised by STD NMR when taking into account the particle-to-solvent 1H-1H spin diffusion transfer using the 1D diffusion equation. EXPERIMENTS We have carried out a systematic study on effect of gelator and solvent concentrations, and gelator surface charge, affecting the behaviour of the classical STD NMR build-up curves. To do so, we have characterised solvent interactions in dispersions of starch and cellulose-like particles prepared in deuterated water and alcohol/D2O mixtures. FINDINGS The Spin Diffusion Transfer Difference (SDTD) NMR protocol is independent of the gelator and solvent concentrations, hence allowing the estimation of the degree of solvent structuration within different particle networks. In addition, the simulation of SDTD build-up curves using the general one-dimensional diffusion equation allows the determination of minimum distances (r) and spin diffusion rates (D) at the particle/solvent interface. This novel NMR protocol can be readily extended to characterise the solvent(s) organisation in any type of colloidal systems constituted by large particles.
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Affiliation(s)
- Valeria Gabrielli
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Agne Kuraite
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | | | - Karen J Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Juan C Muñoz-García
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
| | - Yaroslav Z Khimyak
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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5
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Guzzo T, Barile F, Marras C, Bellini D, Mandaliti W, Nepravishta R, Paci M, Topai A. Stability Evaluation and Degradation Studies of DAC ® Hyaluronic-Polylactide Based Hydrogel by DOSY NMR Spectroscopy. Biomolecules 2020; 10:E1478. [PMID: 33114342 PMCID: PMC7690892 DOI: 10.3390/biom10111478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/30/2022] Open
Abstract
The stability and the degradation of polymers in physiological conditions are very important issues in biomedical applications. The copolymer of hyaluronic acid and poly-D,L-lactic acid (made available in a product called DAC®) produces a hydrogel which retains the hydrophobic character of the poly-D,L-lactide sidechains and the hydrophilic character of a hyaluronic acid backbone. This hydrogel is a suitable device for the coating of orthopedic implants with structured surfaces. In fact, this gel creates a temporary barrier to bacterial adhesion by inhibiting colonization, thus preventing the formation of the biofilm and the onset of an infection. Reabsorbed in about 72 h after the implant, this hydrogel does not hinder bone growth processes. In the need to assess stability and degradation of both the hyaluronan backbone and of the polylactic chains along time and temperature, we identified NMR spectroscopy as a privileged technique for the characterization of the released species, and we applied diffusion-ordered NMR spectroscopy (DOSY-NMR) for the investigation of molecular weight dispersion. Our diffusion studies of DAC® in physiological conditions provided a full understanding of the product degradation by overcoming the limitations observed in applying classical chromatography approaches by gel permeation UV.
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Affiliation(s)
- Tatiana Guzzo
- Colosseum Combinatorial Chemistry Centre for Technology S.r.l (C4T), Via della Ricerca Scientifica snc, 00133 Rome, Italy; (T.G.); (F.B.); (C.M.)
| | - Fabio Barile
- Colosseum Combinatorial Chemistry Centre for Technology S.r.l (C4T), Via della Ricerca Scientifica snc, 00133 Rome, Italy; (T.G.); (F.B.); (C.M.)
| | - Cecilia Marras
- Colosseum Combinatorial Chemistry Centre for Technology S.r.l (C4T), Via della Ricerca Scientifica snc, 00133 Rome, Italy; (T.G.); (F.B.); (C.M.)
| | | | - Walter Mandaliti
- Department of Chemical Science and Technology, University of Rome, Tor Vergata, 00133 Rome, Italy; (W.M.); (R.N.); (M.P.)
| | - Ridvan Nepravishta
- Department of Chemical Science and Technology, University of Rome, Tor Vergata, 00133 Rome, Italy; (W.M.); (R.N.); (M.P.)
| | - Maurizio Paci
- Department of Chemical Science and Technology, University of Rome, Tor Vergata, 00133 Rome, Italy; (W.M.); (R.N.); (M.P.)
| | - Alessandra Topai
- Colosseum Combinatorial Chemistry Centre for Technology S.r.l (C4T), Via della Ricerca Scientifica snc, 00133 Rome, Italy; (T.G.); (F.B.); (C.M.)
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6
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Nepravishta R, Pletka CC, Iwahara J. Racemic phosphorothioate as a tool for NMR investigations of protein-DNA complexes. J Biomol NMR 2020; 74:421-429. [PMID: 32683519 PMCID: PMC7511421 DOI: 10.1007/s10858-020-00333-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/09/2020] [Indexed: 05/05/2023]
Abstract
A major driving force for protein-nucleic acid association is electrostatic interactions via ion pairs of the positively charged basic side chains and negatively charged phosphates. For a better understanding of how proteins scan DNA and recognize particular signatures, it is important to gain atomic-level insight into the behavior of basic side chains at the protein-DNA interfaces. NMR spectroscopy is a powerful tool for investigating the structural, dynamic, and kinetic aspects of protein-DNA interactions. However, resonance assignment of basic side-chain cationic moieties at the molecular interfaces remains to be a major challenge. Here, we propose a fast, robust, and inexpensive approach that greatly facilitates resonance assignment of interfacial moieties and also allows for kinetic measurements of protein translocation between two DNA duplexes. This approach utilizes site-specific incorporation of racemic phosphorothioate at the position of a phosphate that interacts with a protein side chain. This modification retains the electric charge of phosphate and therefore is mild, but causes significant chemical shift perturbations for the proximal protein side chains, which facilitates resonance assignment. Due to the racemic nature of the modification, two different chemical shifts are observed for the species with different diastereomers RP and SP of the incorporated phosphorothioate group. Kinetic information on the exchange of the protein molecule between RP and SP DNA duplexes can be obtained by 15Nz exchange spectroscopy. We demonstrate the applications of this approach to the Antennapedia homeodomain-DNA complex and the CREB1 basic leucine-zipper (bZIP)-DNA complex.
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Affiliation(s)
- Ridvan Nepravishta
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-1068, USA
| | - Channing C Pletka
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, 77555-1068, USA.
