1
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Dialpuri J, Agirre J, Cowtan K, Bond P. NucleoFind: a deep-learning network for interpreting nucleic acid electron density. Nucleic Acids Res 2024; 52:e84. [PMID: 39162213 PMCID: PMC11417358 DOI: 10.1093/nar/gkae715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
Nucleic acid electron density interpretation after phasing by molecular replacement or other methods remains a difficult problem for computer programs to deal with. Programs tend to rely on time-consuming and computationally exhaustive searches to recognise characteristic features. We present NucleoFind, a deep-learning-based approach to interpreting and segmenting electron density. Using an electron density map from X-ray crystallography obtained after molecular replacement, the positions of the phosphate group, sugar ring and nitrogenous base group can be predicted with high accuracy. On average, 78% of phosphate atoms, 85% of sugar atoms and 83% of base atoms are positioned in predicted density after giving NucleoFind maps produced following successful molecular replacement. NucleoFind can use the wealth of context these predicted maps provide to build more accurate and complete nucleic acid models automatically.
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Affiliation(s)
- Jordan S Dialpuri
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Kathryn D Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Paul S Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
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2
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Wang K, Yin Z, Sang C, Xia W, Wang Y, Sun T, Xu X. Geometric deep learning for the prediction of magnesium-binding sites in RNA structures. Int J Biol Macromol 2024; 262:130150. [PMID: 38365157 DOI: 10.1016/j.ijbiomac.2024.130150] [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: 11/30/2023] [Revised: 01/24/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
Magnesium ions (Mg2+) are essential for the folding, functional expression, and structural stability of RNA molecules. However, predicting Mg2+-binding sites in RNA molecules based solely on RNA structures is still challenging. The molecular surface, characterized by a continuous shape with geometric and chemical properties, is important for RNA modelling and carries essential information for understanding the interactions between RNAs and Mg2+ ions. Here, we propose an approach named RNA-magnesium ion surface interaction fingerprinting (RMSIF), a geometric deep learning-based conceptual framework to predict magnesium ion binding sites in RNA structures. To evaluate the performance of RMSIF, we systematically enumerated decoy Mg2+ ions across a full-space grid within the range of 2 to 10 Å from the RNA molecule and made predictions accordingly. Visualization techniques were used to validate the prediction results and calculate success rates. Comparative assessments against state-of-the-art methods like MetalionRNA, MgNet, and Metal3DRNA revealed that RMSIF achieved superior success rates and accuracy in predicting Mg2+-binding sites. Additionally, in terms of the spatial distribution of Mg2+ ions within the RNA structures, a majority were situated in the deep grooves, while a minority occupied the shallow grooves. Collectively, the conceptual framework developed in this study holds promise for advancing insights into drug design, RNA co-transcriptional folding, and structure prediction.
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Affiliation(s)
- Kang Wang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China
| | - Zuode Yin
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Chunjiang Sang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China
| | - Wentao Xia
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China
| | - Yan Wang
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China
| | - Tingting Sun
- Department of Physics, Zhejiang University of Science and Technology, Hangzhou 310008, China.
| | - Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou 213001, China.
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3
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Amadei F, Reichenbach M, Gallo S, Sigel RKO. The structural features of the ligand-free moaA riboswitch and its ion-dependent folding. J Inorg Biochem 2023; 242:112153. [PMID: 36774787 DOI: 10.1016/j.jinorgbio.2023.112153] [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: 10/10/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023]
Abstract
Riboswitches are structural elements of mRNA involved in the regulation of gene expression by responding to specific cellular metabolites. To fulfil their regulatory function, riboswitches prefold into an active state, the so-called binding competent form, that guarantees metabolite binding and allows a consecutive refolding of the RNA. Here, we describe the folding pathway to the binding competent form as well as the ligand free structure of the moaA riboswitch of E. coli. This RNA proposedly responds to the molybdenum cofactor (Moco), a highly oxygen-sensitive metabolite, essential in the carbon and sulfur cycles of eukaryotes. K+- and Mg2+-dependent footprinting assays and spectroscopic investigations show a high degree of structure formation of this RNA already at very low ion-concentrations. Mg2+ facilitates additionally a general compaction of the riboswitch towards its proposed active structure. We show that this fold agrees with the earlier suggested secondary structure which included also a long-range tetraloop/tetraloop-receptor like interaction. Metal ion cleavage assays revealed specific Mg2+-binding pockets within the moaA riboswitch. These Mg2+ binding pockets are good indicators for the potential Moco binding site, since in riboswitches, Mg2+ was shown to be necessary to bind phosphate-carrying metabolites. The importance of the phosphate and of other functional groups of Moco is highlighted by binding assays with tetrahydrobiopterin, the reduced and oxygen-sensitive core moiety of Moco. We demonstrate that the general molecular shape of pterin by its own is insufficient for the recognition by the riboswitch.
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Affiliation(s)
- Fabio Amadei
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - María Reichenbach
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Sofia Gallo
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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4
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Luo B, Zhang C, Ling X, Mukherjee S, Jia G, Xie J, Jia X, Liu L, Baulin EF, Luo Y, Jiang L, Dong H, Wei X, Bujnicki JM, Su Z. Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing. Nat Catal 2023. [DOI: 10.1038/s41929-023-00934-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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5
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Hirano S, Kappel K, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F. Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA. Nature 2022; 610:575-581. [PMID: 36224386 PMCID: PMC9581776 DOI: 10.1038/s41586-022-05324-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022]
Abstract
RNA-guided systems, such as CRISPR-Cas, combine programmable substrate recognition with enzymatic function, a combination that has been used advantageously to develop powerful molecular technologies1,2. Structural studies of these systems have illuminated how the RNA and protein jointly recognize and cleave their substrates, guiding rational engineering for further technology development3. Recent work identified a new class of RNA-guided systems, termed OMEGA, which include IscB, the likely ancestor of Cas9, and the nickase IsrB, a homologue of IscB lacking the HNH nuclease domain4. IsrB consists of only around 350 amino acids, but its small size is counterbalanced by a relatively large RNA guide (roughly 300-nt ωRNA). Here, we report the cryogenic-electron microscopy structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with its cognate ωRNA and a target DNA. We find the overall structure of the IsrB protein shares a common scaffold with Cas9. In contrast to Cas9, however, which uses a recognition (REC) lobe to facilitate target selection, IsrB relies on its ωRNA, part of which forms an intricate ternary structure positioned analogously to REC. Structural analyses of IsrB and its ωRNA as well as comparisons to other RNA-guided systems highlight the functional interplay between protein and RNA, advancing our understanding of the biology and evolution of these diverse systems.
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Affiliation(s)
- Seiichi Hirano
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Kalli Kappel
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Han Altae-Tran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Max E Wilkinson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Soumya Kannan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - F Esra Demircioglu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Rui Yan
- CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Momoko Shiozaki
- CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Zhiheng Yu
- CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Rhiannon K Macrae
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA.
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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6
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Liu D, Thélot FA, Piccirilli JA, Liao M, Yin P. Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly. Nat Methods 2022; 19:576-585. [PMID: 35501384 DOI: 10.1038/s41592-022-01455-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 03/09/2022] [Indexed: 12/29/2022]
Abstract
High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering strategy for efficient structural determination of RNA-only structures using single-particle cryogenic electron microscopy (cryo-EM). This strategy-ROCK (RNA oligomerization-enabled cryo-EM via installing kissing loops)-involves installing kissing-loop sequences onto the functionally nonessential stems of RNAs for homomeric self-assembly into closed rings with multiplied molecular weights and mitigated structural flexibility. ROCK enables cryo-EM reconstruction of the Tetrahymena group I intron at 2.98-Å resolution overall (2.85 Å for the core), allowing de novo model building of the complete RNA, including the previously unknown peripheral domains. ROCK is further applied to two smaller RNAs-the Azoarcus group I intron and the FMN riboswitch, revealing the conformational change of the former and the bound ligand in the latter. ROCK holds promise to greatly facilitate the use of cryo-EM in RNA structural studies.
