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High-Resolution Conformational Analysis of RGDechi-Derived Peptides Based on a Combination of NMR Spectroscopy and MD Simulations. Int J Mol Sci 2022; 23:ijms231911039. [PMID: 36232339 PMCID: PMC9569650 DOI: 10.3390/ijms231911039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022] Open
Abstract
The crucial role of integrin in pathological processes such as tumor progression and metastasis formation has inspired intense efforts to design novel pharmaceutical agents modulating integrin functions in order to provide new tools for potential therapies. In the past decade, we have investigated the biological proprieties of the chimeric peptide RGDechi, containing a cyclic RGD motif linked to an echistatin C-terminal fragment, able to specifically recognize αvβ3 without cross reacting with αvβ5 and αIIbβ3 integrin. Additionally, we have demonstrated using two RGDechi-derived peptides, called RGDechi1-14 and ψRGDechi, that chemical modifications introduced in the C-terminal part of the peptide alter or abolish the binding to the αvβ3 integrin. Here, to shed light on the structural and dynamical determinants involved in the integrin recognition mechanism, we investigate the effects of the chemical modifications by exploring the conformational space sampled by RGDechi1-14 and ψRGDechi using an integrated natural-abundance NMR/MD approach. Our data demonstrate that the flexibility of the RGD-containing cycle is driven by the echistatin C-terminal region of the RGDechi peptide through a coupling mechanism between the N- and C-terminal regions.
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Farina B, Andrea C, Del Gatto A, Comegna D, Di Gaetano S, Capasso D, Paladino A, Acconcia C, Teresa Gentile M, Saviano M, Fattorusso R, Zaccaro L, Russo L. A novel approach for studying receptor-ligand interactions on living cells surface by using NUS/T1ρ-NMR methodologies combined with computational techniques: The RGDechi15D-α vβ 5 integrin complex. Comput Struct Biotechnol J 2021; 19:3303-3318. [PMID: 34188779 PMCID: PMC8207173 DOI: 10.1016/j.csbj.2021.05.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 11/30/2022] Open
Abstract
Structural investigations of receptor-ligand interactions on living cells surface by high-resolution Nuclear Magnetic Resonance (NMR) are problematic due to their short lifetime, which often prevents the acquisition of experiments longer than few hours. To overcome these limitations, we developed an on-cell NMR-based approach for exploring the molecular determinants driving the receptor-ligand recognition mechanism under native conditions. Our method relies on the combination of high-resolution structural and dynamics NMR data with Molecular Dynamics simulations and Molecular Docking studies. The key point of our strategy is the use of Non Uniform Sampling (NUS) and T1ρ-NMR techniques to collect atomic-resolution structural and dynamics information on the receptor-ligand interactions with living cells, that can be used as conformational constraints in computational studies. In fact, the application of these two NMR methodologies allows to record spectra with high S/N ratio and resolution within the lifetime of cells. In particular, 2D NUS [1H–1H] trNOESY spectra are used to explore the ligand conformational changes induced by receptor binding; whereas T1ρ-based experiments are applied to characterize the ligand binding epitope by defining two parameters: T1ρ Attenuation factor and T1ρ Binding Effect. This approach has been tested to characterize the molecular determinants regulating the recognition mechanism of αvβ5-integrin by a selective cyclic binder peptide named RGDechi15D. Our data demonstrate that the developed strategy represents an alternative in-cell NMR tool for studying, at atomic resolution, receptor-ligand recognition mechanism on living cells surface. Additionally, our application may be extremely useful for screening of the interaction profiling of drugs with their therapeutic targets in their native cellular environment.