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7
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Monaco S, Walpole S, Doukani H, Nepravishta R, Martínez‐Bailén M, Carmona AT, Ramos‐Soriano J, Bergström M, Robina I, Angulo J. Exploring Multi-Subsite Binding Pockets in Proteins: DEEP-STD NMR Fingerprinting and Molecular Dynamics Unveil a Cryptic Subsite at the GM1 Binding Pocket of Cholera Toxin B. Chemistry 2020; 26:10024-10034. [PMID: 32449563 PMCID: PMC7496166 DOI: 10.1002/chem.202001723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/08/2020] [Revised: 05/08/2020] [Indexed: 11/30/2022]
Abstract
Ligand-based NMR techniques to study protein-ligand interactions are potent tools in drug design. Saturation transfer difference (STD) NMR spectroscopy stands out as one of the most versatile techniques, allowing screening of fragments libraries and providing structural information on binding modes. Recently, it has been shown that a multi-frequency STD NMR approach, differential epitope mapping (DEEP)-STD NMR, can provide additional information on the orientation of small ligands within the binding pocket. Here, the approach is extended to a so-called DEEP-STD NMR fingerprinting technique to explore the binding subsites of cholera toxin subunit B (CTB). To that aim, the synthesis of a set of new ligands is presented, which have been subject to a thorough study of their interactions with CTB by weak affinity chromatography (WAC) and NMR spectroscopy. Remarkably, the combination of DEEP-STD NMR fingerprinting and Hamiltonian replica exchange molecular dynamics has proved to be an excellent approach to explore the geometry, flexibility, and ligand occupancy of multi-subsite binding pockets. In the particular case of CTB, it allowed the existence of a hitherto unknown binding subsite adjacent to the GM1 binding pocket to be revealed, paving the way to the design of novel leads for inhibition of this relevant toxin.
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Affiliation(s)
- Serena Monaco
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Samuel Walpole
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Hassan Doukani
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
| | - Ridvan Nepravishta
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
- Department of Biochemistry & Molecular BiologySealy Center for Structural Biology & Molecular BiophysicsUniversity of Texas Medical Branch301 University BlvdGalvestonTX77555-1068USA
| | | | - Ana T. Carmona
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Javier Ramos‐Soriano
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Maria Bergström
- Department of Chemistry and Biomedical SciencesLinnaeus University391 82KalmarSweden
| | - Inmaculada Robina
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
| | - Jesus Angulo
- School of PharmacyUniversity of East AngliaNorwich Research ParkNR4 7TJNorwichUK
- Department of Organic ChemistryFaculty of ChemistryUniversity of Seville41012SevilleSpain
- Instituto de Investigaciones Químicas (CSIC-US)Avda. Américo Vespucio, 4941092SevillaSpain
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8
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Montis C, Joseph P, Magnani C, Marín-Menéndez A, Barbero F, Estrada AR, Nepravishta R, Angulo J, Checcucci A, Mengoni A, Morris CJ, Berti D. Multifunctional nanoassemblies target bacterial lipopolysaccharides for enhanced antimicrobial DNA delivery. Colloids Surf B Biointerfaces 2020; 195:111266. [PMID: 32739771 DOI: 10.1016/j.colsurfb.2020.111266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/07/2020] [Revised: 06/10/2020] [Accepted: 07/19/2020] [Indexed: 10/23/2022]
Abstract
The development of new therapeutic strategies against multidrug resistant Gram-negative bacteria is a major challenge for pharmaceutical research. In this respect, it is increasingly recognized that an efficient treatment for resistant bacterial infections should combine antimicrobial and anti-inflammatory effects. Here, we explore the multifunctional therapeutic potential of nanostructured self-assemblies from a cationic bolaamphiphile, which target bacterial lipopolysaccharides (LPSs) and associates with an anti-bacterial nucleic acid to form nanoplexes with therapeutic efficacy against Gram-negative bacteria. To understand the mechanistic details of these multifunctional antimicrobial-anti-inflammatory properties, we performed a fundamental study, comparing the interaction of these nanostructured therapeutics with synthetic biomimetic bacterial membranes and live bacterial cells. Combining a wide range of experimental techniques (Confocal Microscopy, Fluorescence Correlation Spectroscopy, Microfluidics, NMR, LPS binding assays), we demonstrate that the LPS targeting capacity of the bolaamphiphile self-assemblies, comparable to that exerted by Polymixin B, is a key feature of these nanoplexes and one that permits entry of therapeutic nucleic acids in Gram-negative bacteria. These findings enable a new approach to the design of efficient multifunctional therapeutics with combined antimicrobial and anti-inflammatory effects and have therefore the potential to broadly impact fundamental and applied research on self-assembled nano-sized antibacterials for antibiotic resistant infections.
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Affiliation(s)
- Costanza Montis
- Department of Chemistry and CSGI, University of Florence, Florence, Italy
| | - Pierre Joseph
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Chiara Magnani
- Department of Chemistry and CSGI, University of Florence, Florence, Italy
| | | | | | | | | | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - Alice Checcucci
- Department of Biology, University of Florence, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | | | - Debora Berti
- Department of Chemistry and CSGI, University of Florence, Florence, Italy.
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9
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Nepravishta R, Yu B, Iwahara J. Hydrogen-exchange kinetics studied through analysis of self-decoupling of nuclear magnetic resonance. J Magn Reson 2020; 312:106687. [PMID: 31982802 PMCID: PMC7067644 DOI: 10.1016/j.jmr.2020.106687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
Hydrogen exchange between solute and water molecules occurs across a wide range of timescales. Rapid hydrogen-exchange processes can effectively diminish 1H-15N scalar couplings. We demonstrate that the self-decoupling of 15N nuclear magnetic resonance can allow quantitative investigations of hydrogen exchange on a micro- to millisecond timescale, which is relatively difficult to analyze with other methods. Using a Liouvillian matrix incorporating hydrogen exchange as a mechanism for scalar relaxation, the hydrogen exchange rate can be determined from 15N NMR line shapes recorded with and without 1H decoupling. Self-decoupling offers a simple approach to analyze the kinetics of hydrogen exchange in a wide range of timescale.
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Affiliation(s)
- Ridvan Nepravishta
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Binhan Yu
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA.
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10
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Affiliation(s)
- Channing C. Pletka
- Department of Biochemistry & Molecular Biology Sealy Center for Structural Biology & Molecular Biophysics University of Texas Medical Branch 301 University Blvd Galveston TX 77555-1068 USA
| | - Ridvan Nepravishta
- Department of Biochemistry & Molecular Biology Sealy Center for Structural Biology & Molecular Biophysics University of Texas Medical Branch 301 University Blvd Galveston TX 77555-1068 USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology Sealy Center for Structural Biology & Molecular Biophysics University of Texas Medical Branch 301 University Blvd Galveston TX 77555-1068 USA
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11
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Abstract
Due to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so-called "ion atmosphere". Although the release of counterions upon DNA-protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA-protein association. NMR-based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA-protein association.