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Affiliation(s)
- Di Liu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - François A Thélot
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joseph A Piccirilli
- Department of Chemistry, the University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, the University of Chicago, Chicago, IL, USA
| | - Maofu Liao
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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7
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Cascarano GL, Giacovazzo C. Towards the automatic crystal structure solution of nucleic acids: automated model building using the new CAB program. Acta Crystallogr D Struct Biol 2021; 77:1602-1613. [PMID: 34866615 DOI: 10.1107/s2059798321010937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/20/2021] [Indexed: 11/10/2022] Open
Abstract
CAB, a recently described automated model-building (AMB) program, has been modified to work effectively with nucleic acids. To this end, several new algorithms have been introduced and the libraries have been updated. To reduce the input average phase error, ligand heavy atoms are now located before starting the CAB interpretation of the electron-density maps. Furthermore, alternative approaches are used depending on whether the ligands belong to the target or to the model chain used in the molecular-replacement step. Robust criteria are then applied to decide whether the AMB model is acceptable or whether it must be modified to fit prior information on the target structure. In the latter case, the model chains are rearranged to fit prior information on the target chains. Here, the performance of the new AMB program CAB applied to various nucleic acid structures is discussed. Other well documented programs such as Nautilus, ARP/wARP and phenix.autobuild were also applied and the experimental results are described.
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Affiliation(s)
| | - Carmelo Giacovazzo
- Istituto di Cristallografia, CNR, Via G. Amendola 122/o, I-70126 Bari, Italy
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8
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Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution. Nature 2021; 596:603-607. [PMID: 34381213 PMCID: PMC8405103 DOI: 10.1038/s41586-021-03803-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution1-3. However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure-function relationships4, but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure-function relationships in ribozymes.
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9
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Abaeva IS, Vicens Q, Bochler A, Soufari H, Simonetti A, Pestova TV, Hashem Y, Hellen CUT. The Halastavi árva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism. Cell Rep 2020; 33:108476. [PMID: 33296660 DOI: 10.1016/j.celrep.2020.108476] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/05/2020] [Accepted: 11/12/2020] [Indexed: 01/01/2023] Open
Abstract
Dicistrovirus intergenic region internal ribosomal entry sites (IGR IRESs) do not require initiator tRNA, an AUG codon, or initiation factors and jumpstart translation from the middle of the elongation cycle via formation of IRES/80S complexes resembling the pre-translocation state. eEF2 then translocates the [codon-anticodon]-mimicking pseudoknot I (PKI) from ribosomal A sites to P sites, bringing the first sense codon into the decoding center. Halastavi árva virus (HalV) contains an IGR that is related to previously described IGR IRESs but lacks domain 2, which enables these IRESs to bind to individual 40S ribosomal subunits. By using in vitro reconstitution and cryoelectron microscopy (cryo-EM), we now report that the HalV IGR IRES functions by the simplest initiation mechanism that involves binding to 80S ribosomes such that PKI is placed in the P site, so that the A site contains the first codon that is directly accessible for decoding without prior eEF2-mediated translocation of PKI.
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Affiliation(s)
- Irina S Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA
| | - Quentin Vicens
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 15 rue René Descartes, 67000 Strasbourg, France
| | - Anthony Bochler
- INSERM U1212 Acides Nucléiques: Régulations Naturelle et Artificielle, Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France; Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 15 rue René Descartes, 67000 Strasbourg, France
| | - Heddy Soufari
- INSERM U1212 Acides Nucléiques: Régulations Naturelle et Artificielle, Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France
| | - Angelita Simonetti
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 15 rue René Descartes, 67000 Strasbourg, France
| | - Tatyana V Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA.
| | - Yaser Hashem
- INSERM U1212 Acides Nucléiques: Régulations Naturelle et Artificielle, Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France.
| | - Christopher U T Hellen
- Department of Cell Biology, SUNY Downstate Health Sciences University, 450 Clarkson Avenue, MSC 44, Brooklyn, NY 11203, USA.
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10
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Zou A, Lee S, Li J, Zhou R. Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg2+ Ion Bound at the Double Mg-Clamp Structure. J Phys Chem B 2020; 124:701-707. [DOI: 10.1021/acs.jpcb.9b06428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Aodong Zou
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Sangyun Lee
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jingyuan Li
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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11
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Hexahydrated Mg 2+ Binding and Outer-Shell Dehydration on RNA Surface. Biophys J 2019; 114:1274-1284. [PMID: 29590585 DOI: 10.1016/j.bpj.2018.01.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 10/17/2022] Open
Abstract
The interaction between metal ions, especially Mg2+ ions, and RNA plays a critical role in RNA folding. Upon binding to RNA, a metal ion that is fully hydrated in bulk solvent can become dehydrated. Here we use molecular dynamics simulation to investigate the dehydration of bound hexahydrated Mg2+ ions. We find that a hydrated Mg2+ ion in the RNA groove region can involve significant dehydration in the outer hydration shell. The first or innermost hydration shell of the Mg2+ ion, however, is retained during the simulation because of the strong ion-water electrostatic attraction. As a result, water-mediated hydrogen bonding remains an important form for Mg2+-RNA interaction. Analysis for ions at different binding sites shows that the most pronounced water deficiency relative to the fully hydrated state occurs at a radial distance of around 11 Å from the center of the ion. Based on the independent 200 ns molecular dynamics simulations for three different RNA structures (Protein Data Bank: 1TRA, 2TPK, and 437D), we find that Mg2+ ions overwhelmingly dominate over monovalent ions such as Na+ and K+ in ion-RNA binding. Furthermore, application of the free energy perturbation method leads to a quantitative relationship between the Mg2+ dehydration free energy and the local structural environment. We find that ΔΔGhyd, the change of the Mg2+ hydration free energy upon binding to RNA, varies linearly with the inverse distance between the Mg2+ ion and the nearby nonbridging oxygen atoms of the phosphate groups, and ΔΔGhyd can reach -2.0 kcal/mol and -3.0 kcal/mol for an Mg2+ ion bound to the surface and to the groove interior, respectively. In addition, the computation results in an analytical formula for the hydration ratio as a function of the average inverse Mg2+-O distance. The results here might be useful for further quantitative investigations of ion-RNA interactions in RNA folding.
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12
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Leonarski F, D'Ascenzo L, Auffinger P. Nucleobase carbonyl groups are poor Mg 2+ inner-sphere binders but excellent monovalent ion binders-a critical PDB survey. RNA (NEW YORK, N.Y.) 2019; 25:173-192. [PMID: 30409785 PMCID: PMC6348993 DOI: 10.1261/rna.068437.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/16/2018] [Indexed: 05/04/2023]
Abstract
Precise knowledge of Mg2+ inner-sphere binding site properties is vital for understanding the structure and function of nucleic acid systems. Unfortunately, the PDB, which represents the main source of Mg2+ binding sites, contains a substantial number of assignment issues that blur our understanding of the functions of these ions. Here, following a previous study devoted to Mg2+ binding to nucleobase nitrogens, we surveyed nucleic acid X-ray structures from the PDB with resolutions ≤2.9 Å to classify the Mg2+ inner-sphere binding patterns to nucleotide carbonyl, ribose hydroxyl, cyclic ether, and phosphodiester oxygen atoms. From this classification, we derived a set of "prior-knowledge" nucleobase Mg2+ binding sites. We report that crystallographic examples of trustworthy nucleobase Mg2+ binding sites are fewer than expected since many of those are associated with misidentified Na+ or K+ We also emphasize that binding of Na+ and K+ to nucleic acids is much more frequent than anticipated. Overall, we provide evidence derived from X-ray structures that nucleobases are poor inner-sphere binders for Mg2+ but good binders for monovalent ions. Based on strict stereochemical criteria, we propose an extended set of guidelines designed to help in the assignment and validation of ions directly contacting nucleobase and ribose atoms. These guidelines should help in the interpretation of X-ray and cryo-EM solvent density maps. When borderline Mg2+ stereochemistry is observed, alternative placement of Na+, K+, or Ca2+ must be considered. We also critically examine the use of lanthanides (Yb3+, Tb3+) as Mg2+ substitutes in crystallography experiments.
