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Evans NM, Shivers LR, To AJ, Murphy GK, Dieckmann T. Biophysical characterization and design of a minimal version of the Hoechst RNA aptamer. Biochem Biophys Res Commun 2024; 711:149908. [PMID: 38613867 DOI: 10.1016/j.bbrc.2024.149908] [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: 02/02/2024] [Revised: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/15/2024]
Abstract
RNA aptamers are oligonucleotides, selected through Systematic Evolution of Ligands by EXponential Enrichment (SELEX), that can bind to specific target molecules with high affinity. One such molecule is the RNA aptamer that binds to a blue-fluorescent Hoechst dye that was modified with bulky t-Bu groups to prevent non-specific binding to DNA. This aptamer has potential for biosensor applications; however, limited information is available regarding its conformation, molecular interactions with the ligand, and binding mechanism. The study presented here aims to biophysically characterize the Hoechst RNA aptamer when complexed with the t-Bu Hoechst dye and to further optimize the RNA sequence by designing and synthesizing new sequence variants. Each variant aptamer-t-Bu Hoechst complex was evaluated through a combination of fluorescence emission, native polyacrylamide gel electrophoresis, fluorescence titration, and isothermal titration calorimetry experiments. The results were used to design a minimal version of the aptamer consisting of only 21 nucleotides. The performed study also describes a more efficient method for synthesizing the t-Bu Hoechst dye derivative. Understanding the biophysical properties of the t-Bu Hoechst dye-RNA complex lays the foundation for nuclear magnetic resonance spectroscopy studies and its potential development as a building block for an aptamer-based biosensor that can be used in medical, environmental or laboratory settings.
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Affiliation(s)
- Natasha M Evans
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Lindsey R Shivers
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Avery J To
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Graham K Murphy
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
| | - Thorsten Dieckmann
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
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Valenciano-Bellido S, Caaveiro JMM, Morante K, Sushko T, Nakakido M, Nagatoishi S, Tsumoto K. Structure and role of the linker domain of the iron surface-determinant protein IsdH in heme transportation in Staphylococcus aureus. J Biol Chem 2022; 298:101995. [PMID: 35500652 PMCID: PMC9163592 DOI: 10.1016/j.jbc.2022.101995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus is a major cause of deadly nosocomial infections, a severe problem fueled by the steady increase of resistant bacteria. The iron surface determinant (Isd) system is a family of proteins that acquire nutritional iron from the host organism, helping the bacterium to proliferate during infection, and therefore represents a promising antibacterial target. In particular, the surface protein IsdH captures hemoglobin (Hb) and acquires the heme moiety containing the iron atom. Structurally, IsdH comprises three distinctive NEAr-iron Transporter (NEAT) domains connected by linker domains. The objective of this study was to characterize the linker region between NEAT2 and NEAT3 from various biophysical viewpoints and thereby advance our understanding of its role in the molecular mechanism of heme extraction. We demonstrate the linker region contributes to the stability of the bound protein, likely influencing the flexibility and orientation of the NEAT3 domain in its interaction with Hb, but only exerts a modest contribution to the affinity of IsdH for heme. Based on these data, we suggest that the flexible nature of the linker facilitates the precise positioning of NEAT3 to acquire heme. In addition, we also found that residues His45 and His89 of Hb located in the heme transfer route toward IsdH do not play a critical role in the transfer rate-determining step. In conclusion, this study clarifies key elements of the mechanism of heme extraction of human Hb by IsdH, providing key insights into the Isd system and other protein systems containing NEAT domains.
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Affiliation(s)
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
| | - Koldo Morante
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tatyana Sushko
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan; Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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3
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Kumar A, Planchais C, Fronzes R, Mouquet H, Reyes N. Binding mechanisms of therapeutic antibodies to human CD20. Science 2020; 369:793-799. [DOI: 10.1126/science.abb8008] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 12/25/2022]
Abstract
Monoclonal antibodies (mAbs) targeting human antigen CD20 (cluster of
differentiation 20) constitute important immunotherapies for the treatment
of B cell malignancies and autoimmune diseases. Type I and II therapeutic
mAbs differ in B cell binding properties and cytotoxic effects, reflecting
differential interaction mechanisms with CD20. Here we present 3.7- to
4.7-angstrom cryo–electron microscopy structures of full-length CD20 in
complexes with prototypical type I rituximab and ofatumumab and type II
obinutuzumab. The structures and binding thermodynamics demonstrate that
upon binding to CD20, type II mAbs form terminal complexes that preclude
recruitment of additional mAbs and complement components, whereas type I
complexes act as molecular seeds to increase mAb local concentration for
efficient complement activation. Among type I mAbs, ofatumumab complexes
display optimal geometry for complement recruitment. The uncovered
mechanisms should aid rational design of next-generation immunotherapies
targeting CD20.
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Affiliation(s)
- Anand Kumar
- Membrane Protein Mechanisms Unit, Institut Pasteur, 75015 Paris, France
- Membrane Protein Mechanisms Group, European Institute of Chemistry and Biology, University of Bordeaux, 33607 Pessac, France
- CNRS UMR 5234 Fundamental Microbiology and Pathogenicity, Bordeaux, France
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France
- INSERM U1222, Paris, France
| | - Rémi Fronzes
- CNRS UMR 5234 Fundamental Microbiology and Pathogenicity, Bordeaux, France
- Structure and Function of Bacterial Nanomachines Group, European Institute of Chemistry and Biology, University of Bordeaux, 33607 Pessac, France
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France
- INSERM U1222, Paris, France
| | - Nicolas Reyes
- Membrane Protein Mechanisms Unit, Institut Pasteur, 75015 Paris, France
- Membrane Protein Mechanisms Group, European Institute of Chemistry and Biology, University of Bordeaux, 33607 Pessac, France
- CNRS UMR 5234 Fundamental Microbiology and Pathogenicity, Bordeaux, France
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Bernacchi S, Ennifar E. Analysis of the HIV-1 Genomic RNA Dimerization Initiation Site Binding to Aminoglycoside Antibiotics Using Isothermal Titration Calorimetry. Methods Mol Biol 2020; 2113:237-250. [PMID: 32006318 DOI: 10.1007/978-1-0716-0278-2_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Isothermal titration calorimetry (ITC) provides a sensitive, powerful, and accurate tool to suitably analyze the thermodynamic of RNA binding events. This approach does not require any modification or labeling of the system under analysis and is performed in solution. ITC is a very convenient technique that provides an accurate determination of binding parameters, as well as a complete thermodynamic profile of the molecular interactions. Here we show how this approach can be used to characterize the interactions between the dimerization initiation site (DIS) RNA localized within the HIV-1 viral genome and aminoglycoside antibiotics. Our ITC study showed that the 4,5-disubstituted 2-desoxystreptamine (2-DOS) aminoglycosides can bind the DIS with a nanomolar affinity and a high specificity.
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Affiliation(s)
- Serena Bernacchi
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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