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Affiliation(s)
- Channing C Pletka
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1068, USA
| | - Ridvan Nepravishta
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX, 77555-1068, USA
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12
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Fenn J, Nepravishta R, Guy CS, Harrison J, Angulo J, Cameron AD, Fullam E. Structural Basis of Glycerophosphodiester Recognition by the Mycobacterium tuberculosis Substrate-Binding Protein UgpB. ACS Chem Biol 2019; 14:1879-1887. [PMID: 31433162 PMCID: PMC6757277 DOI: 10.1021/acschembio.9b00204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/07/2019] [Indexed: 11/28/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB) and has evolved an incredible ability to survive latently within the human host for decades. The Mtb pathogen encodes for a low number of ATP-binding cassette (ABC) importers for the acquisition of carbohydrates that may reflect the nutrient poor environment within the host macrophages. Mtb UgpB (Rv2833c) is the substrate binding domain of the UgpABCE transporter that recognizes glycerophosphocholine (GPC), indicating that this transporter has a role in recycling glycerophospholipid metabolites. By using a combination of saturation transfer difference (STD) NMR and X-ray crystallography, we report the structural analysis of Mtb UgpB complexed with GPC and have identified that Mtb UgpB not only recognizes GPC but is also promiscuous for a broad range of glycerophosphodiesters. Complementary biochemical analyses and site-directed mutagenesis precisely define the molecular basis and specificity of glycerophosphodiester recognition. Our results provide critical insights into the structural and functional role of the Mtb UgpB transporter and reveal that the specificity of this ABC-transporter is not limited to GPC, therefore optimizing the ability of Mtb to scavenge scarce nutrients and essential glycerophospholipid metabolites via a single transporter during intracellular infection.
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Affiliation(s)
- Jonathan
S. Fenn
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Ridvan Nepravishta
- School
of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, United Kingdom
| | - Collette S. Guy
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - James Harrison
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Jesus Angulo
- School
of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, United Kingdom
| | - Alexander D. Cameron
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
| | - Elizabeth Fullam
- School
of Life Sciences, University of Warwick, Coventry, West Midlands CV4 7AL, United Kingdom
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13
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Şenkardeş S, Tatar E, Nepravishta R, Cela D, Paci M, Özakpınar ÖB, Şekerler T, De Clercq E, Pannecouque C, Küçükgüzel ŞG, Küçükgüzel İ. Synthesis and Biological Activity of N-(arylsulfonyl) Valine Hydrazones and Assistance of NMR Spectroscopy for Definitive 3D Structure. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180810120609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Background:Hydrazide-hydrazones constitute an important class of compounds for new drug development. In this study, a series of 39 new acylhydrazones (3-41), derived from (2S)-3-methyl- 2-[[(4-methylphenyl)sulfonyl]amino]butanoic acid hydrazide were synthesized with further aim to achieve biologically active acylhydrazones carrying an amino acid side chain.Methods:Compounds 3-41 were synthesized by microwave-assisted method. All synthesized compounds have been tested for their anti-HIV activity compound 21 was subjected to a new set of 2DNMR analysis for the characterization of the isomers in solution and determination of its 3D structure.Results:The IC50 values for compounds 2-40 were found between >125-10.90 µg/ml against HIV- 1(IIIB) and HIV-2(ROD) strains in MT-4 cells. Compounds 3, 6, 10, 12, 23, 24, 27, 32, and 37 with CC50 values between 10.90-14.50 µg/ml were selected to evaluate for their antileukemia activity. IC50 values for these mentioned compounds were found as >100μM on human chronic myelogenous leukemia, K562 cell line.Conclusion:Some compounds with IC50 values between 10.90-14.50 μg/ml will be of benefit in the development of novel leads.
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Affiliation(s)
- Sevil Şenkardeş
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, Haydarpasa 34668, Istanbul, Turkey
| | - Esra Tatar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, Haydarpasa 34668, Istanbul, Turkey
| | - Ridvan Nepravishta
- Dipartimento di Scienze e Technologie Chimiche, Universita di Roma "Tor Vergata", Roma, Italy
| | - Dorisa Cela
- Dipartimento di Scienze e Technologie Chimiche, Universita di Roma "Tor Vergata", Roma, Italy
| | - Maurizio Paci
- Dipartimento di Scienze e Technologie Chimiche, Universita di Roma "Tor Vergata", Roma, Italy
| | - Özlem Bingöl Özakpınar
- Department of Biochemistry, Faculty of Pharmacy, Marmara University, Haydarpasa 34668, Istanbul, Turkey
| | - Turgut Şekerler
- Department of Biochemistry, Faculty of Pharmacy, Marmara University, Haydarpasa 34668, Istanbul, Turkey
| | - Erik De Clercq
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Ş. Güniz Küçükgüzel
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, Haydarpasa 34668, Istanbul, Turkey
| | - İlkay Küçükgüzel
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Marmara University, Haydarpasa 34668, Istanbul, Turkey
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14
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Nepravishta R, Ferrentino F, Mandaliti W, Mattioni A, Weber J, Polo S, Castagnoli L, Cesareni G, Paci M, Santonico E. CoCUN, a Novel Ubiquitin Binding Domain Identified in N4BP1. Biomolecules 2019; 9:biom9070284. [PMID: 31319543 PMCID: PMC6681339 DOI: 10.3390/biom9070284] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin binding domains (UBDs) are modular elements that bind non-covalently to ubiquitin and act as downstream effectors and amplifiers of the ubiquitination signal. With few exceptions, UBDs recognize the hydrophobic path centered on Ile44, including residues Leu8, Ile44, His68, and Val70. A variety of different orientations, which can be attributed to specific contacts between each UBD and surface residues surrounding the hydrophobic patch, specify how each class of UBD specifically contacts ubiquitin. Here, we describe the structural model of a novel ubiquitin-binding domain that we identified in NEDD4 binding protein 1 (N4BP1). By performing protein sequence analysis, mutagenesis, and nuclear magnetic resonance (NMR) spectroscopy of the 15N isotopically labeled protein, we demonstrate that a Phe-Pro motif in N4BP1 recognizes the canonical hydrophobic patch of ubiquitin. This recognition mode resembles the molecular mechanism evolved in the coupling of ubiquitin conjugation to endoplasmic-reticulum (ER) degradation (CUE) domain family, where an invariant proline, usually following a phenylalanine, is required for ubiquitin binding. Interestingly, this novel UBD, which is not evolutionary related to CUE domains, shares a 40% identity and 47% similarity with cullin binding domain associating with NEDD8 (CUBAN), a protein module that also recognizes the ubiquitin-like NEDD8. Based on these features, we dubbed the region spanning the C-terminal 50 residues of N4BP1 the CoCUN domain, for Cousin of CUBAN. By performing circular dichroism and 15N NMR chemical shift perturbation of N4BP1 in complex with ubiquitin, we demonstrate that the CoCUN domain lacks the NEDD8 binding properties observed in CUBAN. We also show that, in addition to mediating the interaction with ubiquitin and ubiquitinated substrates, both CUBAN and CoCUN are poly-ubiquitinated in cells. The structural and the functional characterization of this novel UBD can contribute to a deeper understanding of the molecular mechanisms governing N4BP1 function, providing at the same time a valuable tool for clarifying how the discrimination between ubiquitin and the highly related NEDD8 is achieved.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy East Anglia, University of Norwich, Norwich NR4 7TJ, UK
| | | | - Walter Mandaliti
- Department of Chemical Sciences and Technologies, Tor Vergata University, 00133 Rome, Italy
| | - Anna Mattioni
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy. (G.C.)
| | - Janine Weber
- IFOM, The FIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Simona Polo
- IFOM, The FIRC Institute for Molecular Oncology, 20139 Milan, Italy
| | - Luisa Castagnoli
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy. (G.C.)
| | - Gianni Cesareni
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy. (G.C.)
