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Banna HA, Das NK, Ojha M, Koirala D. Advances in chaperone-assisted RNA crystallography using synthetic antibodies. BBA ADVANCES 2023; 4:100101. [PMID: 37655005 PMCID: PMC10466895 DOI: 10.1016/j.bbadva.2023.100101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/13/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023] Open
Abstract
RNA molecules play essential roles in many biological functions, from gene expression regulation, cellular growth, and metabolism to catalysis. They frequently fold into three-dimensional structures to perform their functions. Therefore, determining RNA structure represents a key step for understanding the structure-function relationships and developing RNA-targeted therapeutics. X-ray crystallography remains a method of choice for determining high-resolution RNA structures, but it has been challenging due to difficulties associated with RNA crystallization and phasing. Several natural and synthetic RNA binding proteins have been used to facilitate RNA crystallography. Having unique properties to help crystal packing and phasing, synthetic antibody fragments, specifically the Fabs, have emerged as promising RNA crystallization chaperones, and so far, over a dozen of RNA structures have been solved using this strategy. Nevertheless, multiple steps in this approach need to be improved, including the recombinant expression of these anti-RNA Fabs, to warrant the full potential of these synthetic Fabs as RNA crystallization chaperones. This review highlights the nuts and bolts and recent advances in the chaperone-assisted RNA crystallography approach, specifically emphasizing the Fab antibody fragments as RNA crystallization chaperones.
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Affiliation(s)
- Hasan Al Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Naba Krishna Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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Abstract
In recent years, it has become clear that RNA molecules are involved in almost all vital cellular processes and pathogenesis of human disorders. The functional diversity of RNA comes from its structural richness. Although composed of only four nucleotides, RNA molecules present a plethora of secondary and tertiary structures critical for intra and intermolecular contacts with other RNAs and ligands (proteins, small metabolites, etc.). In order to fully understand RNA function it is necessary to define its spatial structure. Crystallography, nuclear magnetic resonance and cryogenic electron microscopy have demonstrated considerable success in determining the structures of biologically important RNA molecules. However, these powerful methods require large amounts of sample. Despite their limitations, chemical synthesis and in vitro transcription are usually employed to obtain milligram quantities of RNA for structural studies, delivering simple and effective methods for large-scale production of homogenous samples. The aim of this paper is to provide an overview of methods for large-scale RNA synthesis with emphasis on chemical synthesis and in vitro transcription. We also present our own results of testing the efficiency of these approaches in order to adapt the material acquisition strategy depending on the desired RNA construct.
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Pujari N, Saundh SL, Acquah FA, Mooers BHM, Ferré-D’Amaré AR, Leung AKW. Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals. CRYSTALS 2021; 11:952. [PMID: 34745656 PMCID: PMC8570644 DOI: 10.3390/cryst11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
X-ray crystallography remains a powerful method to gain atomistic insights into the catalytic and regulatory functions of RNA molecules. However, the technique requires the preparation of diffraction-quality crystals. This is often a resource- and time-consuming venture because RNA crystallization is hindered by the conformational heterogeneity of RNA, as well as the limited opportunities for stereospecific intermolecular interactions between RNA molecules. The limited success at crystallization explains in part the smaller number of RNA-only structures in the Protein Data Bank. Several approaches have been developed to aid the formation of well-ordered RNA crystals. The majority of these are construct-engineering techniques that aim to introduce crystal contacts to favor the formation of well-diffracting crystals. A typical example is the insertion of tetraloop-tetraloop receptor pairs into non-essential RNA segments to promote intermolecular association. Other methods of promoting crystallization involve chaperones and crystallization-friendly molecules that increase RNA stability and improve crystal packing. In this review, we discuss the various techniques that have been successfully used to facilitate crystal packing of RNA molecules, recent advances in construct engineering, and directions for future research in this vital aspect of RNA crystallography.
