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Mathivanan J, Bai Z, Chen A, Sheng J. Design, Synthesis, and Characterization of a Novel 2'-5'-Linked Amikacin-Binding Aptamer: An Experimental and MD Simulation Study. ACS Chem Biol 2022; 17:3478-3488. [PMID: 36453647 PMCID: PMC10400016 DOI: 10.1021/acschembio.2c00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
To extend the approach of using RNA aptamers as transient protective groups for the synthesis of novel small-molecule drug derivatives from the existing aminoglycosides, we incorporated 2'-5' phosphodiester backbone modification in a structurally known neomycin RNA aptamer and studied the binding of a series of aminoglycosides using isothermal calorimetry (ITC) and molecular dynamics (MD) simulation. Experimental characterization of amikacin, a commercially available and widely used aminoglycoside for treating bacterial infections, shows that the aptamer A1 with a 2'-5' linkage between G15 and U16 exhibits a sevenfold increase in binding affinity with a lower binding energy compared to the native aptamer. Molecular dynamics (MD) simulation studies rationalize that this noncanonical linkage generates a narrower binding pocket by creating a superspiral RNA helical structure, which improves the ligand's fit in the binding pocket. These results provide new insights into applying 2'-5' linkages to diversify functional RNA aptamers as noncovalent protective groups in the synthesis of aminoglycoside derivatives, which can be further extended to other current drug molecules and complex natural compounds to make new pools of drug candidates more efficiently.
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Affiliation(s)
- Johnsi Mathivanan
- Department of Chemistry and the RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Zhixue Bai
- Department of Chemistry and the RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Alan Chen
- Department of Chemistry and the RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Jia Sheng
- Department of Chemistry and the RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
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2
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Lee G, MacLean D, Ulrich H, Zhao X, Aronowski J, Jayaraman V. RNA based antagonist of NMDA receptors. ACS Chem Neurosci 2014; 5:559-67. [PMID: 24708087 PMCID: PMC4102967 DOI: 10.1021/cn500041k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/07/2014] [Indexed: 11/30/2022] Open
Abstract
The N-methyl d-aspartate (NMDA) class of ionotropic glutamate receptors plays important roles in learning and memory as well as in a number of neurological disorders including Huntington's disease and cerebral ischemia. Here, we describe the isolation and characterization of a 2' F-modified RNA aptamers directed against GluN2A-containing NMDA receptors. By adding a negative selection step toward the closely related AMPA and kainate receptors, the RNA aptamers specifically recognize NMDA receptors with dissociation constants in the nanomolar range. Electrophysiological characterization of these aptamers using rapid perfusion in outside-out patches reveals that they selectively inhibit the GluN2A containing subtype of NMDA receptors with little effect on the AMPA and kainate receptor subtypes. We also demonstrate that this RNA aptamer significantly reduces neurotoxicity in an in vitro model of cerebral ischemia. Given that the RNA based antagonist can be readily modified, it can be used as a tool in targeted drug delivery or for imaging purposes in addition to having the potential use as a therapeutic intervention in disorders involving glutamate receptors.
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MESH Headings
- Animals
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/pharmacology
- Base Sequence
- Cell Hypoxia/drug effects
- Cell Survival/drug effects
- Cells, Cultured
- Cerebral Cortex/drug effects
- Cerebral Cortex/physiology
- Consensus Sequence
- Glucose/deficiency
- Molecular Sequence Data
- Neurons/drug effects
- Neurons/physiology
- Neuroprotective Agents/chemistry
- Neuroprotective Agents/pharmacology
- Nucleic Acid Conformation
- Patch-Clamp Techniques
- Radioligand Assay
- Rats
- Receptors, AMPA/antagonists & inhibitors
- Receptors, AMPA/metabolism
- Receptors, Kainic Acid/antagonists & inhibitors
- Receptors, Kainic Acid/metabolism
- Receptors, N-Methyl-D-Aspartate/antagonists & inhibitors
- Receptors, N-Methyl-D-Aspartate/metabolism
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Affiliation(s)
- Garam Lee
- Center for Membrane Biology, Department of Biochemistry
and Molecular Biology, and Department of Neurology, University of Texas Health Science Center, 6431 Fannin, Houston, Texas 77030, United States