- DIPO, Dipartimento di Oncologia ed Emato-oncologia, Università degli Studi di Milano, 20122 Milan, Italy
- Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00143 Rome, Italy
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, Tor Vergata University, 00133 Rome, Italy
| | - Elena Santonico
- Department of Biology, University of Tor Vergata, 00133 Rome, Italy. (G.C.)
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15
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Nepravishta R, Monaco S, Muñoz-García JC, Khimyak YZ, Angulo J. Spatially Resolved STD-NMR Applied to the Study of Solute Transport in Biphasic Systems: Application to Protein-Ligand Interactions. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19849789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Fluid biphasic systems are one of the most interesting dynamic systems in chemistry and biochemistry. In nuclear magnetic resonance (NMR) spectroscopy, the study of the solute dynamics across fluid biphasic systems requires the introduction of dedicated NMR methods, due to their intrinsic heterogeneity. Diffusion and spatially resolved NMR techniques represent a useful approach for dealing with the study of solutes in biphasic systems and have been applied lately with success. Nevertheless, other potential applications of NMR spectroscopy for biphasic systems remain to be explored. In this proof-of-concept communication, we specifically aimed to investigate whether solute exchange between two immiscible phases can be followed by NMR experiments involving transfer of magnetization. To that aim, we have used spatially resolved saturation transfer difference NMR (SR-STD NMR) experiments to analyze solute exchange by transfer of saturation from one phase to the other in a biphasic system and have explored which are the underlying mechanisms leading to the transfer of magnetization between phases and the limits of the approach. We hereby demonstrate that SR-STD NMR is feasible and that it might be implemented in pharmacological screening for binders of biological receptors or in the study of chemical and biochemical reactions occurring at interfaces.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Juan C. Muñoz-García
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Yaroslav Z. Khimyak
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
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16
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Santonico E, Nepravishta R, Mandaliti W, Castagnoli L, Cesareni G, Paci M. CUBAN, a Case Study of Selective Binding: Structural Details of the Discrimination between Ubiquitin and NEDD8. Int J Mol Sci 2019; 20:ijms20051185. [PMID: 30857167 PMCID: PMC6429362 DOI: 10.3390/ijms20051185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/02/2019] [Accepted: 03/05/2019] [Indexed: 11/22/2022] Open
Abstract
The newly identified CUBAN (Cullin binding domain associating with NEDD8) domain recognizes both ubiquitin and the ubiquitin-like NEDD8. Despite the high similarity between the two molecules, CUBAN shows a clear preference for NEDD8, free and conjugated to cullins. We previously characterized the domain structure, both alone and in complex with NEDD8. The results here reported are addressed to investigate the determinants that drive the selective binding of CUBAN towards NEDD8 and ubiquitin. The 15N HSQC NMR perturbation pattern of the labeled CUBAN domain, when combined with either NEDD8 or ubiquitin, shows a clear involvement of hydrophobic residues that characterize the early stages of these interactions. After a slow conformational selection step, hydrophobic and then neutral and polar interactions take place, which drive the correct orientation of the CUBAN domain, leading to differences in the recognition scheme of NEDD8 and ubiquitin. As a result, a cascade of induced fit steps seems to determine the structural preference shown for NEDD8 and therefore the basis of the selectivity of the CUBAN domain. Finally, molecular dynamics analysis was performed to determine by fluctuations the internal flexibility of the CUBAN/NEDD8 complex. We consider that our results, based on a structural investigation mainly focused on the early stages of the recognition, provide a fruitful opportunity to report the different behavior of the same protein with two highly similar binding partners.
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Affiliation(s)
- Elena Santonico
- Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy.
| | | | - Walter Mandaliti
- Department of Chemical Science and Technologies, Tor Vergata University of Rome, 00133 Rome, Italy.
| | - Luisa Castagnoli
- Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy.
| | - Gianni Cesareni
- Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy.
- Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00179 Rome, Italy.
| | - Maurizio Paci
- Department of Chemical Science and Technologies, Tor Vergata University of Rome, 00133 Rome, Italy.
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17
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Castagnoli L, Mandaliti W, Nepravishta R, Valentini E, Mattioni A, Procopio R, Iannuccelli M, Polo S, Paci M, Cesareni G, Santonico E. Selectivity of the CUBAN domain in the recognition of ubiquitin and NEDD8. FEBS J 2019; 286:653-677. [PMID: 30659753 DOI: 10.1111/febs.14752] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 07/23/2018] [Revised: 09/25/2018] [Accepted: 12/28/2018] [Indexed: 12/27/2022]
Abstract
Among the members of the ubiquitin-like (Ubl) protein family, neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) is the closest in sequence to ubiquitin (57% identity). The two modification mechanisms and their functions, however, are highly distinct and the two Ubls are not interchangeable. A complex network of interactions between modifying enzymes and adaptors, most of which are specific while others are promiscuous, ensures selectivity. Many domains that bind the ubiquitin hydrophobic patch also bind NEDD8 while no domain that specifically binds NEDD8 has yet been described. Here, we report an unbiased selection of domains that bind ubiquitin and/or NEDD8 and we characterize their specificity/promiscuity. Many ubiquitin-binding domains bind ubiquitin preferentially and, to a lesser extent, NEDD8. In a few cases, the affinity of these domains for NEDD8 can be increased by substituting the alanine at position 72 with arginine, as in ubiquitin. We have also identified a unique domain, mapping to the carboxyl end of the protein KHNYN, which has a stark preference for NEDD8. Given its ability to bind neddylated cullins, we have named this domain CUBAN (Cullin-Binding domain Associating with NEDD8). We present here the solution structure of the CUBAN domain both in the isolated form and in complex with NEDD8. The results contribute to the understanding of the discrimination mechanism between ubiquitin and the Ubl. They also provide new insights on the biological role of a ill-defined protein, whose function is hitherto only predicted.