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Affiliation(s)
- Narsimha Pujari
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Stephanie L. Saundh
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian R. Ferré-D’Amaré
- Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD 20892, USA
| | - Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
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Stanek KA, Mura C. Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly. Methods Mol Biol 2019; 1737:273-299. [PMID: 29484599 DOI: 10.1007/978-1-4939-7634-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hfq is a bacterial RNA-binding protein that plays key roles in the post-transcriptional regulation of gene expression. Like other Sm proteins, Hfq assembles into toroidal discs that bind RNAs with varying affinities and degrees of sequence specificity. By simultaneously binding to a regulatory small RNA (sRNA) and an mRNA target, Hfq hexamers facilitate productive RNA∙∙∙RNA interactions; the generic nature of this chaperone-like functionality makes Hfq a hub in many sRNA-based regulatory networks. That Hfq is crucial in diverse cellular pathways-including stress response, quorum sensing, and biofilm formation-has motivated genetic and "RNAomic" studies of its function and physiology (in vivo), as well as biochemical and structural analyses of Hfq∙∙∙RNA interactions (in vitro). Indeed, crystallographic and biophysical studies first established Hfq as a member of the phylogenetically conserved Sm superfamily. Crystallography and other biophysical methodologies enable the RNA-binding properties of Hfq to be elucidated in atomic detail, but such approaches have stringent sample requirements, viz.: reconstituting and characterizing an Hfq·RNA complex requires ample quantities of well-behaved (sufficient purity, homogeneity) specimens of Hfq and RNA (sRNA, mRNA fragments, short oligoribonucleotides, or even single nucleotides). The production of such materials is covered in this chapter, with a particular focus on recombinant Hfq proteins for crystallization experiments.
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Affiliation(s)
- Kimberly A Stanek
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| | - Cameron Mura
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
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Ferré-D'Amaré AR. Use of the U1A Protein to Facilitate Crystallization and Structure Determination of Large RNAs. Methods Mol Biol 2016; 1320:67-76. [PMID: 26227038 PMCID: PMC5178131 DOI: 10.1007/978-1-4939-2763-0_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The preparation of well-ordered crystals of RNAs with complex three-dimensional architecture can be facilitated by engineering a binding site for the spliceosomal protein U1A into a functionally and structurally dispensable stem-loop of the RNA of interest. Once suitable crystals are obtained, the U1A protein, of known structure, can be employed to facilitate preparation of heavy atom or anomalously scattering atom derivatives, or as a source of partial model phases for the molecular replacement method. Here, we describe the methods for making U1A preparations suitable for cocrystallization with RNA. As an example, the cocrystallization of the tetracycline aptamer with U1A is also described.
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Affiliation(s)
- Adrian R Ferré-D'Amaré
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, 50 South Drive, MSC8012, Bethesda, MD, 20892-8012, USA,
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Veeraraghavan N, Ganguly A, Chen JH, Bevilacqua PC, Hammes-Schiffer S, Golden BL. Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry 2011; 50:2672-82. [PMID: 21348498 PMCID: PMC3068245 DOI: 10.1021/bi2000164] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The hepatitis delta virus (HDV) ribozyme uses both metal ion and nucleobase catalysis in its cleavage mechanism. A reverse G·U wobble was observed in a recent crystal structure of the precleaved state. This unusual base pair positions a Mg(2+) ion to participate in catalysis. Herein, we used molecular dynamics (MD) and X-ray crystallography to characterize the conformation and metal binding characteristics of this base pair in product and precleaved forms. Beginning with a crystal structure of the product form, we observed formation of the reverse G·U wobble during MD trajectories. We also demonstrated that this base pair is compatible with the diffraction data for the product-bound state. During MD trajectories of the product form, Na(+) ions interacted with the reverse G·U wobble in the RNA active site, and a Mg(2+) ion, introduced in certain trajectories, remained bound at this site. Beginning with a crystal structure of the precleaved form, the reverse G·U wobble with bound Mg(2+) remained intact during MD simulations. When we removed Mg(2+) from the starting precleaved structure, Na(+) ions interacted with the reverse G·U wobble. In support of the computational results, we observed competition between Na(+) and Mg(2+) in the precleaved ribozyme crystallographically. Nonlinear Poisson-Boltzmann calculations revealed a negatively charged patch near the reverse G·U wobble. This anionic pocket likely serves to bind metal ions and to help shift the pK(a) of the catalytic nucleobase, C75. Thus, the reverse G·U wobble motif serves to organize two catalytic elements, a metal ion and catalytic nucleobase, within the active site of the HDV ribozyme.
