1
|
Frumenzio G, Chandramouli B, Besker N, Grottesi A, Talarico C, Frigerio F, Emerson A, Musiani F. Conformational response to ligand binding of TMPRSS2, a protease involved in SARS-CoV-2 infection: Insights through computational modeling. Proteins 2023; 91:1288-1297. [PMID: 37409524 DOI: 10.1002/prot.26548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
Thanks to the considerable research which has been undertaken in the last few years to improve our understanding of the biology and mechanism of action of SARS-CoV-2, we know how the virus uses its surface spike protein to infect host cells. The transmembrane prosthesis, serine 2 (TMPRSS2) protein, located on the surface of human cells, recognizes the cleavage site in the spike protein, leading to the release of the fusion peptide and entry of the virus into the host cells. Because of its role, TMPRSS2 has been proposed as a drug target to prevent infection by the virus. In this study, we aim to increase our understanding of TMPRSS2 using long scale microsecond atomistic molecular dynamics simulations, focusing on the conformational changes over time. The comparison between simulations conducted on the protein in the native (apo) and inhibited form (holo), has shown that in the holo form the inhibitor stabilizes the catalytic site and induces rearrangements in the extracellular domain of the protein. In turn, it leads to the formation of a new cavity in the vicinity of the ligand binding pocket that is stable in the microsecond time scale. Given the low specificity of known protease inhibitors, these findings suggest a new potential drug target site that can be used to improve TMPRSS2 specific recognition by newly designed inhibitors.
Collapse
Affiliation(s)
- Giorgia Frumenzio
- Super Computing Applications and Innovation, Department HPC, CINECA, Casalecchio di Reno, Italy
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | | | | | | | | | - Andrew Emerson
- Super Computing Applications and Innovation, Department HPC, CINECA, Casalecchio di Reno, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| |
Collapse
|
2
|
Mohanty A, Parida A, Raut RK, Behera RK. Ferritin: A Promising Nanoreactor and Nanocarrier for Bionanotechnology. ACS BIO & MED CHEM AU 2022; 2:258-281. [PMID: 37101573 PMCID: PMC10114856 DOI: 10.1021/acsbiomedchemau.2c00003] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The essence of bionanotechnology lies in the application of nanotechnology/nanomaterials to solve the biological problems. Quantum dots and nanoparticles hold potential biomedical applications, but their inherent problems such as low solubility and associated toxicity due to their interactions at nonspecific target sites is a major concern. The self-assembled, thermostable, ferritin protein nanocages possessing natural iron scavenging ability have emerged as a potential solution to all the above-mentioned problems by acting as nanoreactor and nanocarrier. Ferritins, the cellular iron repositories, are hollow, spherical, symmetric multimeric protein nanocages, which sequester the excess of free Fe(II) and synthesize iron biominerals (Fe2O3·H2O) inside their ∼5-8 nm central cavity. The electrostatics and dynamics of the pore residues not only drives the natural substrate Fe2+ inside ferritin nanocages but also uptakes a set of other metals ions/counterions during in vitro synthesis of nanomaterial. The current review aims to report the recent developments/understanding on ferritin structure (self-assembly, surface/pores electrostatics, metal ion binding sites) and chemistry occurring inside these supramolecular protein cages (protein mediated metal ion uptake and mineralization/nanoparticle formation) along with its surface modification to exploit them for various nanobiotechnological applications. Furthermore, a better understanding of ferritin self-assembly would be highly useful for optimizing the incorporation of nanomaterials via the disassembly/reassembly approach. Several studies have reported the successful engineering of these ferritin protein nanocages in order to utilize them as potential nanoreactor for synthesizing/incorporating nanoparticles and as nanocarrier for delivering imaging agents/drugs at cell specific target sites. Therefore, the combination of nanoscience (nanomaterials) and bioscience (ferritin protein) projects several benefits for various applications ranging from electronics to medicine.
Collapse
|
3
|
Del Frate G, Macchiagodena M, Akhunzada MJ, D'Autilia F, Catte A, Bhattacharjee N, Barone V, Cardarelli F, Brancato G. Probing Liquid-Ordered and Disordered Phases in Lipid Model Membranes: A Combined Theoretical and Spectroscopic Study of a Fluorescent Molecular Rotor. J Phys Chem B 2022; 126:480-491. [PMID: 35001625 PMCID: PMC8785181 DOI: 10.1021/acs.jpcb.1c08324] [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] [Indexed: 11/30/2022]
Abstract
![]()
An integrated theoretical/experimental
strategy has been applied
to the study of environmental effects on the spectroscopic parameters
of 4-(diphenylamino)phtalonitrile (DPAP), a fluorescent molecular
rotor. The computational part starts from the development of an effective
force field for the first excited electronic state of DPAP and proceeds
through molecular dynamics simulations in solvents of different polarities
toward the evaluation of Stokes shifts by quantum mechanics/molecular
mechanics (QM/MM) approaches. The trends of the computed results closely
parallel the available experimental results thus giving confidence
to the interpretation of new experimental studies of the photophysics
of DPAP in lipid bilayers. In this context, results show unambiguously
that both flexible dihedral angles and global rotations are significantly
retarded in a cholesterol/DPPC lipid matrix with respect to the DOPC
matrix, thus confirming the sensitivity of DPAP to probe different
environments and, therefore, its applicability as a probe for detecting
different structures and levels of plasma membrane organization.