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Affiliation(s)
| | - Walter Mandaliti
- Department of Chemical Sciences and Technologies, Tor Vergata University, Rome, Italy
| | - Ridvan Nepravishta
- Department of Chemical Sciences and Technologies, Tor Vergata University, Rome, Italy.,School of Pharmacy East Anglia, University of Norwich, UK
| | | | - Anna Mattioni
- Department of Biology, Tor Vergata University, Rome, Italy
| | - Radha Procopio
- Department of Biology, Tor Vergata University, Rome, Italy.,Institute of Molecular Bioimaging and Physiology, CNR, Catanzaro, Italy
| | | | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.,DIPO, Dipartimento di Oncologia ed Emato-oncologia, University of Milan, Italy
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, Tor Vergata University, Rome, Italy
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18
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Latousakis D, Nepravishta R, Rejzek M, Wegmann U, Le Gall G, Kavanaugh D, Colquhoun IJ, Frese S, MacKenzie DA, Walter J, Angulo J, Field RA, Juge N. Serine-rich repeat protein adhesins from Lactobacillus reuteri display strain specific glycosylation profiles. Glycobiology 2019; 29:45-58. [PMID: 30371779 PMCID: PMC6291802 DOI: 10.1093/glycob/cwy100] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 01/24/2023] Open
Abstract
Lactobacillus reuteri is a gut symbiont inhabiting the gastrointestinal tract of numerous vertebrates. The surface-exposed serine-rich repeat protein (SRRP) is a major adhesin in Gram-positive bacteria. Using lectin and sugar nucleotide profiling of wild-type or L. reuteri isogenic mutants, MALDI-ToF-MS, LC-MS and GC-MS analyses of SRRPs, we showed that L. reuteri strains 100-23C (from rodent) and ATCC 53608 (from pig) can perform protein O-glycosylation and modify SRRP100-23 and SRRP53608 with Hex-Glc-GlcNAc and di-GlcNAc moieties, respectively. Furthermore, in vivo glycoengineering in E. coli led to glycosylation of SRRP53608 variants with α-GlcNAc and GlcNAcβ(1→6)GlcNAcα moieties. The glycosyltransferases involved in the modification of these adhesins were identified within the SecA2/Y2 accessory secretion system and their sugar nucleotide preference determined by saturation transfer difference NMR spectroscopy and differential scanning fluorimetry. Together, these findings provide novel insights into the cellular O-protein glycosylation pathways of gut commensal bacteria and potential routes for glycoengineering applications.
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Affiliation(s)
- Dimitrios Latousakis
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Udo Wegmann
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Gwenaelle Le Gall
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Devon Kavanaugh
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Ian J Colquhoun
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Donald A MacKenzie
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Nathalie Juge
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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19
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Nepravishta R, Walpole S, Tailford L, Juge N, Angulo J. Deriving Ligand Orientation in Weak Protein-Ligand Complexes by DEEP-STD NMR Spectroscopy in the Absence of Protein Chemical-Shift Assignment. Chembiochem 2018; 20:340-344. [PMID: 30379391 PMCID: PMC6468252 DOI: 10.1002/cbic.201800568] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 01/07/2023]
Abstract
Differential epitope mapping saturation transfer difference (DEEP‐STD) NMR spectroscopy is a recently developed powerful approach for elucidating the structure and pharmacophore of weak protein–ligand interactions, as it reports key information on the orientation of the ligand and the architecture of the binding pocket.1 The method relies on selective saturation of protein residues in the binding site and the generation of a differential epitope map by observing the ligand, which depicts the nature of the protein residues making contact with the ligand in the bound state. Selective saturation requires knowledge of the chemical‐shift assignment of the protein residues, which can be obtained either experimentally by NMR spectroscopy or predicted from 3D structures. Herein, we propose a simple experimental procedure to expand the DEEP‐STD NMR methodology to protein–ligand cases in which the spectral assignment of the protein is not available. This is achieved by experimentally identifying the chemical shifts of the residues present in binding hot‐spots on the surface of the receptor protein by using 2D NMR experiments combined with a paramagnetic probe.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Louise Tailford
- The Gut Microbes and Health Institute Strategic Program, Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Nathalie Juge
- The Gut Microbes and Health Institute Strategic Program, Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
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20
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Abstract
STD NMR is a powerful ligand-based tool for screening small molecules and low molecular weight fragments for their interaction with a given macromolecule. Such information is invaluable both in the drug discovery sector and in understanding fundamental biological interactions. Recently, powerful methods have been developed to extract a greater wealth of information from the STD NMR experiment, including ligand binding epitopes, dissociation constant determination, and mapping of binding site properties. Herein we describe these STD NMR experiments, giving practical examples for each approach, and highlight the important parameters and common pitfalls that must be considered for a successful experiment.
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Affiliation(s)
- Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
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21
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Mandaliti W, Nepravishta R, Pica F, Vallebona PS, Garaci E, Paci M. Potential mechanism of thymosin-α1-membrane interactions leading to pleiotropy: experimental evidence and hypotheses. Expert Opin Biol Ther 2018; 18:33-42. [DOI: 10.1080/14712598.2018.1456527] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Walter Mandaliti
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
| | - Ridvan Nepravishta
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
- School of Pharmacy, East Anglia University, Norwich, UK
| | - Francesca Pica
- Department of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Rome, Italy
| | | | - Enrico Garaci
- San Raffaele Pisana Scientific Institute for Research, Hospitalization and Health Care, Rome, Italy
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
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22
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Cela D, Nepravishta R, Mandaliti W, Tatar E, Şenkardeş S, Küçükgüzel İ, Küçükgüzel ŞG, Paci M. Three-dimensional structure syn/ anti isomers of a valin hydrazone. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317089331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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23
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Giachin G, Nepravishta R, Mandaliti W, Melino S, Margon A, Scaini D, Mazzei P, Piccolo A, Legname G, Paci M, Leita L. The mechanisms of humic substances self-assembly with biological molecules: The case study of the prion protein. PLoS One 2017; 12:e0188308. [PMID: 29161325 PMCID: PMC5697873 DOI: 10.1371/journal.pone.0188308] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/04/2017] [Indexed: 12/17/2022] Open
Abstract
Humic substances (HS) are the largest constituent of soil organic matter and are considered as a key component of the terrestrial ecosystem. HS may facilitate the transport of organic and inorganic molecules, as well as the sorption interactions with environmentally relevant proteins such as prions. Prions enter the environment through shedding from live hosts, facilitating a sustained incidence of animal prion diseases such as Chronic Wasting Disease and scrapie in cervid and ovine populations, respectively. Changes in prion structure upon environmental exposure may be significant as they can affect prion infectivity and disease pathology. Despite its relevance, the mechanisms of prion interaction with HS are still not completely understood. The goal of this work is to advance a structural-level picture of the encapsulation of recombinant, non-infectious, prion protein (PrP) into different natural HS. We observed that PrP precipitation upon addition of HS is mainly driven by a mechanism of "salting-out" whereby PrP molecules are rapidly removed from the solution and aggregate in insoluble adducts with humic molecules. Importantly, this process does not alter the protein folding since insoluble PrP retains its α-helical content when in complex with HS. The observed ability of HS to promote PrP insolubilization without altering its secondary structure may have potential relevance in the context of "prion ecology". These results suggest that soil organic matter interacts with prions possibly without altering the protein structures. This may facilitate prions preservation from biotic and abiotic degradation leading to their accumulation in the environment.