| | - David
M. MacLean
- Center for Membrane Biology, Department of Biochemistry
and Molecular Biology, and Department of Neurology, University of Texas Health Science Center, 6431 Fannin, Houston, Texas 77030, United States
| | - Henning Ulrich
- Department
of Biochemistry, Instituto de Química, Universidade de São Paulo, São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, S.P. 05508-900, Brazil
| | - Xiurong Zhao
- Center for Membrane Biology, Department of Biochemistry
and Molecular Biology, and Department of Neurology, University of Texas Health Science Center, 6431 Fannin, Houston, Texas 77030, United States
| | - Jaroslaw Aronowski
- Center for Membrane Biology, Department of Biochemistry
and Molecular Biology, and Department of Neurology, University of Texas Health Science Center, 6431 Fannin, Houston, Texas 77030, United States
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry
and Molecular Biology, and Department of Neurology, University of Texas Health Science Center, 6431 Fannin, Houston, Texas 77030, United States
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3
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Baird NJ, Ferré-D’Amaré AR. Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches. RNA 2013; 19:167-76. [PMID: 23249744 PMCID: PMC3543082 DOI: 10.1261/rna.036269.112] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [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: 09/04/2012] [Accepted: 11/03/2012] [Indexed: 05/21/2023]
Abstract
Most known glycine riboswitches have two homologous aptamer domains arranged in tandem and separated by a short linker. The two aptamers associate through reciprocal "quaternary" interactions that have been proposed to result in cooperative glycine binding. Recently, the interaptamer linker was found to form helix P0 with a previously unrecognized segment 5' to the first aptamer domain. P0 was shown to increase glycine affinity, abolish cooperativity, and conform to the K-turn motif consensus. We examine the global thermodynamic and structural role of P0 using isothermal titration calorimetry (ITC) and small-angle X-ray scattering (SAXS), respectively. To evaluate the generality of P0 function, we prepared glycine riboswitch constructs lacking and including P0 from Bacillus subtilis, Fusobacterium nucleatum, and Vibrio cholerae. We find that P0 indeed folds into a K-turn, supports partial pre-folding of all three glycine-free RNAs, and is required for ITC observation of glycine binding under physiologic Mg(2+) concentrations. Except for the unusually small riboswitch from F. nucleatum, the K-turn is needed for maximally compacting the glycine-bound states of the RNAs. Formation of a ribonucleoprotein complex between the B. subtilis or the F. nucleatum RNA constructs and the bacterial K-turn binding protein YbxF promotes additional folding of the free riboswitch, and enhances glycine binding. Consistent with the previously reported loss of cooperativity, P0-containing B. subtilis and V. cholerae tandem aptamers bound no more than one glycine molecule per riboswitch. Our results indicate that the P0 K-turn helps organize the quaternary structure of tandem glycine riboswitches, thereby facilitating ligand binding under physiologic conditions.
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4
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Cirillo D, Agostini F, Klus P, Marchese D, Rodriguez S, Bolognesi B, Tartaglia GG. Neurodegenerative diseases: quantitative predictions of protein-RNA interactions. RNA 2013; 19:129-140. [PMID: 23264567 PMCID: PMC3543085 DOI: 10.1261/rna.034777.112] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 11/16/2012] [Indexed: 06/01/2023]
Abstract
Increasing evidence indicates that RNA plays an active role in a number of neurodegenerative diseases. We recently introduced a theoretical framework, catRAPID, to predict the binding ability of protein and RNA molecules. Here, we use catRAPID to investigate ribonucleoprotein interactions linked to inherited intellectual disability, amyotrophic lateral sclerosis, Creutzfeuld-Jakob, Alzheimer's, and Parkinson's diseases. We specifically focus on (1) RNA interactions with fragile X mental retardation protein FMRP; (2) protein sequestration caused by CGG repeats; (3) noncoding transcripts regulated by TAR DNA-binding protein 43 TDP-43; (4) autogenous regulation of TDP-43 and FMRP; (5) iron-mediated expression of amyloid precursor protein APP and α-synuclein; (6) interactions between prions and RNA aptamers. Our results are in striking agreement with experimental evidence and provide new insights in processes associated with neuronal function and misfunction.