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Affiliation(s)
- Filip Leonarski
- Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
| | - Luigi D'Ascenzo
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, 67084, France
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13
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Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L. Revealing the distinct folding phases of an RNA three-helix junction. Nucleic Acids Res 2018; 46:7354-7365. [PMID: 29762712 PMCID: PMC6101490 DOI: 10.1093/nar/gky363] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 01/08/2023] Open
Abstract
Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Ron Elber
- Department of Chemistry and Institute for Computational Engineering and Sciences (ICES) University of Texas at Austin, Austin, TX, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
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14
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Shoffner GM, Wang R, Podell E, Cech TR, Guo F. In Crystallo Selection to Establish New RNA Crystal Contacts. Structure 2018; 26:1275-1283.e3. [PMID: 29910185 DOI: 10.1016/j.str.2018.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/03/2018] [Accepted: 05/10/2018] [Indexed: 11/25/2022]
Abstract
Crystallography is a major technique for determining large RNA structures. Obtaining diffraction-quality crystals has been the bottleneck. Although several RNA crystallization methods have been developed, the field strongly needs additional approaches. Here we invented an in crystallo selection strategy for identifying mutations that enhance a target RNA's crystallizability. The strategy includes constructing an RNA pool containing random mutations, obtaining crystals, and amplifying the sequences enriched by crystallization. We demonstrated a proof-of-principle application to the P4-P6 domain from the Tetrahymena ribozyme. We further determined the structures of four selected mutants. All four establish new crystal lattice contacts while maintaining the native structure. Three mutants achieve this by relocating bulges and one by making a helix more flexible. In crystallo selection provides opportunities to improve crystals of RNAs or RNA-ligand complexes. Our results also suggest that mutants may be rationally designed for crystallization by "walking" a bulge along the RNA chain.
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Affiliation(s)
- Grant M Shoffner
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Ruixuan Wang
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Elaine Podell
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, Boulder, CO 80309-0596, USA
| | - Thomas R Cech
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado BioFrontiers Institute, Boulder, CO 80309-0596, USA
| | - Feng Guo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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15
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Leonarski F, D'Ascenzo L, Auffinger P. Mg2+ ions: do they bind to nucleobase nitrogens? Nucleic Acids Res 2017; 45:987-1004. [PMID: 27923930 PMCID: PMC5314772 DOI: 10.1093/nar/gkw1175] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 01/28/2023] Open
Abstract
Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for divalent metals. Further, Mg2+ coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg2+ assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na+, K+, NH4+ ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg2+ ions do not bind to N7 atoms. Without much of a surprise, Mn2+, Zn2+ and Cd2+, which have a higher affinity for nitrogens, may contact N7 atoms when present in crystallization buffers. In this respect, we describe for the first time a potential Zn2+ ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg2+ in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments.
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Affiliation(s)
- Filip Leonarski
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Luigi D'Ascenzo
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
| | - Pascal Auffinger
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, F-67000 Strasbourg, France
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16
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Zhang W, Tam CP, Wang J, Szostak JW. Unusual Base-Pairing Interactions in Monomer-Template Complexes. ACS CENTRAL SCIENCE 2016; 2:916-926. [PMID: 28058281 PMCID: PMC5200924 DOI: 10.1021/acscentsci.6b00278] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 06/06/2023]
Abstract
Many high-resolution crystal structures have contributed to our understanding of the reaction pathway for catalysis by DNA and RNA polymerases, but the structural basis of nonenzymatic template-directed RNA replication has not been studied in comparable detail. Here we present crystallographic studies of the binding of ribonucleotide monomers to RNA primer-template complexes, with the goal of improving our understanding of the mechanism of nonenzymatic RNA copying, and of catalysis by polymerases. To explore how activated ribonucleotides recognize and bind to RNA templates, we synthesized an unreactive phosphonate-linked pyrazole analogue of guanosine 5'-phosphoro-2-methylimidazolide (2-MeImpG), a highly activated nucleotide that has been used extensively to study nonenzymatic primer extension. We cocrystallized this analogue with structurally rigidified RNA primer-template complexes carrying single or multiple monomer binding sites, and obtained high-resolution X-ray structures of these complexes. In addition to Watson-Crick base pairing, we repeatedly observed noncanonical guanine:cytidine base pairs in our crystal structures. In most structures, the phosphate and leaving group moieties of the monomers were highly disordered, while in others the distance from O3' of the primer to the phosphorus of the incoming monomer was too great to allow for reaction. We suggest that these effects significantly influence the rate and fidelity of nonenzymatic RNA replication, and that even primitive ribozyme polymerases could enhance RNA replication by enforcing Watson-Crick base pairing between monomers and primer-template complexes, and by bringing the reactive functional groups into closer proximity.
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Affiliation(s)
- Wen Zhang
- Howard Hughes Medical Institute, Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Chun Pong Tam
- Howard Hughes Medical Institute, Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
| | - Jiawei Wang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jack W. Szostak
- Howard Hughes Medical Institute, Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford
Street, Cambridge, Massachusetts 02138, United States
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17
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Zhang S, Stevens D, Goyal P, Bingaman JL, Bevilacqua PC, Hammes-Schiffer S. Assessing the Potential Effects of Active Site Mg 2+ Ions in the glmS Ribozyme-Cofactor Complex. J Phys Chem Lett 2016; 7:3984-3988. [PMID: 27677922 PMCID: PMC5117136 DOI: 10.1021/acs.jpclett.6b01854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/14/2016] [Indexed: 06/06/2023]
Abstract
Ribozymes employ diverse catalytic strategies in their self-cleavage mechanisms, including the use of divalent metal ions. This work explores the effects of Mg2+ ions in the active site of the glmS ribozyme-GlcN6P cofactor complex using computational methods. Deleterious and potentially beneficial effects of an active site Mg2+ ion on the self-cleavage reaction were identified. The presence of a Mg2+ ion near the scissile phosphate oxygen atoms at the cleavage site was determined to be deleterious, and thereby anticatalytic, due to electrostatic repulsion of the cofactor, disruption of key hydrogen-bonding interactions, and obstruction of nucleophilic attack. On the other hand, the presence of a Mg2+ ion at another position in the active site, the Hoogsteen face of the putative base, was found to avoid these deleterious effects and to be potentially catalytically favorable owing to the stabilization of negative charge and pKa shifting of the guanine base.
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Affiliation(s)
- Sixue Zhang
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
| | - David
R. Stevens
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
| | - Puja Goyal
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
| | - Jamie L. Bingaman
- Department of Chemistry and Center
for RNA Molecular Biology and Department of Biochemistry
and Molecular Biology, The Pennsylvania
State University, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department of Chemistry and Center
for RNA Molecular Biology and Department of Biochemistry
and Molecular Biology, The Pennsylvania
State University, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
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18
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Zhou H, Kimsey IJ, Nikolova EN, Sathyamoorthy B, Grazioli G, McSally J, Bai T, Wunderlich CH, Kreutz C, Andricioaei I, Al-Hashimi HM. m(1)A and m(1)G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat Struct Mol Biol 2016; 23:803-10. [PMID: 27478929 PMCID: PMC5016226 DOI: 10.1038/nsmb.3270] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 07/05/2016] [Indexed: 12/13/2022]
Abstract
The B-DNA double helix can dynamically accommodate G-C and A-T base pairs in either Watson-Crick or Hoogsteen configurations. Here, we show that G-C(+) (in which + indicates protonation) and A-U Hoogsteen base pairs are strongly disfavored in A-RNA. As a result,N(1)-methyladenosine and N(1)-methylguanosine, which occur in DNA as a form of alkylation damage and in RNA as post-transcriptional modifications, have dramatically different consequences. Whereas they create G-C(+) and A-T Hoogsteen base pairs in duplex DNA, thereby maintaining the structural integrity of the double helix, they block base-pairing and induce local duplex melting in RNA. These observations provide a mechanism for disrupting RNA structure through post-transcriptional modifications. The different propensities to form Hoogsteen base pairs in B-DNA and A-RNA may help cells meet the opposing requirements of maintaining genome stability, on the one hand, and of dynamically modulating the structure of the epitranscriptome, on the other.