Collapse
Affiliation(s)
| | | | | | - Francesca D'Autilia
- Center for Nanotechnology Innovation@NEST (CNI@NEST), Piazza San Silvestro 12, I-56127 Pisa, Italy
| | - Andrea Catte
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare(INFN), Largo Pontecorvo 3, I-56 127 Pisa, Italy.,Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, I-50 019 Sesto Fiorentino, Florence, Italy
| | | | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare(INFN), Largo Pontecorvo 3, I-56 127 Pisa, Italy.,Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Via della Lastruccia 3, I-50 019 Sesto Fiorentino, Florence, Italy
| |
Collapse
|
4
|
Wang Y, Zang J, Wang C, Zhang X, Zhao G. Structural Insights for the Stronger Ability of Shrimp Ferritin to Coordinate with Heavy Metal Ions as Compared to Human H-Chain Ferritin. Int J Mol Sci 2021; 22:ijms22157859. [PMID: 34360624 PMCID: PMC8346123 DOI: 10.3390/ijms22157859] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022] Open
Abstract
Although apoferritin has been widely utilized as a new class of natural protein nanovehicles for encapsulation and delivery of nutraceuticals, its ability to remove metal heavy ions has yet to be explored. In this study, for the first time, we demonstrated that the ferritin from kuruma prawns (Marsupenaeus japonicus), named MjF, has a pronouncedly larger ability to resist denaturation induced by Cd2+ and Hg2+ as compared to its analogue, human H-chain ferritin (HuHF), despite the fact that these two proteins share a high similarity in protein structure. Treatment of HuHF with Cd2+ or Hg2+ at a metal ion/protein shell ratio of 100/1 resulted in marked protein aggregation, while the MjF solution was kept constantly clear upon treatment with Cd2+ and Hg2+ at different protein shell/metal ion ratios (50/1, 100/1, 250/1, 500/1, 1000/1, and 2500/1). Structural comparison analyses in conjunction with the newly solved crystal structure of the complex of MjF plus Cd2+ or Hg2+ revealed that cysteine (Cys) is a major residue responsible for such binding, and that the large difference in the ability to resist denaturation induced by these two heavy metal ions between MjF and HuHF is mainly derived from the different positions of Cys residues in these two proteins; namely, Cys residues in HuHF are located on the outer surface, while Cys residues from MjF are buried within the protein shell. All of these findings raise the high possibility that prawn ferritin, as a food-derived protein, could be developed into a novel bio-template to remove heavy metal ions from contaminated food systems.
Collapse
Affiliation(s)
- Yingjie Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China; (Y.W.); (J.Z.)
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China; (Y.W.); (J.Z.)
| | - Chengtao Wang
- Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology & Business University, No. 11 Fucheng Road, Haidian District, Beijing 100048, China;
| | - Xiuqing Zhang
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China; (Y.W.); (J.Z.)
- Correspondence: (X.Z.); (G.Z.); Tel.: +86-10-62736710 (G.Z.); Fax: +86-10-62738737 (G.Z.)
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China; (Y.W.); (J.Z.)
- Correspondence: (X.Z.); (G.Z.); Tel.: +86-10-62736710 (G.Z.); Fax: +86-10-62738737 (G.Z.)
| |
Collapse
|
5
|
Plays M, Müller S, Rodriguez R. Chemistry and biology of ferritin. Metallomics 2021; 13:6244244. [PMID: 33881539 PMCID: PMC8083198 DOI: 10.1093/mtomcs/mfab021] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
Iron is an essential element required by cells and has been described as a key player in ferroptosis. Ferritin operates as a fundamental iron storage protein in cells forming multimeric assemblies with crystalline iron cores. We discuss the latest findings on ferritin structure and activity and its link to cell metabolism and ferroptosis. The chemistry of iron, including its oxidation states, is important for its biological functions, its reactivity, and the biology of ferritin. Ferritin can be localized in different cellular compartments and secreted by cells with a variety of functions depending on its spatial context. Here, we discuss how cellular ferritin localization is tightly linked to its function in a tissue-specific manner, and how impairment of iron homeostasis is implicated in diseases, including cancer and coronavirus disease 2019. Ferritin is a potential biomarker and we discuss latest research where it has been employed for imaging purposes and drug delivery.
Collapse
Affiliation(s)
- Marina Plays
- Chemical Biology of Cancer Laboratory, Institut Curie, 26 rue d'Ulm, 75005 Paris, France.,Centre national de la recherche scientifique UMR 3666, Paris, France.,Institut national de la santé et de la recherche médicale U1143, Paris, France.,PSL Université Paris, Paris, France
| | - Sebastian Müller
- Chemical Biology of Cancer Laboratory, Institut Curie, 26 rue d'Ulm, 75005 Paris, France.,Centre national de la recherche scientifique UMR 3666, Paris, France.,Institut national de la santé et de la recherche médicale U1143, Paris, France.,PSL Université Paris, Paris, France
| | - Raphaël Rodriguez
- Chemical Biology of Cancer Laboratory, Institut Curie, 26 rue d'Ulm, 75005 Paris, France.,Centre national de la recherche scientifique UMR 3666, Paris, France.,Institut national de la santé et de la recherche médicale U1143, Paris, France.,PSL Université Paris, Paris, France
| |
Collapse
|
6
|
Rana S, Kherb J. Validation of specific cation partitioning to molecular surfaces using fluorescent carbon quantum dots. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
7
|
Maity B, Hishikawa Y, Lu D, Ueno T. Recent progresses in the accumulation of metal ions into the apo-ferritin cage: Experimental and theoretical perspectives. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.03.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|