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Affiliation(s)
- Narayanan Veeraraghavan
- Huck Institutes of Life Sciences, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Abir Ganguly
- Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jui-Hui Chen
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907
| | - Philip C. Bevilacqua
- Huck Institutes of Life Sciences, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802,Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802,To whom correspondence should be addressed. B.L.G.: telephone (765) 496-6165; fax (765) 494-7897; . S.H.-S. telephone (814) 865-6442; fax (814) 865-2927; . P.C.B. telephone (814) 863-3812; fax (814) 865-2927.
| | - Sharon Hammes-Schiffer
- Department of Chemistry, 104 Chemistry Building, The Pennsylvania State University, University Park, Pennsylvania 16802,To whom correspondence should be addressed. B.L.G.: telephone (765) 496-6165; fax (765) 494-7897; . S.H.-S. telephone (814) 865-6442; fax (814) 865-2927; . P.C.B. telephone (814) 863-3812; fax (814) 865-2927.
| | - Barbara L. Golden
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907,To whom correspondence should be addressed. B.L.G.: telephone (765) 496-6165; fax (765) 494-7897; . S.H.-S. telephone (814) 865-6442; fax (814) 865-2927; . P.C.B. telephone (814) 863-3812; fax (814) 865-2927.
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Wang YX, Zuo X, Wang J, Yu P, Butcher SE. Rapid global structure determination of large RNA and RNA complexes using NMR and small-angle X-ray scattering. Methods 2010; 52:180-91. [PMID: 20554045 PMCID: PMC5370570 DOI: 10.1016/j.ymeth.2010.06.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Indexed: 12/21/2022] Open
Abstract
Among the greatest advances in biology today are the discoveries of various roles played by RNA in biological processes. However, despite significant advances in RNA structure determination using X-ray crystallography [1] and solution NMR [2-4], the number of bona fide RNA structures is very limited, in comparison with the growing number of known functional RNAs. This is because of great difficulty in growing crystals or/and obtaining phase information, and severe size constraints on structure determination by solution NMR spectroscopy. Clearly, there is an acute need for new methodologies for RNA structure determination. The prevailing approach for structure determination of RNA in solution is a "bottom-up" approach that was basically transplanted from the approach used for determining protein structures, despite vast differences in both structural features and chemical compositions between these two types of biomacromolecules. In this chapter, we describe a new method, which has been reported recently, for rapid global structure determination of RNAs using solution-based NMR spectroscopy and small-angle X-ray scattering. The method treats duplexes as major building blocks of RNA structures. By determining the global orientations of the duplexes and the overall shape, the global structure of an RNA can be constructed and further regularized using Xplor-NIH. The utility of the method was demonstrated in global structure determination of two RNAs, a 71-nt and 102-nt RNAs with an estimated backbone RMSD ∼3.0Å. The global structure opens door to high-resolution structure determination in solution.