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Affiliation(s)
- Huiqing Zhou
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Isaac J. Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | - Evgenia N. Nikolova
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California USA
| | | | - Gianmarc Grazioli
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - James McSally
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Tianyu Bai
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
| | | | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck Austria
| | - Ioan Andricioaei
- Department of Chemistry, University of California Irvine, Irvine, California USA
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina USA
- Department of Chemistry, Duke University, Durham, North Carolina USA
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19
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Zhang Y, Baranovskiy AG, Tahirov ET, Tahirov TH, Pavlov YI. Divalent ions attenuate DNA synthesis by human DNA polymerase α by changing the structure of the template/primer or by perturbing the polymerase reaction. DNA Repair (Amst) 2016; 43:24-33. [PMID: 27235627 DOI: 10.1016/j.dnarep.2016.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/09/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022]
Abstract
DNA polymerases (pols) are sophisticated protein machines operating in the replication, repair and recombination of genetic material in the complex environment of the cell. DNA pol reactions require at least two divalent metal ions for the phosphodiester bond formation. We explore two understudied roles of metals in pol transactions with emphasis on polα, a crucial enzyme in the initiation of DNA synthesis. We present evidence that the combination of many factors, including the structure of the template/primer, the identity of the metal, the metal turnover in the pol active site, and the influence of the concentration of nucleoside triphosphates, affect DNA pol synthesis. On the poly-dT70 template, the increase of Mg(2+) concentration within the range typically used for pol reactions led to the severe loss of the ability of pol to extend DNA primers and led to a decline in DNA product sizes when extending RNA primers, simulating the effect of "counting" of the number of nucleotides in nascent primers by polα. We suggest that a high Mg(2+) concentration promotes the dynamic formation of unconventional DNA structure(s), thus limiting the apparent processivity of the enzyme. Next, we found that Zn(2+) supported robust polα reactions when the concentration of nucleotides was above the concentration of ions; however, there was only one nucleotide incorporation by the Klenow fragment of DNA pol I. Zn(2+) drastically inhibited polα, but had no effect on Klenow, when Mg(2+) was also present. It is possible that Zn(2+) perturbs metal-mediated transactions in pol active site, for example affecting the step of pyrophosphate removal at the end of each pol cycle necessary for continuation of polymerization.
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Affiliation(s)
- Yinbo Zhang
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States
| | - Emin T Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States.
| | - Youri I Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, United States.
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20
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Grzybkowska A, Jędrzejczyk D, Rostkowski M, Chworos A, Dybala-Defratyka A. RNA model evaluation based on MD simulation of four tRNA analogs. RSC Adv 2016. [DOI: 10.1039/c6ra14933b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Characteristic of 3D structures of tRNA analogs generated from primary sequence, subjected to all-atom MD simulation and assessed using selected RNA model evaluation methods.
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Affiliation(s)
- Anna Grzybkowska
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Dominika Jędrzejczyk
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
| | - Michał Rostkowski
- Institute of Applied Radiation Chemistry
- Faculty of Chemistry
- Lodz University of Technology
- Lodz
- Poland
| | - Arkadiusz Chworos
- Center of Molecular and Macromolecular Studies
- Polish Academy of Sciences
- 90-363 Lodz
- Poland
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21
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Zhao C, Rajashankar KR, Marcia M, Pyle AM. Crystal structure of group II intron domain 1 reveals a template for RNA assembly. Nat Chem Biol 2015; 11:967-72. [PMID: 26502156 PMCID: PMC4651773 DOI: 10.1038/nchembio.1949] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/18/2015] [Indexed: 12/17/2022]
Abstract
Although the importance of large noncoding RNAs is increasingly appreciated, our understanding of their structures and architectural dynamics remains limited. In particular, we know little about RNA folding intermediates and how they facilitate the productive assembly of RNA tertiary structures. Here, we report the crystal structure of an obligate intermediate that is required during the earliest stages of group II intron folding. Composed of domain 1 from the Oceanobacillus iheyensis group II intron (266 nucleotides), this intermediate retains native-like features but adopts a compact conformation in which the active site cleft is closed. Transition between this closed and the open (native) conformation is achieved through discrete rotations of hinge motifs in two regions of the molecule. The open state is then stabilized by sequential docking of downstream intron domains, suggesting a 'first come, first folded' strategy that may represent a generalizable pathway for assembly of large RNA and ribonucleoprotein structures.
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Affiliation(s)
- Chen Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Dept. of Chemistry and Chemical Biology, Cornell University Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439
| | - Marco Marcia
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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22
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Thaplyal P, Ganguly A, Hammes-Schiffer S, Bevilacqua PC. Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density. Biochemistry 2015; 54:2160-75. [PMID: 25799319 PMCID: PMC4824481 DOI: 10.1021/acs.biochem.5b00190] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
The
hepatitis delta virus (HDV) ribozyme self-cleaves in the presence
of a wide range of monovalent and divalent ions. Prior theoretical
studies provided evidence that self-cleavage proceeds via a concerted
or stepwise pathway, with the outcome dictated by the valency of the
metal ion. In the present study, we measure stereospecific thio effects
at the nonbridging oxygens of the scissile phosphate under a wide
range of experimental conditions, including varying concentrations
of diverse monovalent and divalent ions, and combine these with quantum
mechanical/molecular mechanical (QM/MM) free energy simulations on
the stereospecific thio substrates. The RP substrate gives large normal thio effects in the presence of all
monovalent ions. The SP substrate also
gives normal or no thio effects, but only for smaller monovalent and
divalent cations, such as Li+, Mg2+, Ca2+, and Sr2+; in contrast, sizable inverse thio
effects are found for larger monovalent and divalent cations, including
Na+, K+, NH4+, and Ba2+. Proton inventories are found to be unity in the presence
of the larger monovalent and divalent ions, but two in the presence
of Mg2+. Additionally, rate–pH profiles are inverted
for the low charge density ions, and only imidazole plus ammonium
ions rescue an inactive C75Δ variant in the absence of Mg2+. Results from the thio effect experiments, rate–pH
profiles, proton inventories, and ammonium/imidazole rescue experiments,
combined with QM/MM free energy simulations, support a change in the
mechanism of HDV ribozyme self-cleavage from concerted and metal ion-stabilized
to stepwise and proton transfer-stabilized as the charge density of
the metal ion decreases.
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Affiliation(s)
- Pallavi Thaplyal
- †Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Abir Ganguly
- ‡Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sharon Hammes-Schiffer
- ‡Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Philip C Bevilacqua
- †Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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23
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Cowtan K. Automated nucleic acid chain tracing in real time. IUCRJ 2014; 1:387-92. [PMID: 25485119 PMCID: PMC4224457 DOI: 10.1107/s2052252514019290] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/26/2014] [Indexed: 06/04/2023]
Abstract
The crystallographic structure solution of nucleotides and nucleotide complexes is now commonplace. The resulting electron-density maps are often poorer than for proteins, and as a result interpretation in terms of an atomic model can require significant effort, particularly in the case of large structures. While model building can be performed automatically, as with proteins, the process is time-consuming, taking minutes to days depending on the software and the size of the structure. A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software, with extended chain fragments built around the current view position in a fraction of a second. The speed of the method arises from the determination of the 'fingerprint' of the sugar and phosphate groups in terms of conserved high-density and low-density features, coupled with a highly efficient scoring algorithm. Use cases include the rapid evaluation of an initial electron-density map, addition of nucleotide fragments to prebuilt protein structures, and in favourable cases the completion of the structure while automated model-building software is still running. The method has been incorporated into the Coot software package.
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Affiliation(s)
- Kevin Cowtan
- Department of Chemistry, University of York, York YO1 5DD, England
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24
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Sherman EM, Holmes S, Ye JD. Specific RNA-binding antibodies with a four-amino-acid code. J Mol Biol 2014; 426:2145-57. [PMID: 24631830 DOI: 10.1016/j.jmb.2014.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 02/28/2014] [Accepted: 03/01/2014] [Indexed: 01/23/2023]
Abstract
Numerous large non-coding RNAs are rapidly being discovered, and many of them have been shown to play vital roles in gene expression, gene regulation, and human diseases. Given their often structured nature, specific recognition with an antibody fragment becomes feasible and may help define the structure and function of these non-coding RNAs. As demonstrated for protein antigens, specific antibodies may aid in RNA crystal structure elucidation or the development of diagnostic tools and therapeutic drugs targeting disease-causing RNAs. Recent success and limitation of RNA antibody development has made it imperative to generate an effective antibody library specifically targeting RNA molecules. Adopting the reduced chemical diversity design and further restricting the interface diversity to tyrosines, serines, glycines, and arginines only, we have constructed a RNA-targeting Fab library. Phage display selection and downstream characterization showed that this library yielded high-affinity Fabs for all three RNA targets tested. Using a quantitative specificity assay, we found that these Fabs are highly specific, possibly due to the alternate codon design we used to avoid consecutive arginines in the Fab interface. In addition, the effectiveness of the minimal Fab library may challenge our view of the protein-RNA binding interface and provide a unique solution for future design of RNA-binding proteins.
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Affiliation(s)
- Eileen M Sherman
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
| | - Sean Holmes
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
| | - Jing-Dong Ye
- Department of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA.