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Affiliation(s)
- Gabriele Giachin
- Department of Neurosciences, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- * E-mail: (GG); (LL)
| | - Ridvan Nepravishta
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
- School of Pharmacy, East Anglia University, Norwich, United Kingdom
| | - Walter Mandaliti
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
| | - Sonia Melino
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
| | - Alja Margon
- CREA Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (Council for Agricultural Research and Economics), Gorizia, Italy
| | - Denis Scaini
- Life Science Department, University of Trieste, Trieste, Italy
- ELETTRA Synchrotron Light Source, Trieste, Italy
| | - Pierluigi Mazzei
- Interdepartmental Research Centre (CERMANU), University of Naples Federico II, Napoli, Italy
| | - Alessandro Piccolo
- Interdepartmental Research Centre (CERMANU), University of Naples Federico II, Napoli, Italy
| | - Giuseppe Legname
- Department of Neurosciences, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy
- ELETTRA Synchrotron Light Source, Trieste, Italy
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Rome, Italy
| | - Liviana Leita
- CREA Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (Council for Agricultural Research and Economics), Gorizia, Italy
- * E-mail: (GG); (LL)
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Mandaliti W, Nepravishta R, Pica F, Vallebona PS, Garaci E, Paci M. Thymosin α1 Interacts with Hyaluronic Acid Electrostatically by Its Terminal Sequence LKEKK. Molecules 2017; 22:E1843. [PMID: 29077041 PMCID: PMC6150299 DOI: 10.3390/molecules22111843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/19/2017] [Accepted: 10/24/2017] [Indexed: 11/17/2022] Open
Abstract
Thymosin α1 (Tα1), is a peptidic hormone, whose immune regulatory properties have been demonstrated both in vitro and in vivo and approved in different countries for treatment of several viral infections and cancers. Tα1 assumes a conformation in negative membranes upon insertion into the phosphatidylserine exposure as found in several pathologies and in apoptosis. These findings are in agreement with the pleiotropy of Tα1, which targets both normal and tumor cells, interacting with multiple cellular components, and have generated renewed interest in the topic. Hyaluronan (HA) occurs ubiquitously in the extracellular matrix and on cell surfaces and has been related to a variety of diseases, and developmental and physiological processes. Proteins binding HA, among them CD44 and the Receptor for HA-mediated motility (RHAMM) receptors, mediate its biological effects. NMR spectroscopy indicated preliminarily that an interaction of Tα1 with HA occurs specifically around lysine residues of the sequence LKEKK of Tα1 and is suggestive of a possible interference of Tα1 in the binding of HA with CD44 and RHAMM. Further studies are needed to deepen these observations because Tα1 is known to potentiate the T-cell immunity and anti-tumor effect. The binding inhibitory activity of Tα1 on HA-CD44 or HA-RHAMM interactions can suppress both T-cell reactivity and tumor progression.
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Affiliation(s)
- Walter Mandaliti
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", via della Ricerca Scientifica 1, 00133 Rome, Italy.
| | - Ridvan Nepravishta
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", via della Ricerca Scientifica 1, 00133 Rome, Italy.
- School of Pharmacy, East Anglia University, Norwich NR4 7TJ, UK.
| | - Francesca Pica
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", via Montpellier 1, 00133 Rome, Italy.
| | - Paola Sinibaldi Vallebona
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", via Montpellier 1, 00133 Rome, Italy.
| | - Enrico Garaci
- San Raffaele Pisana Scientific Institute for Research, Hospitalization and Health Care, 00163 Rome, Italy.
| | - Maurizio Paci
- Department of Chemical Sciences and Technologies, University of Rome "Tor Vergata", via della Ricerca Scientifica 1, 00133 Rome, Italy.
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25
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Guzzo T, Mandaliti W, Nepravishta R, Aramini A, Bodo E, Daidone I, Allegretti M, Topai A, Paci M. Conformational Change in the Mechanism of Inclusion of Ketoprofen in β-Cyclodextrin: NMR Spectroscopy, Ab Initio Calculations, Molecular Dynamics Simulations, and Photoreactivity. J Phys Chem B 2016; 120:10668-10678. [PMID: 27689813 DOI: 10.1021/acs.jpcb.6b07913] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inclusion of drugs in cyclodextrins (CDs) is a recognized tool for modifying several properties such as solubility, stability, bioavailability, and so on. The photoreactive behavior of the β-CD/ketoprofen (KP) complex upon UV exposure showed a significant increase in photodecarboxylation, whereas the secondary degradation products by hydroxylation of the benzophenone moiety were inhibited. The results may account for an improvement of KP photophysical properties upon inclusion, thus better fostering its topical use. To correlate the structural details of the inclusion with these results, an NMR spectroscopic study of KP upon inclusion in β-CD was performed. Effects of the magnetically anisotropic centers of KP, changing their orientations upon inclusion and giving chemical shift variations, were specifically correlated with the results of the molecular dynamic simulations and ab initio calculations. In the large variety of papers focusing on the structural analysis of β-CD complexes, this work represents one of the few examples in which a detailed analysis of these simultaneous upfield-downfield NMR shifts of the same aromatic molecule upon inclusion is reported. Interestingly, the results demonstrate that the observed upfield and downfield shifts upon inclusion are not related to any direct magnetic role of β-CD. The conformational change of KP upon the inclusion process consists of a slight reduction in the angle between the two phenyl rings and in a remarkable reduction in the mobility of the carboxyl group, the latter being one of the main contributions to the NMR resonance shifts. These structural details help in understanding the features of the inclusion complex and, eventually, the driving force for its formation.
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Affiliation(s)
- T Guzzo
- C4T (Colosseum Combinatorial Chemistry Centre for Technology) S.C.a r.l. , Via della Ricerca Scientifica s.n.c., 00133 Rome, Italy
| | - W Mandaliti
- Department of Chemical Science and Technology, University of Rome "Tor Vergata" , 00133 Rome, Italy
| | - R Nepravishta
- Department of Chemical Science and Technology, University of Rome "Tor Vergata" , 00133 Rome, Italy.,Department of Chemical Pharmaceutical and Biomolecular Technologies, Faculty of Pharmacy Catholic University "Our Lady of Good Counsel" , Rr. D. Hoxha, 1000 Tirane, Albania
| | - A Aramini
- Department of Discovery, Dompé Farmaceutici SpA Research Center , Via Campo di Pile, 67100 L'Aquila, Italy
| | - E Bodo
- Department of Chemistry, University of Rome "Sapienza" , 00133 Rome, Italy
| | - I Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila , Via Vetoio (Coppito 1), 67010 L'Aquila, Italy
| | - M Allegretti
- Department of Discovery, Dompé Farmaceutici SpA Research Center , Via Campo di Pile, 67100 L'Aquila, Italy
| | - A Topai
- C4T (Colosseum Combinatorial Chemistry Centre for Technology) S.C.a r.l. , Via della Ricerca Scientifica s.n.c., 00133 Rome, Italy
| | - M Paci
- Department of Chemical Science and Technology, University of Rome "Tor Vergata" , 00133 Rome, Italy
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26
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Nepravishta R, Mandaliti W, Vallebona PS, Pica F, Garaci E, Paci M. Mechanism of Action of Thymosinα1: Does It Interact with Membrane by Recognition of Exposed Phosphatidylserine on Cell Surface? A Structural Approach. Vitam Horm 2016; 102:101-19. [PMID: 27450732 DOI: 10.1016/bs.vh.2016.04.002] [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] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymosinα1 is a peptidic hormone with pleiotropic activity, which is used in the therapy of several diseases. It is unstructured in water solution and interacts with negative regions of micelles and vesicles assuming two tracts of helical conformation with a structural flexible break in between. The studies of the interaction of Thymosinα1 with micelles of mixed dipalmitoylphosphatidylcholine and sodium dodecylsulfate and vesicles with mixed dipalmitoylphosphatidylcholine/dipalmitoylphosphatidylserine, the latter the negative component of the membranes, by (1)H and natural abundance (15)N NMR are herewith reported, reviewed, and discussed. The results indicate that the preferred interactions are those where the surface is negatively charged due to sodium dodecylsulfate or due to the presence of dipalmitoylphosphatidylserine exposed on the surface. In fact the unbalance of dipalmitoylphosphatidylserine on the cellular surface is an important phenomenon present in pathological conditions of cells. Moreover, the direct interaction of Thymosinα1 with K562 cells presenting an overexposure of phosphatidylserine as a consequence of resveratrol-induced apoptosis was carried out.