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Affiliation(s)
- Davide Cirillo
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Federico Agostini
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Petr Klus
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Domenica Marchese
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Silvia Rodriguez
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Benedetta Bolognesi
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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5
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Kolesnikova O, Kazakova H, Comte C, Steinberg S, Kamenski P, Martin RP, Tarassov I, Entelis N. Selection of RNA aptamers imported into yeast and human mitochondria. RNA 2010; 16:926-941. [PMID: 20348443 PMCID: PMC2856887 DOI: 10.1261/rna.1914110] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2009] [Accepted: 02/01/2010] [Indexed: 05/29/2023]
Abstract
In the yeast Saccharomyces cerevisiae, nuclear DNA-encoded is partially imported into mitochondria. We previously found that the synthetic transcripts of yeast tRNA(Lys) and a number of their mutant versions could be specifically internalized by isolated yeast and human mitochondria. The mitochondrial targeting of tRNA(Lys) in yeast was shown to depend on the cytosolic precursor of mitochondrial lysyl-tRNA synthetase and the glycolytic enzyme enolase. Here we applied the approach of in vitro selection (SELEX) to broaden the spectrum of importable tRNA-derived molecules. We found that RNAs selected for their import into isolated yeast mitochondria have lost the potential to acquire a classical tRNA-shape. Analysis of conformational rearrangements in the importable RNAs by in-gel fluorescence resonance energy transfer (FRET) approach permitted us to suggest that protein factor binding and subsequent import require formation of an alternative structure, different from a classic L-form tRNA model. We show that in the complex with targeting protein factor, enolase 2, tRK1 adopts a particular conformation characterized by bringing together the 3'-end and the TPsiC loop. This is a first evidence for implication of RNA secondary structure rearrangement in the mechanism of mitochondrial import selectivity. Based on these data, a set of small RNA molecules with significantly improved efficiency of import into yeast and human mitochondria was constructed, opening the possibility of creating a new mitochondrial vector system able to target therapeutic oligoribonucleotides into deficient human mitochondria.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Base Sequence
- Biological Transport, Active
- Fluorescence Resonance Energy Transfer
- Humans
- In Vitro Techniques
- Lysine-tRNA Ligase/metabolism
- Mitochondria/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Phosphopyruvate Hydratase/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- SELEX Aptamer Technique
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Olga Kolesnikova
- UMR 7156, Université de Strasbourg/Centre National de la Recherche Scientifique (UdS/CNRS), 67084 Strasbourg, France
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6
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Lipfert J, Sim AYL, Herschlag D, Doniach S. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. RNA 2010; 16:708-19. [PMID: 20194520 PMCID: PMC2844619 DOI: 10.1261/rna.1985110] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [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] [Indexed: 05/10/2023]
Abstract
Riboswitches are gene-regulating RNAs that are usually found in the 5'-untranslated regions of messenger RNA. As the sugar-phosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested mono- and divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann calculations using SAXS-derived low-resolution structural models allowed us to perform an energetic dissection of this process. The results showed that a model with a constant favorable contribution to folding that is opposed by an unfavorable electrostatic term that varies with ion concentration and valency provides a reasonable quantitative description of the observed folding behavior. Glycine binding, on the other hand, requires specific divalent ions binding based on the observation that Mg(2+), Ca(2+), and Mn(2+) facilitated glycine binding, whereas other divalent cations did not. The results provide a case study of how ion-dependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected.
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Affiliation(s)
- Jan Lipfert
- Department of Physics, Stanford University, Stanford, California 94305, USA
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7
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Sugiyama S, Nomura Y, Sakamoto T, Kitatani T, Kobayashi A, Miyakawa S, Takahashi Y, Adachi H, Takano K, Murakami S, Inoue T, Mori Y, Nakamura Y, Matsumura H. Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:942-4. [PMID: 18931441 PMCID: PMC2564881 DOI: 10.1107/s1744309108028236] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 09/03/2008] [Indexed: 11/10/2022]
Abstract
Aptamers, which are folded DNA or RNA molecules, bind to target molecules with high affinity and specificity. An RNA aptamer specific for the Fc fragment of human immunoglobulin G (IgG) has recently been identified and it has been demonstrated that an optimized 24-nucleotide RNA aptamer binds to the Fc fragment of human IgG and not to other species. In order to clarify the structural basis of the high specificity of the RNA aptamer, it was crystallized in complex with the Fc fragment of human IgG1. Preliminary X-ray diffraction studies revealed that the crystals belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 83.7, b = 107.2, c = 79.0 A. A data set has been collected to 2.2 A resolution.