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25
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Kraemer-Chant CM, Heckman JE, Lambert D, Burke JM. Cobalt(III)hexaammine-dependent photocrosslinks in the hairpin ribozyme. J Inorg Biochem 2013; 131:87-98. [PMID: 24295878 DOI: 10.1016/j.jinorgbio.2013.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 10/26/2022]
Abstract
We have utilized the hairpin ribozyme, an RNA enzyme whose structure has been solved by high-resolution methods, to develop a new tool for mapping nucleobase-stacking interactions and potential metal-binding sites in RNA molecules. This tool involves the photoactivation of a specifically bound cobalt(III)hexaammine molecule at wavelengths corresponding to excitation of the metal ion complex only; no base excitation is involved. The photoexcitation initiates a process which strongly promotes the formation of a novel covalent bond or crosslink between one base (termed the "first base"), which is close in space to the excited cobalt(III)hexaammine complex, and another base upon which the first base is closely stacked. These crosslinked species can be isolated and sequenced; their activities can be analyzed to ensure that the crosslinked structures represent an active conformation of the molecule. We have shown that, as in electron transfer in DNA, several criteria must be met to result in the successful formation of these crosslinks. These include the appropriate oxidation potential of the first donor base, the stacking and close interaction of the two donor bases involved in the crosslink, and the binding of a specific cobalt(III)hexaammine molecule to the first donor base. Additionally, we have determined that this crosslinking is pH-sensitive, although the cause of this sensitivity remains unknown. This tool has proven useful in the past for the analysis of the hairpin ribozyme folded structure, and has been applied to identify potential metal-binding sites on the hairpin and extended hammerhead ribozymes.
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Affiliation(s)
- Christina M Kraemer-Chant
- Department of Microbiology and Molecular Genetics, 95 Carrigan Drive, University of Vermont, Burlington, VT 05405, USA.
| | - Joyce E Heckman
- Department of Microbiology and Molecular Genetics, 95 Carrigan Drive, University of Vermont, Burlington, VT 05405, USA
| | - Dominic Lambert
- Department of Microbiology and Molecular Genetics, 95 Carrigan Drive, University of Vermont, Burlington, VT 05405, USA
| | - John M Burke
- Department of Microbiology and Molecular Genetics, 95 Carrigan Drive, University of Vermont, Burlington, VT 05405, USA
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26
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Abstract
Nearly two decades after Westhof and Michel first proposed that RNA tetraloops may interact with distal helices, tetraloop–receptor interactions have been recognized as ubiquitous elements of RNA tertiary structure. The unique architecture of GNRA tetraloops (N=any nucleotide, R=purine) enables interaction with a variety of receptors, e.g., helical minor grooves and asymmetric internal loops. The most common example of the latter is the GAAA tetraloop–11 nt tetraloop receptor motif. Biophysical characterization of this motif provided evidence for the modularity of RNA structure, with applications spanning improved crystallization methods to RNA tectonics. In this review, we identify and compare types of GNRA tetraloop–receptor interactions. Then we explore the abundance of structural, kinetic, and thermodynamic information on the frequently occurring and most widely studied GAAA tetraloop–11 nt receptor motif. Studies of this interaction have revealed powerful paradigms for structural assembly of RNA, as well as providing new insights into the roles of cations, transition states and protein chaperones in RNA folding pathways. However, further research will clearly be necessary to characterize other tetraloop–receptor and long-range tertiary binding interactions in detail – an important milestone in the quantitative prediction of free energy landscapes for RNA folding.
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27
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Islam B, Sgobba M, Laughton C, Orozco M, Sponer J, Neidle S, Haider S. Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Nucleic Acids Res 2013; 41:2723-35. [PMID: 23293000 PMCID: PMC3575793 DOI: 10.1093/nar/gks1331] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 11/26/2012] [Accepted: 11/27/2012] [Indexed: 01/12/2023] Open
Abstract
The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. Although G-quartet stems have been well characterized, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 μs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology.
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Affiliation(s)
- Barira Islam
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Miriam Sgobba
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Charlie Laughton
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Modesto Orozco
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Jiri Sponer
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Stephen Neidle
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Shozeb Haider
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
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28
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Kraft JJ, Treder K, Peterson MS, Miller WA. Cation-dependent folding of 3' cap-independent translation elements facilitates interaction of a 17-nucleotide conserved sequence with eIF4G. Nucleic Acids Res 2013; 41:3398-413. [PMID: 23361463 PMCID: PMC3597692 DOI: 10.1093/nar/gkt026] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The 3′-untranslated regions of many plant viral RNAs contain cap-independent translation elements (CITEs) that drive translation initiation at the 5′-end of the mRNA. The barley yellow dwarf virus-like CITE (BTE) stimulates translation by binding the eIF4G subunit of translation initiation factor eIF4F with high affinity. To understand this interaction, we characterized the dynamic structural properties of the BTE, mapped the eIF4G-binding sites on the BTE and identified a region of eIF4G that is crucial for BTE binding. BTE folding involves cooperative uptake of magnesium ions and is driven primarily by charge neutralization. Footprinting experiments revealed that functional eIF4G fragments protect the highly conserved stem–loop I and a downstream bulge. The BTE forms a functional structure in the absence of protein, and the loop that base pairs the 5′-untranslated region (5′-UTR) remains solvent-accessible at high eIF4G concentrations. The region in eIF4G between the eIF4E-binding site and the MIF4G region is required for BTE binding and translation. The data support the model in which the eIF4F complex binds directly to the BTE which base pairs simultaneously to the 5′-UTR, allowing eIF4F to recruit the 40S ribosomal subunit to the 5′-end.
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Affiliation(s)
- Jelena J Kraft
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA
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29
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Coonrod LA, Lohman JR, Berglund JA. Utilizing the GAAA tetraloop/receptor to facilitate crystal packing and determination of the structure of a CUG RNA helix. Biochemistry 2012; 51:8330-7. [PMID: 23025897 DOI: 10.1021/bi300829w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is a microsatellite expansion disorder caused by the aberrant expansion of CTG repeats in the 3'-untranslated region of the DMPK gene. When transcribed, the toxic RNA CUG repeats sequester RNA binding proteins, which leads to disease symptoms. The expanded CUG repeats can adopt a double-stranded structure, and targeting this helix is a therapeutic strategy for DM1. To improve our understanding of the 5'CUG/3'GUC motif and how it may interact with proteins and small molecules, we designed a short CUG helix attached to a GAAA tetraloop/receptor to facilitate crystal packing. Here we report the highest-resolution structure (1.95 Å) to date of a GAAA tetraloop/receptor and the CUG helix it was used to crystallize. Within the CUG helix, we identify two different forms of noncanonical U-U pairs and reconfirm that CUG repeats are essentially A-form. An analysis of all noncanonical U-U pairs in the context of CUG repeats revealed six different classes of conformations that the noncanonical U-U pairs are able to adopt.
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Affiliation(s)
- Leslie A Coonrod
- Institute of Molecular Biology and Department of Chemistry, University of Oregon, Eugene, OR 97403, USA
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30
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Frederiksen JK, Li NS, Das R, Herschlag D, Piccirilli JA. Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding. RNA (NEW YORK, N.Y.) 2012; 18:1123-1141. [PMID: 22539523 PMCID: PMC3358636 DOI: 10.1261/rna.028738.111] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 01/17/2012] [Indexed: 05/27/2023]
Abstract
Within the three-dimensional architectures of RNA molecules, divalent metal ions populate specific locations, shedding their water molecules to form chelates. These interactions help the RNA adopt and maintain specific conformations and frequently make essential contributions to function. Defining the locations of these site-bound metal ions remains challenging despite the growing database of RNA structures. Metal-ion rescue experiments have provided a powerful approach to identify and distinguish catalytic metal ions within RNA active sites, but the ability of such experiments to identify metal ions that contribute to tertiary structure acquisition and structural stability is less developed and has been challenged. Herein, we use the well-defined P4-P6 RNA domain of the Tetrahymena group I intron to reevaluate prior evidence against the discriminatory power of metal-ion rescue experiments and to advance thermodynamic descriptions necessary for interpreting these experiments. The approach successfully identifies ligands within the RNA that occupy the inner coordination sphere of divalent metal ions and distinguishes them from ligands that occupy the outer coordination sphere. Our results underscore the importance of obtaining complete folding isotherms and establishing and evaluating thermodynamic models in order to draw conclusions from metal-ion rescue experiments. These results establish metal-ion rescue as a rigorous tool for identifying and dissecting energetically important metal-ion interactions in RNAs that are noncatalytic but critical for RNA tertiary structure.