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Affiliation(s)
- Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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Kulshina N, Edwards TE, Ferré-D'Amaré AR. Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch. RNA (NEW YORK, N.Y.) 2010; 16:186-96. [PMID: 19948769 PMCID: PMC2802028 DOI: 10.1261/rna.1847310] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Accepted: 10/05/2009] [Indexed: 05/24/2023]
Abstract
The thi-box riboswitch regulates gene expression in response to the intracellular concentration of thiamine pyrophosphate (TPP) in archaea, bacteria, and eukarya. To complement previous biochemical, genetic, and structural studies of this phylogenetically widespread RNA domain, we have characterized its interaction with TPP by isothermal titration calorimetry. This shows that TPP binding is highly dependent on Mg(2+) concentration. The dissociation constant decreases from approximately 200 nM at 0.5 mM Mg(2+) concentration to approximately 9 nM at 2.5 mM Mg(2+) concentration. Binding is enthalpically driven, but the unfavorable entropy of binding decreases as Mg(2+) concentration rises, suggesting that divalent cations serve to pre-organize the RNA. Mutagenesis, biochemical analysis, and a new crystal structure of the riboswitch suggest that a critical element that participates in organizing the riboswitch structure is the tertiary interaction formed between the P3 and L5 regions. This tertiary contact is distant from the TPP binding site, but calorimetric analysis reveals that even subtle mutations in L5 can have readily detectable effects on TPP binding. The thermodynamic signatures of these mutations, namely decreased favorable enthalpy of binding and small effects on entropy of binding, are consistent with the P3-L5 association contributing allosterically to TPP-induced compaction of the RNA.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Base Sequence
- Binding Sites/genetics
- Crystallography, X-Ray
- Escherichia coli/genetics
- Ligands
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- Sequence Analysis, RNA
- Thermodynamics
- Thiamine Pyrophosphate/chemistry
- Thiamine Pyrophosphate/metabolism
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Affiliation(s)
- Nadia Kulshina
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195, USA
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Gong B, Chen JH, Yajima R, Chen Y, Chase E, Chadalavada DM, Golden BL, Carey PR, Bevilacqua PC. Raman crystallography of RNA. Methods 2009; 49:101-11. [PMID: 19409996 PMCID: PMC2753759 DOI: 10.1016/j.ymeth.2009.04.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 04/21/2009] [Accepted: 04/23/2009] [Indexed: 01/30/2023] Open
Abstract
Raman crystallography is the application of Raman spectroscopy to single crystals. This technique has been applied to a variety of protein molecules where it has provided unique information about biopolymer folding, substrate binding, and catalysis. Here, we describe the application of Raman crystallography to functional RNA molecules. RNA represents unique opportunities and challenges for Raman crystallography. One issue that confounds studies of RNA is its tendency to adopt multiple non-functional folds. Raman crystallography has the advantage that it isolates a single state of the RNA within the crystal and can evaluate its fold, metal ion binding properties (ligand identity, stoichiometry, and affinity), proton binding properties (identity, stoichiometry, and affinity), and catalytic potential. In particular, base-specific stretches can be identified and then associated with the binding of metal ions and protons. Because measurements are carried out in the hanging drop at ambient, rather than cryo, conditions and because RNA crystals tend to be approximately 70% solvent, RNA dynamics and conformational changes become experimentally accessible. This review focuses on experimental setup and procedures, acquisition and interpretation of Raman data, and determination of physicochemical properties of the RNA. Raman crystallographic and solution biochemical experiments on the HDV RNA enzyme are summarized and found to be in excellent agreement. Remarkably, characterization of the crystalline state has proven to help rather than hinder functional characterization of functional RNA, most likely because the tendency of RNA to fold heterogeneously is limited in a crystalline environment. Future applications of Raman crystallography to RNA are briefly discussed.
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Affiliation(s)
- Bo Gong
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Jui-Hui Chen
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907
| | - Rieko Yajima
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Yuanyuan Chen
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Elaine Chase
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907
| | - Durga M. Chadalavada
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
| | - Barbara L. Golden
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, Indiana 47907
| | - Paul R. Carey
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106
| | - Philip C. Bevilacqua
- Department of Chemistry, The Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802
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Abstract
Procedures that were critical for crystallization of the glmS ribozyme-riboswitch RNA domain from the thermophilic Gram-positive bacterium Thermoanaerobacter tengcongensis are described. Experimental design based on screening multiple variant RNA sequences and techniques used to identify initial crystallization conditions were similar to those employed for most RNAs. However, serendipitous in-drop digestion of one RNA construct at a specific internucleotide linkage was crucial for the growth of high-quality glmS ribozyme crystals. Biochemical analysis of crystalline RNA identified the site of scission and guided design of an optimized bimolecular RNA construct. Finally, modifications of ionic strength and pH of solutions used for stabilization of the crystals were essential for optimal diffraction and binding of the activator glucosamine-6-phosphate, respectively. Although their details are specific to the glmS ribozyme, these general strategies may be useful for analyzing and improving crystals of other RNAs.
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