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Affiliation(s)
- Shigeru Sugiyama
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- CREST JST, Suita, Osaka 565-0871, Japan
| | - Yusuke Nomura
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino-shi, Chiba 275-0016, Japan
- CREST JST, Minato-ku, Tokyo 108-8639, Japan
| | - Taiichi Sakamoto
- Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino-shi, Chiba 275-0016, Japan
- CREST JST, Minato-ku, Tokyo 108-8639, Japan
| | - Tomoya Kitatani
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- CREST JST, Suita, Osaka 565-0871, Japan
| | | | - Shin Miyakawa
- CREST JST, Minato-ku, Tokyo 108-8639, Japan
- Ribomic Inc., 3-16-13 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan
| | - Yoshinori Takahashi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- CREST JST, Suita, Osaka 565-0871, Japan
| | - Hiroaki Adachi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- CREST JST, Suita, Osaka 565-0871, Japan
- SOSHO Inc., Osaka 541-0053, Japan
| | - Kazufumi Takano
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- CREST JST, Suita, Osaka 565-0871, Japan
- SOSHO Inc., Osaka 541-0053, Japan
| | - Satoshi Murakami
- CREST JST, Suita, Osaka 565-0871, Japan
- SOSHO Inc., Osaka 541-0053, Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
| | - Tsuyoshi Inoue
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- CREST JST, Suita, Osaka 565-0871, Japan
- SOSHO Inc., Osaka 541-0053, Japan
| | - Yusuke Mori
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- CREST JST, Suita, Osaka 565-0871, Japan
- SOSHO Inc., Osaka 541-0053, Japan
| | - Yoshikazu Nakamura
- CREST JST, Minato-ku, Tokyo 108-8639, Japan
- Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Hiroyoshi Matsumura
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- CREST JST, Suita, Osaka 565-0871, Japan
- SOSHO Inc., Osaka 541-0053, Japan
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8
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Du M, Ulrich H, Zhao X, Aronowski J, Jayaraman V. Water soluble RNA based antagonist of AMPA receptors. Neuropharmacology 2007; 53:242-51. [PMID: 17588619 PMCID: PMC2001231 DOI: 10.1016/j.neuropharm.2007.05.007] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 04/27/2007] [Accepted: 05/14/2007] [Indexed: 11/18/2022]
Abstract
Alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are one of the important receptor classes involved in glutamate-mediated excitotoxicity. Although small molecule antagonists of this receptor have been shown to have neuroprotective properties, their low solubilities pose severe side effects in clinical trials. Here we have used the SELEX method to obtain water-soluble nuclease-resistant RNA ligands that bind to the agonist binding site of AMPA receptors. Using whole-cell current recordings, we have characterized the functional consequences of a representative aptamer from this class and show that it is a competitive antagonist of AMPA receptors and in the concentration range where it acts as an inhibitor of the AMPA receptor the RNA has no effect on the GluR6 homomeric kainate receptors. Additionally, using a fluorescence resonance energy transfer (FRET) probe, we show that this RNA ligand stabilizes the open cleft conformation of the ligand binding domain, consistent with the known structures of small antagonist-bound states of the soluble domain of this protein. Finally, using rat primary cortical neurons, we show that this RNA ligand significantly reduces neurotoxicity associated with oxygen glucose deprivation. The water-soluble and antagonistic properties of this aptamer coupled with its neuroprotective properties make it an excellent candidate for potential use in diseases or pathological conditions involving glutamate-mediated excitotoxicity.
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Affiliation(s)
- Mei Du
- 6431 Fannin, Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center, Houston, TX 77030, USA
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9
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Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J Mol Biol 2007; 365:1393-406. [PMID: 17118400 PMCID: PMC1941672 DOI: 10.1016/j.jmb.2006.10.022] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 09/28/2006] [Accepted: 10/09/2006] [Indexed: 01/05/2023]
Abstract
Riboswitches are complex folded RNA domains found in noncoding regions of mRNA that regulate gene expression upon small molecule binding. Recently, Breaker and coworkers reported a tandem aptamer riboswitch (VCI-II) that binds glycine cooperatively. Here, we use hydroxyl radical footprinting and small-angle X-ray scattering (SAXS) to study the conformations of this tandem aptamer as a function of Mg(2+) and glycine concentration. We fit a simple three-state thermodynamic model that describes the energetic coupling between magnesium-induced folding and glycine binding. Furthermore, we characterize the structural conformations of each of the three states: In low salt with no magnesium present, the VCI-II construct has an extended overall conformation, presumably representing unfolded structures. Addition of millimolar concentrations of Mg(2+) in the absence of glycine leads to a significant compaction and partial folding as judged by hydroxyl radical protections. In the presence of millimolar Mg(2+) concentrations, the tandem aptamer binds glycine cooperatively. The glycine binding transition involves a further compaction, additional tertiary packing interactions and further uptake of magnesium ions relative to the state in high Mg(2+) but no glycine. Employing density reconstruction algorithms, we obtain low resolution 3-D structures for all three states from the SAXS measurements. These data provide a first glimpse into the structural conformations of the VCI-II aptamer, establish rigorous constraints for further modeling, and provide a framework for future mechanistic studies.
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Affiliation(s)
- Jan Lipfert
- Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Physics, Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Vincent B. Chu
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | | | - Nathan Boyd
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Sebastian Doniach
- Department of Physics, Stanford University, Stanford, CA 94305, USA
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
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