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Affiliation(s)
- John K. Frederiksen
- The Pritzker School of Medicine
- Department of Biochemistry and Molecular Biology
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rhiju Das
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, California 94305-5307, USA
| | - Daniel Herschlag
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, California 94305-5307, USA
| | - Joseph A. Piccirilli
- Department of Biochemistry and Molecular Biology
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
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31
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Koculi E, Cho SS, Desai R, Thirumalai D, Woodson SA. Folding path of P5abc RNA involves direct coupling of secondary and tertiary structures. Nucleic Acids Res 2012; 40:8011-20. [PMID: 22641849 PMCID: PMC3439887 DOI: 10.1093/nar/gks468] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Folding mechanisms in which secondary structures are stabilized through the formation of tertiary interactions are well documented in protein folding but challenge the folding hierarchy normally assumed for RNA. However, it is increasingly clear that RNA could fold by a similar mechanism. P5abc, a small independently folding tertiary domain of the Tetrahymena thermophila group I ribozyme, is known to fold by a secondary structure rearrangement involving helix P5c. However, the extent of this rearrangement and the precise stage of folding that triggers it are unknown. We use experiments and simulations to show that the P5c helix switches to the native secondary structure late in the folding pathway and is directly coupled to the formation of tertiary interactions in the A-rich bulge. P5c mutations show that the switch in P5c is not rate-determining and suggest that non-native interactions in P5c aid folding rather than impede it. Our study illustrates that despite significant differences in the building blocks of proteins and RNA, there may be common ways in which they self-assemble.
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Affiliation(s)
- Eda Koculi
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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32
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Bowman JC, Lenz TK, Hud NV, Williams LD. Cations in charge: magnesium ions in RNA folding and catalysis. Curr Opin Struct Biol 2012; 22:262-72. [PMID: 22595008 DOI: 10.1016/j.sbi.2012.04.006] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 04/24/2012] [Accepted: 04/24/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Jessica C Bowman
- School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332-0400, United States
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33
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Piccirilli JA, Koldobskaya Y. Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment. Philos Trans R Soc Lond B Biol Sci 2012; 366:2918-28. [PMID: 21930583 DOI: 10.1098/rstb.2011.0144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
All models of the RNA world era invoke the presence of ribozymes that can catalyse RNA polymerization. The class I ligase ribozyme selected in vitro 15 years ago from a pool of random RNA sequences catalyses formation of a 3',5'-phosphodiester linkage analogous to a single step of RNA polymerization. Recently, the three-dimensional structure of the ligase was solved in complex with U1A RNA-binding protein and independently in complex with an antibody fragment. The RNA adopts a tripod arrangement and appears to use a two-metal ion mechanism similar to protein polymerases. Here, we discuss structural implications for engineering a true polymerase ribozyme and describe the use of the antibody framework both as a portable chaperone for crystallization of other RNAs and as a platform for exploring steps in evolution from the RNA world to the RNA-protein world.
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Affiliation(s)
- Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Gordon Center for Integrative Science, Room W406, Chicago, IL 60637, USA.
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34
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Mládek A, Šponer JE, Kulhánek P, Lu XJ, Olson WK, Šponer J. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. J Chem Theory Comput 2012; 8:335-347. [PMID: 22712001 PMCID: PMC3375708 DOI: 10.1021/ct200712b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Folded RNA molecules are shaped by an astonishing variety of highly conserved noncanonical molecular interactions and backbone topologies. The dinucleotide platform is a widespread recurrent RNA modular building submotif formed by the side-by-side pairing of bases from two consecutive nucleotides within a single strand, with highly specific sequence preferences. This unique arrangement of bases is cemented by an intricate network of noncanonical hydrogen bonds and facilitated by a distinctive backbone topology. The present study investigates the gas-phase intrinsic stabilities of the three most common RNA dinucleotide platforms - 5'-GpU-3', ApA, and UpC - via state-of-the-art quantum-chemical (QM) techniques. The mean stability of base-base interactions decreases with sequence in the order GpU > ApA > UpC. Bader's atoms-in-molecules analysis reveals that the N2(G)…O4(U) hydrogen bond of the GpU platform is stronger than the corresponding hydrogen bonds in the other two platforms. The mixed-pucker sugar-phosphate backbone conformation found in most GpU platforms, in which the 5'-ribose sugar (G) is in the C2'-endo form and the 3'-sugar (U) in the C3'-endo form, is intrinsically more stable than the standard A-RNA backbone arrangement, partially as a result of a favorable O2'…O2P intra-platform interaction. Our results thus validate the hypothesis of Lu et al. (Lu Xiang-Jun, et al. Nucleic Acids Res. 2010, 38, 4868-4876), that the superior stability of GpU platforms is partially mediated by the strong O2'…O2P hydrogen bond. In contrast, ApA and especially UpC platform-compatible backbone conformations are rather diverse and do not display any characteristic structural features. The average stabilities of ApA and UpC derived backbone conformers are also lower than those of GpU platforms. Thus, the observed structural and evolutionary patterns of the dinucleotide platforms can be accounted for, to a large extent, by their intrinsic properties as described by modern QM calculations. In contrast, we show that the dinucleotide platform is not properly described in the course of atomistic explicit-solvent simulations. Our work also gives methodological insights into QM calculations of experimental RNA backbone geometries. Such calculations are inherently complicated by rather large data and refinement uncertainties in the available RNA experimental structures, which often preclude reliable energy computations.
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Affiliation(s)
- Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Kulhánek
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Xiang-Jun Lu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Wilma K. Olson
- Department of Chemistry & Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers - The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jiřĺ Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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35
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Abstract
Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.
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Affiliation(s)
- Maria Pechlaner
- Institute of Inorganic Chemistry, University of Zürich, Zürich, Switzerland
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36
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Forconi M, Schwans JP, Porecha RH, Sengupta RN, Piccirilli JA, Herschlag D. 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA. ACTA ACUST UNITED AC 2011; 18:949-54. [PMID: 21867910 DOI: 10.1016/j.chembiol.2011.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 06/20/2011] [Accepted: 07/06/2011] [Indexed: 10/17/2022]
Abstract
The ability of fluorine in a C-F bond to act as a hydrogen bond acceptor is controversial. To test such ability in complex RNA macromolecules, we have replaced native 2'-OH groups with 2'-F and 2'-H groups in two related systems, the Tetrahymena group I ribozyme and the ΔC209 P4-P6 RNA domain. In three cases the introduced 2'-F mimics the native 2'-OH group, suggesting that the fluorine atom can accept a hydrogen bond. In each of these cases the native hydroxyl group interacts with a purine exocyclic amine. Our results give insight about the properties of organofluorine and suggest a possible general biochemical signature for tertiary interactions between 2'-hydroxyl groups and exocyclic amino groups within RNA.
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Affiliation(s)
- Marcello Forconi
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
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37
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Golden BL. Two distinct catalytic strategies in the hepatitis δ virus ribozyme cleavage reaction. Biochemistry 2011; 50:9424-33. [PMID: 22003985 DOI: 10.1021/bi201157t] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The hepatitis delta virus (HDV) ribozyme and related RNAs are widely dispersed in nature. This RNA is a small nucleolytic ribozyme that self-cleaves to generate products with a 2',3'-cyclic phosphate and a free 5'-hydroxyl. Although small ribozymes are dependent on divalent metal ions under biologically relevant buffer conditions, they function in the absence of divalent metal ions at high ionic strengths. This characteristic suggests that a functional group within the covalent structure of small ribozymes is facilitating catalysis. Structural and mechanistic analyses have demonstrated that the HDV ribozyme active site contains a cytosine with a perturbed pK(a) that serves as a general acid to protonate the leaving group. The reaction of the HDV ribozyme in monovalent cations alone never approaches the velocity of the Mg(2+)-dependent reaction, and there is significant biochemical evidence that a Mg(2+) ion participates directly in catalysis. A recent crystal structure of the HDV ribozyme revealed that there is a metal binding pocket in the HDV ribozyme active site. Modeling of the cleavage site into the structure suggested that this metal ion can interact directly with the scissile phosphate and the nucleophile. In this manner, the Mg(2+) ion can serve as a Lewis acid, facilitating deprotonation of the nucleophile and stabilizing the conformation of the cleavage site for in-line attack of the nucleophile at the scissile phosphate. This catalytic strategy had previously been observed only in much larger ribozymes. Thus, in contrast to most large and small ribozymes, the HDV ribozyme uses two distinct catalytic strategies in its cleavage reaction.