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Affiliation(s)
- Biancamaria Farina
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy.,Advanced Accelerator Applications, a Novartis Company, via Vivaldi 43, 81100 Caserta, Italy
| | - Corvino Andrea
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Daniela Comegna
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Domenica Capasso
- Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy.,Center for Life Sciences and Technologies (CESTEV) University of Naples Federico II, Via Tommaso De Amicis 95, 80145 Naples, Italy
| | - Antonella Paladino
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis, Benevento 82100, Italy
| | - Clementina Acconcia
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy
| | - Maria Teresa Gentile
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy
| | - Michele Saviano
- Institute of Crystallography-CNR, Via Amendola 122/O, 70126 Bari, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy.,Interdepartmental Center of Bioactive Peptide, University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania - Luigi Vanvitelli, via Vivaldi 43, 81100 Caserta, Italy
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Pagano K, Carminati L, Tomaselli S, Molinari H, Taraboletti G, Ragona L. Molecular Basis of the Antiangiogenic Action of Rosmarinic Acid, a Natural Compound Targeting Fibroblast Growth Factor-2/FGFR Interactions. Chembiochem 2021; 22:160-169. [PMID: 32975328 DOI: 10.1002/cbic.202000610] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Indexed: 12/12/2022]
Abstract
Fibroblast growth factor (FGF2)/fibroblast growth factor receptor (FGFR) signalling plays a major role both in physiology and in several pathologies, including cancer development, metastasis formation and resistance to therapy. The development of small molecules, acting extracellularly to target FGF2/FGFR interactions, has the advantage of limiting the adverse effects associated with current intracellular FGFR inhibitors. Herein, we discuss the ability of the natural compound rosmarinic acid (RA) to induce FGF2/FGFR complex dissociation. The molecular-level description of the FGF2/FGFR/RA system, by NMR spectroscopy and docking, clearly demonstrates that RA binds to the FGFR-D2 domain and directly competes with FGF2 for the same binding site. Direct and allosteric perturbations combine to destabilise the complex. The proposed molecular mechanism is validated by cellular studies showing that RA inhibits FGF2-induced endothelial cell proliferation and FGFR activation. Our results can serve as the basis for the development of new extracellular inhibitors of the FGF/FGFR pathways.
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Affiliation(s)
- Katiuscia Pagano
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) CNR, Institution, Via Corti 12, 20133, Milano, Italy
| | - Laura Carminati
- Laboratory of Tumour Microenvironment, Department of Oncology Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126, Bergamo, Italy
| | - Simona Tomaselli
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) CNR, Institution, Via Corti 12, 20133, Milano, Italy
| | - Henriette Molinari
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) CNR, Institution, Via Corti 12, 20133, Milano, Italy
| | - Giulia Taraboletti
- Laboratory of Tumour Microenvironment, Department of Oncology Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126, Bergamo, Italy
| | - Laura Ragona
- Istituto di Scienze e Tecnologie Chimiche (SCITEC) CNR, Institution, Via Corti 12, 20133, Milano, Italy
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Ragucci S, Ruggiero A, Russo R, Landi N, Valletta M, Chambery A, Russo L, Di Maro A. Correlation of structure, function and protein dynamics in myoglobins from Eurasian woodcock, chicken and ostrich. J Biomol Struct Dyn 2020; 39:851-866. [DOI: 10.1080/07391102.2020.1719201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sara Ragucci
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Alessio Ruggiero
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Nicola Landi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Mariangela Valletta
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania ‘Luigi Vanvitelli’, Caserta, Italy
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Wang LJ, Gu XD, Yu GH, Shen L, Ji HF. Different effects of lipid on conformational conversion of chicken and murine prion proteins. Vet Microbiol 2018; 224:1-7. [PMID: 30269782 DOI: 10.1016/j.vetmic.2018.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 08/09/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
Prion diseases are characterized by the conformational conversion of the cellular prion protein (PrPC) to the pathogenic isoform (PrPSc). Lipids have been found to interact with PrPC and contribute to the efficient formation of PrPSc. Non-mammalian PrPs are not readily to undergo the conversion process into an infectious isoform, yet the effect of lipid on the conformational conversion of non-mammalian PrPC remains to be explored. Herein, the effects of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) on full-length recombinant chicken PrP (ChPrP) 24-249 and murine PrP (MoPrP) 23-230 were investigated. Firstly, it was found that in the presence of chemical denaturant, POPG remarkably inhibited MoPrP amyloid fibril growth, while had slight effect on that of ChPrP as estimated by amyloid fibril growth and transmissible electronic microscope assays. Secondly, under physiological condition, POPG induced conformation changes in both MoPrP and ChPrP using Thioflavin T (ThT) fluorescence, circular dichroism, proteinase K digestion and transmission electron microscopy assays. With a POPG:PrP molar ratio of 30:1, the ThT fluorescence of MoPrP was found to be lower than that of ChPrP, however, the POPG-induced MoPrP had higher β-sheet content and was more proteinase K-resistant than POPG-induced ChPrP. In summary, the present results suggested that the effects of POPG on conformational conversion of MoPrP and ChPrP were different under both denaturation and physiological conditions.