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Affiliation(s)
- R Nepravishta
- University of Rome "Tor Vergata", Rome, Italy; Faculty of Pharmacy Catholic University "Our Lady of Good Counsel", Tirane, Albania
| | - W Mandaliti
- University of Rome "Tor Vergata", Rome, Italy
| | | | - F Pica
- University of Rome "Tor Vergata", Rome, Italy
| | - E Garaci
- University of Rome "Tor Vergata", Rome, Italy; San Raffaele Pisana Scientific Institute for Research, Hospitalization and Health Care, Rome, Italy
| | - M Paci
- University of Rome "Tor Vergata", Rome, Italy.
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27
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Mandaliti W, Nepravishta R, Sinibaldi Vallebona P, Pica F, Garaci E, Paci M. Thymosin α1 Interacts with Exposed Phosphatidylserine in Membrane Models and in Cells and Uses Serum Albumin as a Carrier. Biochemistry 2016; 55:1462-72. [DOI: 10.1021/acs.biochem.5b01345] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Walter Mandaliti
- Department
of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Ridvan Nepravishta
- Department
of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
- Department
of Chemical Pharmaceutical and Biomolecular Technologies, Faculty of Pharmacy Catholic University “Our Lady of Good Counsel”, Rr. D.
Hoxha, Tirane, Albania
| | - Paola Sinibaldi Vallebona
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Francesca Pica
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
| | - Enrico Garaci
- Department
of Experimental Medicine and Surgery, University of Rome “Tor Vergata”, Via Montpellier 1, 00133 Rome, Italy
- San
Raffaele Pisana Scientific Institute for Research, Hospitalization and Health Care, 00163 Rome, Italy
| | - Maurizio Paci
- Department
of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, 00133 Rome, Italy
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28
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Bellomaria A, Nepravishta R, Marchetti M, Paci M. Profiling proteins in nutraceutical formulations: Characterization of the constituents. Food Chem 2016; 194:733-9. [DOI: 10.1016/j.foodchem.2015.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 07/11/2015] [Accepted: 08/10/2015] [Indexed: 11/15/2022]
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Melino S, Bellomaria A, Nepravishta R, Paci M, Melino G. p63 threonine phosphorylation signals the interaction with the WW domain of the E3 ligase Itch. Cell Cycle 2015; 13:3207-17. [PMID: 25485500 DOI: 10.4161/15384101.2014.951285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Both in epithelial development as well as in epithelial cancers, the p53 family member p63 plays a crucial role acting as a master transcriptional regulator. P63 steady state protein levels are regulated by the E3 ubiquitin ligase Itch, via a physical interaction between the PPxY consensus sequence (PY motif) of p63 and one of the 4 WW domains of Itch; this substrate recognition process leads to protein-ubiquitylation and p63 proteasomal degradation. The interaction of the WW domains, a highly compact protein-protein binding module, with the short proline-rich sequences is therefore a crucial regulatory event that may offer innovative potential therapeutic opportunity. Previous molecular studies on the Itch-p63 recognition have been performed in vitro using the Itch-WW2 domain and the peptide interacting fragment of p63 (pep63), which includes the PY motif. Itch-WW2-pep63 interaction is also stabilized in vitro by the conformational constriction of the S-S cyclization in the p63 peptide. The PY motif of p63, as also for other proteins, is characterized by the nearby presence of a (T/S)P motif, which is a potential recognition site of the WW domain of the IV group present in the prolyl-isomerase Pin1. In this study, we demonstrate, by in silico and spectroscopical studies using both the linear pep63 and its cyclic form, that the threonine phosphorylation of the (T/S)PPPxY motif may represent a crucial regulatory event of the Itch-mediated p63 ubiquitylation, increasing the Itch-WW domains-p63 recognition event and stabilizing in vivo the Itch-WW-p63 complex. Moreover, our studies confirm that the subsequently trans/cis proline isomerization of (T/S)P motif by the Pin1 prolyl-isomerase, could modulate the E3-ligase interaction, and that the (T/S)pPtransPPxY motif represent the best conformer for the ItchWW-(T/S)PPPxY motif recognition.