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Affiliation(s)
- Barbara L Golden
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, United States.
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38
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Ravindran PP, Héroux A, Ye JD. Improvement of the crystallizability and expression of an RNA crystallization chaperone. J Biochem 2011; 150:535-43. [PMID: 21785128 DOI: 10.1093/jb/mvr093] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Crystallizing RNA has been an imperative and challenging task in the world of RNA research. Assistive methods such as chaperone-assisted RNA crystallography (CARC), employing monoclonal antibody fragments (Fabs) as crystallization chaperones have enabled us to obtain RNA crystal structures by forming crystal contacts and providing initial phasing information. Despite the early successes, the crystallization of large RNA-Fab complex remains a challenge in practice. The possible reason for this difficulty is that the Fab scaffold has not been optimized for crystallization in complex with RNA. Here, we have used the surface entropy reduction (SER) technique for the optimization of ΔC209 P4-P6/Fab2 model system. Protruding lysine and glutamate residues were mutated to a set of alanines or serines to construct Fab2SMA or Fab2SMS. Expression with the shake flask approach was optimized to allow large scale production for crystallization. Crystal screening shows that significantly higher crystal-forming ratio was observed for the mutant complexes. As the chosen SER residues are far away from the CDR regions of the Fab, the same set of mutations can now be directly applied to other Fabs binding to a variety of ribozymes and riboswitches to improve the crystallizability of Fab-RNA complex.
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39
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Abstract
Unlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced the RNA backbone torsion angles to two (η and θ, analogous to φ and ψ in proteins). When these torsion angles are calculated for nucleotides in a crystallographic database and plotted against one another, one obtains a plot analogous to a Ramachandran plot (the η/θ plot), with highly populated and unpopulated regions. Nucleotides that occupy proximal positions on the plot have identical structures and are found in the same units of tertiary structure. In this review, we describe the statistical validation of the η/θ formalism and the exploration of features within the η/θ plot. We also describe the application of the η/θ formalism in RNA motif discovery, structural comparison, RNA structure building and tertiary structure prediction. More than a tool, however, the η/θ formalism has provided new insights into RNA structure itself, revealing its fundamental components and the factors underlying RNA architectural form.
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Insights into metalloregulation by M-box riboswitch RNAs via structural analysis of manganese-bound complexes. J Mol Biol 2011; 407:556-70. [PMID: 21315082 DOI: 10.1016/j.jmb.2011.01.049] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2010] [Revised: 01/18/2011] [Accepted: 01/25/2011] [Indexed: 11/23/2022]
Abstract
The M-box riboswitch couples intracellular magnesium levels to expression of bacterial metal transport genes. Structural analyses on other riboswitch RNA classes, which typically respond to a small organic metabolite, have revealed that ligand recognition occurs through a combination of base-stacking, electrostatic, and hydrogen-bonding interactions. In contrast, the M-box RNA triggers a change in gene expression upon association with an undefined population of metals, rather than responding to only a single ligand. Prior biophysical experimentation suggested that divalent ions associate with the M-box RNA to promote a compacted tertiary conformation, resulting in sequestration of a short sequence tract otherwise required for downstream gene expression. Electrostatic shielding from loosely associated metals is undoubtedly an important influence during this metal-mediated compaction pathway. However, it is also likely that a subset of divalent ions specifically occupies cation binding sites and promotes proper positioning of functional groups for tertiary structure stabilization. To better elucidate the role of these metal binding sites, we resolved a manganese-chelated M-box RNA complex to 1.86 Å by X-ray crystallography. These data support the presence of at least eight well-ordered cation binding pockets, including several sites that had been predicted by biochemical studies but were not observed in prior structural analysis. Overall, these data support the presence of three metal-binding cores within the M-box RNA that facilitate a network of long-range interactions within the metal-bound, compacted conformation.
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41
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Petrov AS, Bowman JC, Harvey SC, Williams LD. Bidentate RNA-magnesium clamps: on the origin of the special role of magnesium in RNA folding. RNA (NEW YORK, N.Y.) 2011; 17:291-7. [PMID: 21173199 PMCID: PMC3022278 DOI: 10.1261/rna.2390311] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 11/04/2010] [Indexed: 05/18/2023]
Abstract
Magnesium plays a special role in RNA function and folding. Although water is magnesium's most common first-shell ligand, the oxyanions of RNA have significant affinity for magnesium. Here we provide a quantum mechanical description of first-shell RNA-magnesium and DNA-magnesium interactions, demonstrating the unique features that characterize the energetics and geometry of magnesium complexes within large folded RNAs. Our work focuses on bidentate chelation of magnesium by RNA or DNA, where multiple phosphate oxyanions enter the first coordination shell of magnesium. These bidentate RNA clamps of magnesium occur frequently in large RNAs. The results here suggest that magnesium, compared to calcium and sodium, has an enhanced ability to form bidentate clamps with RNA. Bidentate RNA-sodium clamps, in particular, are unstable and spontaneously open. Due to magnesium's size and charge density it binds more intimately than other cations to the oxyanions of RNA, so that magnesium clamps are stabilized not only by electrostatic interactions, but also by charge transfer, polarization, and exchange interactions. These nonelectrostatic components of the binding are quite substantial with the high charge and small interatomic distances within the magnesium complexes, but are less pronounced for calcium due to its larger size, and for sodium due to its smaller charge. Additionally, bidentate RNA clamps of magnesium are more stable than those with DNA. The source of the additional stability of RNA complexes is twofold: there is a slightly attenuated energetic penalty for ring closure in the formation of RNA bidentate chelation complexes and elevated electrostatic interactions between the RNA and cations. In sum, it can be seen why sodium and calcium cannot replicate the structures or energetics of RNA-magnesium complexes.
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Affiliation(s)
- Anton S Petrov
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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42
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Novikova IV, Hassan BH, Mirzoyan MG, Leontis NB. Engineering cooperative tecto-RNA complexes having programmable stoichiometries. Nucleic Acids Res 2010; 39:2903-17. [PMID: 21138969 PMCID: PMC3074147 DOI: 10.1093/nar/gkq1231] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High affinity and specificity RNA-RNA binding interfaces can be constructed by combining pairs of GNRA loop/loop-receptor interaction motifs. These interactions can be fused using flexible four-way junction motifs to create divalent, self-assembling scaffolding units ('tecto-RNA') that have favorable properties for nanomedicine and other applications. We describe the design and directed assembly of tecto-RNA units ranging from closed, cooperatively assembling ring-shaped complexes of programmable stoichiometries (dimers, trimers and tetramers) to open multimeric structures. The novelty of this work is that tuning of the stoichiometries of self-assembled complexes is achieved by precise positioning of the interaction motifs in the monomer units rather than changing their binding specificities. Structure-probing and transmission electron microscopy studies as well as thermodynamic analysis support formation of closed cooperative complexes that are highly resistant to nuclease digestion. The present designs provide two helical arms per RNA monomer for further functionalization aims.
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Affiliation(s)
- Irina V Novikova
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
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43
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Edwards AL, Reyes FE, Héroux A, Batey RT. Structural basis for recognition of S-adenosylhomocysteine by riboswitches. RNA (NEW YORK, N.Y.) 2010; 16:2144-55. [PMID: 20864509 PMCID: PMC2957054 DOI: 10.1261/rna.2341610] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 08/16/2010] [Indexed: 05/25/2023]
Abstract
S-adenosyl-(L)-homocysteine (SAH) riboswitches are regulatory elements found in bacterial mRNAs that up-regulate genes involved in the S-adenosyl-(L)-methionine (SAM) regeneration cycle. To understand the structural basis of SAH-dependent regulation by RNA, we have solved the structure of its metabolite-binding domain in complex with SAH. This structure reveals an unusual pseudoknot topology that creates a shallow groove on the surface of the RNA that binds SAH primarily through interactions with the adenine ring and methionine main chain atoms and discriminates against SAM through a steric mechanism. Chemical probing and calorimetric analysis indicate that the unliganded RNA can access bound-like conformations that are significantly stabilized by SAH to direct folding of the downstream regulatory switch. Strikingly, we find that metabolites bearing an adenine ring, including ATP, bind this aptamer with sufficiently high affinity such that normal intracellular concentrations of these compounds may influence regulation of the riboswitch.