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Affiliation(s)
- Li-Juan Wang
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China
| | - Xiao-Dan Gu
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China
| | - Guo-Hua Yu
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, School of Life Sciences, Longyan University, Longyan 364012, China
| | - Liang Shen
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China.
| | - Hong-Fang Ji
- Institute of Biomedical Research, Shandong University of Technology, Zibo, Shandong, China; Zibo Key Laboratory of New Drug Development of Neurodegenerative diseases, Shandong Provincial Research Center for Bioinformatic Engineering and Technique, School of Life Sciences, Shandong University of Technology, Zibo, Shandong, China.
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Russo L, Farina B, Del Gatto A, Comegna D, Di Gaetano S, Capasso D, Liguoro A, Malgieri G, Saviano M, Fattorusso R, Zaccaro L. Deciphering RGDechi peptide‐α
5
β
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integrin interaction mode in isolated cell membranes. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Luigi Russo
- Department of EnvironmentalBiological and Pharmaceutical Science and Technology, University of Campania—Luigi Vanvitelli, via Vivaldi 43Caserta81100 Italy
| | - Biancamaria Farina
- Institute of Biostructures and Bioimaging‐CNR, Via Mezzocannone 16Naples80134 Italy
| | - Annarita Del Gatto
- Institute of Biostructures and Bioimaging‐CNR, Via Mezzocannone 16Naples80134 Italy
- Interdepartmental Center of Bioactive PeptideUniversity of Naples Federico II, Via Mezzocannone 16Naples80134 Italy
| | - Daniela Comegna
- Institute of Biostructures and Bioimaging‐CNR, Via Mezzocannone 16Naples80134 Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging‐CNR, Via Mezzocannone 16Naples80134 Italy
- Interdepartmental Center of Bioactive PeptideUniversity of Naples Federico II, Via Mezzocannone 16Naples80134 Italy
| | - Domenica Capasso
- Department of PharmacyUniversity of Naples Federico II, Via Mezzocannone 16Naples80134 Italy
| | - Annamaria Liguoro
- Institute of Biostructures and Bioimaging‐CNR, Via Mezzocannone 16Naples80134 Italy
| | - Gaetano Malgieri
- Department of EnvironmentalBiological and Pharmaceutical Science and Technology, University of Campania—Luigi Vanvitelli, via Vivaldi 43Caserta81100 Italy
| | - Michele Saviano
- Institute of Crystallography‐CNR, Via Amendola 122/OBari70126 Italy
| | - Roberto Fattorusso
- Department of EnvironmentalBiological and Pharmaceutical Science and Technology, University of Campania—Luigi Vanvitelli, via Vivaldi 43Caserta81100 Italy
- Interdepartmental Center of Bioactive PeptideUniversity of Naples Federico II, Via Mezzocannone 16Naples80134 Italy
| | - Laura Zaccaro
- Institute of Biostructures and Bioimaging‐CNR, Via Mezzocannone 16Naples80134 Italy
- Interdepartmental Center of Bioactive PeptideUniversity of Naples Federico II, Via Mezzocannone 16Naples80134 Italy
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Evolutionary implications of metal binding features in different species' prion protein: an inorganic point of view. Biomolecules 2014; 4:546-65. [PMID: 24970230 PMCID: PMC4101497 DOI: 10.3390/biom4020546] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/29/2014] [Accepted: 05/06/2014] [Indexed: 12/21/2022] Open
Abstract
Prion disorders are a group of fatal neurodegenerative conditions of mammals. The key molecular event in the pathogenesis of such diseases is the conformational conversion of prion protein, PrPC, into a misfolded form rich in β-sheet structure, PrPSc, but the detailed mechanistic aspects of prion protein conversion remain enigmatic. There is uncertainty on the precise physiological function of PrPC in healthy individuals. Several evidences support the notion of its role in copper homeostasis. PrPC binds Cu2+ mainly through a domain composed by four to five repeats of eight amino acids. In addition to mammals, PrP homologues have also been identified in birds, reptiles, amphibians and fish. The globular domain of protein is retained in the different species, suggesting that the protein carries out an essential common function. However, the comparison of amino acid sequences indicates that prion protein has evolved differently in each vertebrate class. The primary sequences are strongly conserved in each group, but these exhibit a low similarity with those of mammals. The N-terminal domain of different prions shows tandem amino acid repeats with an increasing amount of histidine residues going from amphibians to mammals. The difference in the sequence affects the number of copper binding sites, the affinity and the coordination environment of metal ions, suggesting that the involvement of prion in metal homeostasis may be a specific characteristic of mammalian prion protein. In this review, we describe the similarities and the differences in the metal binding of different species' prion protein, as revealed by studies carried out on the entire protein and related peptide fragments.
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