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Key Words
- CXCR4, chemokine receptor
- E3 ubiquitin ligases
- HECT, Homologous E6-AP Carboxyl Terminus
- IPTG, isopropyl-β-D-thiogalactoside
- Itch
- Pin1
- Ppep63, phosphorylated pep63
- RHS, Rapp-Hodgkin syndrome
- RP-HPLC, reverse phase high performance chromatography
- TFE, 2, 2, 2-trifluoroethanol
- TNF, tumor necrosis factor
- TRAF6, TNF receptor-associated factor 6
- cPpep63, cyclic phosphorylated pep63
- p53 family
- p63
- pep63, p63(534–551) peptide
- proline isomerization
- ubiquitynation
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Affiliation(s)
- Sonia Melino
- a Dipartimento di Scienze e Tecnologie Chimiche ; University of Rome "Tor Vergata" ; Rome , Italy
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Nepravishta R, Mandaliti W, Eliseo T, Vallebona PS, Pica F, Garaci E, Paci M. Thymosin α1 inserts N terminus into model membranes assuming a helical conformation. Expert Opin Biol Ther 2015; 15 Suppl 1:S71-81. [DOI: 10.1517/14712598.2015.1009034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Desideri E, Vegliante R, Cardaci S, Nepravishta R, Paci M, Ciriolo MR. MAPK14/p38α-dependent modulation of glucose metabolism affects ROS levels and autophagy during starvation. Autophagy 2014; 10:1652-65. [PMID: 25046111 DOI: 10.4161/auto.29456] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Increased glycolytic flux is a common feature of many cancer cells, which have adapted their metabolism to maximize glucose incorporation and catabolism to generate ATP and substrates for biosynthetic reactions. Indeed, glycolysis allows a rapid production of ATP and provides metabolic intermediates required for cancer cells growth. Moreover, it makes cancer cells less sensitive to fluctuations of oxygen tension, a condition usually occurring in a newly established tumor environment. Here, we provide evidence for a dual role of MAPK14 in driving a rearrangement of glucose metabolism that contributes to limiting reactive oxygen species (ROS) production and autophagy activation in condition of nutrient deprivation. We demonstrate that MAPK14 is phosphoactivated during nutrient deprivation and affects glucose metabolism at 2 different levels: on the one hand, it increases SLC2A3 mRNA and protein levels, resulting in a higher incorporation of glucose within the cell. This event involves the MAPK14-mediated enhancement of HIF1A protein stability. On the other hand, MAPK14 mediates a metabolic shift from glycolysis to the pentose phosphate pathway (PPP) through the modulation of PFKFB3 (6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase 3) degradation by the proteasome. This event requires the presence of 2 distinct degradation sequences, KEN box and DSG motif Ser273, which are recognized by 2 different E3 ligase complexes. The mutation of either motif increases PFKFB3 resistance to starvation-induced degradation. The MAPK14-driven metabolic reprogramming sustains the production of NADPH, an important cofactor for many reduction reactions and for the maintenance of the proper intracellular redox environment, resulting in reduced levels of ROS. The final effect is a reduced activation of autophagy and an increased resistance to nutrient deprivation.
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Affiliation(s)
- Enrico Desideri
- Department of Biology; University of Rome "Tor Vergata"; Rome, Italy
| | - Rolando Vegliante
- Department of Biology; University of Rome "Tor Vergata"; Rome, Italy
| | - Simone Cardaci
- Department of Biology; University of Rome "Tor Vergata"; Rome, Italy
| | - Ridvan Nepravishta
- Department of Sciences and Chemical Technologies; University of Rome "Tor Vergata"; Rome, Italy
| | - Maurizio Paci
- Department of Sciences and Chemical Technologies; University of Rome "Tor Vergata"; Rome, Italy
| | - Maria Rosa Ciriolo
- Department of Biology; University of Rome "Tor Vergata"; Rome, Italy; Research Centre IRCCS San Raffaele Pisana; Rome, Italy
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Giovannini D, Cappelli G, Jiang L, Castilletti C, Colone A, Serafino A, Wannenes F, Giacò L, Quintiliani G, Fraziano M, Nepravishta R, Colizzi V, Mariani F. A new Mycobacterium tuberculosis smooth colony reduces growth inside human macrophages and represses PDIM Operon gene expression. Does an heterogeneous population exist in intracellular mycobacteria? Microb Pathog 2012; 53:135-46. [DOI: 10.1016/j.micpath.2012.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 06/18/2012] [Accepted: 06/26/2012] [Indexed: 11/30/2022]
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Nepravishta R, Polizio F, Paci M, Melino S. A metal-binding site in the RTN1-C protein: new perspectives on the physiological role of a neuronal protein. Metallomics 2012; 4:480-7. [PMID: 22522967 DOI: 10.1039/c2mt20035j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Reticulon 1-C (RTN1-C) is an ER-associated neuronal protein characterized by horse-shoe-like topology with two transmembrane helices and the N- and C-terminal regions which are supposed in the cytosolic side of ER. The physiological role of this protein is not completely clarified, but several studies have suggested its involvement in the neuronal differentiation, membrane vesicle trafficking and induction of apoptosis. The C-terminal region of RTN1-C is characterized by the presence of a H4 histone consensus sequence that makes it able to interact with nucleic acids and HDAC enzymes both in vitro and in vivo. In the present study a potential metal ion binding motif (HxE/D) at the C-terminal of the RTN1-C has been identified and its capability to bind metals investigated by UV-vis, CD, multidimensional NMR spectroscopy and biological assays. The results suggest a possible implication of the metal ions in the mechanisms of formation of the recently observed RTNs multiprotein complexes contributing to understand the structure and function of this neuronal membrane protein, suggesting a possible effect of the metal binding property on its biological function.
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Affiliation(s)
- Ridvan Nepravishta
- Department of Sciences and Chemical Technologies, University of Rome Tor Vergata, via della Ricerca Scientifica, 00133 Rome, Italy
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Nepravishta R, Sabelli R, Iorio E, Micheli L, Paci M, Melino S. Oxidative species and S-glutathionyl conjugates in the apoptosis induction by allyl thiosulfate. FEBS J 2011; 279:154-67. [DOI: 10.1111/j.1742-4658.2011.08407.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Nepravishta R, Bellomaria A, Polizio F, Paci M, Melino S. Reticulon RTN1-CCT Peptide: A Potential Nuclease and Inhibitor of Histone Deacetylase Enzymes. Biochemistry 2009; 49:252-8. [DOI: 10.1021/bi9012676] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
| | | | | | | | - Sonia Melino
- Department of Sciences and Chemical Technologies
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36
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Melino S, Nepravishta R, Bellomaria A, Di Marco S, Paci M. Nucleic acid binding of the RTN1-C C-terminal region: toward the functional role of a reticulon protein. Biochemistry 2009; 48:242-53. [PMID: 19140693 DOI: 10.1021/bi801407w] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
RTN1-C protein is a membrane protein localized in the ER and expressed in the nervous system. Its biological role is still unclear, although interactions of the N-terminal region of RTN1-C with proteins involved in vesicle trafficking have been observed, but the role of the C-terminal region of this family protein remains to be investigated. By a homology analysis of the amino acid sequence, we identified in the C-terminal region of RTN1-C a unique consensus sequence characteristic of H4 histone protein. Thus, a 23-mer peptide (RTN1-C(CT)) corresponding to residues 186-208 of RTN1-C was synthesized, and its conformation and its interaction with nucleic acids were investigated. Here we demonstrate the strong ability of RTN1-C(CT) peptide to bind and condense the nucleic acids using electrophoretic and spectroscopic techniques. To determine if the binding of RTN1-C to nucleic acids could be regulated in vivo by an acetylation-deacetylation mechanism, as for the histone proteins, we studied the interaction of RTN1-C with one zinc-dependent histone deacetylase (HDAC) enzyme, HDAC8, with fluorescence and kinetic techniques using an acetylated form of RTN1-C(CT). The results reported here allow us to propose that the nucleic acid binding property of RTN1-C may have an important role in the biological function of this protein, the function of which could be regulated by an acetylation-deacetylation mechanism.
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Affiliation(s)
- Sonia Melino
- Department of Sciences and Chemical Technologies, University of Rome Tor Vergata, Rome, Italy.
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