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Affiliation(s)
- Andrea L Edwards
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215, USA
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44
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Kieft JS, Chase E, Costantino DA, Golden BL. Identification and characterization of anion binding sites in RNA. RNA (NEW YORK, N.Y.) 2010; 16:1118-1123. [PMID: 20410239 PMCID: PMC2874163 DOI: 10.1261/rna.2072710] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Accepted: 02/17/2010] [Indexed: 05/29/2023]
Abstract
Although RNA molecules are highly negatively charged, anions have been observed bound to RNA in crystal structures. It has been proposed that anion binding sites found within isolated RNAs represent regions of the molecule that could be involved in intermolecular interactions, indicating potential contact points for negatively charged amino acids from proteins or phosphate groups from an RNA. Several types of anion binding sites have been cataloged based on available structures. However, currently there is no method for unambiguously assigning anions to crystallographic electron density, and this has precluded more detailed analysis of RNA-anion interaction motifs and their significance. We therefore soaked selenate into two different types of RNA crystals and used the anomalous signal from these anions to identify binding sites in these RNA molecules unambiguously. Examination of these sites and comparison with other suspected anion binding sites reveals features of anion binding motifs, and shows that selenate may be a useful tool for studying RNA-anion interactions.
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Affiliation(s)
- Jeffrey S Kieft
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, 80045, USA.
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45
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Christian EL, Anderson VE, Carey PR, Harris ME. A quantitative Raman spectroscopic signal for metal-phosphodiester interactions in solution. Biochemistry 2010; 49:2869-79. [PMID: 20180599 DOI: 10.1021/bi901866u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate identification and quantification of metal ion-phosphodiester interactions are essential for understanding the role of metal ions as determinants of three-dimensional folding of large RNAs and as cofactors in the active sites of both RNA and protein phosphodiesterases. Accomplishing this goal is difficult due to the dynamic and complex mixture of direct and indirect interactions formed with nucleic acids and other phosphodiesters in solution. To address this issue, Raman spectroscopy has been used to measure changes in bond vibrational energies due to metal interactions. However, the contributions of inner-sphere, H-bonding, and electrostatic interactions to the Raman spectrum of phosphoryl oxygens have not been analyzed quantitatively. Here, we report that all three forms of metal ion interaction result in attenuation of the Raman signal for the symmetric vibration of the nonbridging phosphate oxygens (nu(s)PO(2)(-)), while only inner-sphere coordination gives rise to an apparent shift of nu(s)PO(2)(-) to higher wavenumbers (nu(s)PO(2)(-)M) in solution. Formation of nu(s)PO(2)(-)M is shown to be both dependent on metal ion identity and an accurate measure of site-specific metal ion binding. In addition, the spectroscopic parameter reflecting the energetic difference between nu(s)PO(2)(-) and nu(s)PO(2)(-)M (DeltanuM) is largely insensitive to changes in phosphodiester structure but strongly dependent on the absolute electronegativity and hardness of the interacting metal ion. Together, these studies provide strong experimental support for the use of nu(s)PO(2)(-)M and DeltanuM as general spectroscopic features for the quantitative analysis of metal binding affinity and the identification of metal ions associated with phosphodiesters in solution.
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Affiliation(s)
- Eric L Christian
- Center for RNA Molecular Biology, Case Western Reserve University School of Medicine,Cleveland, Ohio 44106, USA.
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46
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Wang W, Zhao J, Han Q, Wang G, Yang G, Shallop AJ, Liu J, Gaffney BL, Jones RA. Modulation of RNA metal binding by flanking bases: 15N NMR evaluation of GC, tandem GU, and tandem GA sites. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:424-34. [PMID: 20183593 DOI: 10.1080/15257770903044234] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
(15)N NMR chemical shift changes in the presence of Mg(H(2)O)(6)(2+), Zn(2+), Cd(2+), and Co(NH(3))(6)(3+) were used to probe the effect of flanking bases on metal binding sites in three different RNA motifs. We found that: for GC pairs, the presence of a flanking purine creates a site for the soft metals Zn(2+) and Cd(2+) only; a GG.UU motif selectively binds only Co(NH(3))(6)(3+), while a UG.GU motif binds none of these metals; a 3' guanosine flanking the adenosine of a sheared GA.AG pair creates an unusually strong binding site that precludes binding to the cross-strand stacked guanosines within the tandem pair.
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Affiliation(s)
- Weimin Wang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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47
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Montange RK, Mondragón E, van Tyne D, Garst AD, Ceres P, Batey RT. Discrimination between closely related cellular metabolites by the SAM-I riboswitch. J Mol Biol 2009; 396:761-72. [PMID: 20006621 DOI: 10.1016/j.jmb.2009.12.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 11/30/2009] [Accepted: 12/06/2009] [Indexed: 12/17/2022]
Abstract
The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-A X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-A improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.
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Affiliation(s)
- Rebecca K Montange
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Campus Box 215, Boulder, CO 80309-0215, USA
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48
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Hunsicker-Wang L, Vogt M, Derose VJ. EPR methods to study specific metal-ion binding sites in RNA. Methods Enzymol 2009; 468:335-67. [PMID: 20946777 DOI: 10.1016/s0076-6879(09)68016-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The properties of metal-ion interactions with RNA can be explored by spectroscopic methods. In this chapter, we describe the use of paramagnetic Mn(2+) ions and electron paramagnetic resonance (EPR)-based techniques to monitor the association of Mn(2+) with RNA and related nucleotides. Solution EPR methods are used to determine the numbers of Mn(2+) ions associating with RNA. For RNA poised with a single-bound Mn(2+), low-temperature EPR characteristics provide information about the asymmetry of the Mn(2+) coordination site. To identify the RNA groups coordinating to the Mn(2+) ion, ENDOR (electron nuclear double resonance) and ESEEM (electron spin echo envelope modulation) methods are applied. Both continuous-wave (CW) and electron spin echo (ESE)-detected ENDOR methods are described. This chapter includes practical details for RNA sample preparation, including isotope substitution and cryoprotection, and an overview of data acquisition and analysis methods used in these techniques, as well as examples from the current literature.
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Abstract
The 2'-hydroxyl group plays an integral role in RNA structure and catalysis. This ubiquitous component of the RNA backbone can participate in multiple interactions essential for RNA function, such as hydrogen bonding and metal ion coordination, but the multifunctional nature of the 2'-hydroxyl renders identification of these interactions a significant challenge. By virtue of their versatile physicochemical properties, such as distinct metal coordination preferences, hydrogen bonding properties, and ability to be protonated, 2'-amino-2'-deoxyribonucleotides can serve as tools for probing local interactions involving 2'-hydroxyl groups within RNA. The 2'-amino group can also serve as a chemoselective site for covalent modification, permitting the introduction of probes for investigation of RNA structure and dynamics. In this chapter, we describe the use of 2'-aminonucleotides for investigation of local interactions within RNA, focusing on interactions involving 2'-hydroxyl groups required for RNA structure, function, and catalysis.
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50
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Vicens Q, Gooding AR, Duarte LF, Batey RT. Preparation of group I introns for biochemical studies and crystallization assays by native affinity purification. PLoS One 2009; 4:e6740. [PMID: 19710925 PMCID: PMC2729099 DOI: 10.1371/journal.pone.0006740] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Accepted: 07/27/2009] [Indexed: 11/19/2022] Open
Abstract
The study of functional RNAs of various sizes and structures requires efficient methods for their synthesis and purification. Here, 23 group I intron variants ranging in length from 246 to 341 nucleotides—some containing exons—were subjected to a native purification technique previously applied only to shorter RNAs (<160 nucleotides). For the RNAs containing both exons, we adjusted the original purification protocol to allow for purification of radiolabeled molecules. The resulting RNAs were used in folding assays on native gel electrophoresis and in self-splicing assays. The intron-only RNAs were subjected to the regular native purification scheme, assayed for folding and employed in crystallization screens. All RNAs that contained a 3′ overhang of one nucleotide were efficiently cleaved off from the support and were at least 90% pure after the non-denaturing purification. A representative subset of these RNAs was shown to be folded and self-splicing after purification. Additionally, crystals were grown for a 286 nucleotide long variant of the Clostridium botulinum intron. These results demonstrate the suitability of the native affinity purification method for the preparation of group I introns. We hope these findings will stimulate a broader application of this strategy to the preparation of other large RNA molecules.
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Affiliation(s)
- Quentin Vicens
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA.
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