1
|
Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol 2024; 21:1-32. [PMID: 38100535 PMCID: PMC10730233 DOI: 10.1080/15476286.2023.2289709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses remain a global threat to animals, plants, and humans. The type 1 human immunodeficiency virus (HIV-1) is a member of the retrovirus family and carries an RNA genome, which is reverse transcribed into viral DNA and further integrated into the host-cell DNA for viral replication and proliferation. The RNA structures from the HIV-1 genome provide valuable insights into the mechanisms underlying the viral replication cycle. Moreover, these structures serve as models for designing novel therapeutic approaches. Here, we review structural data on RNA from the HIV-1 genome as well as computational studies based on these structural data. The review is organized according to the type of structured RNA element which contributes to different steps in the viral replication cycle. This is followed by an overview of the HIV-1 transactivation response element (TAR) RNA as a model system for understanding dynamics and interactions in the viral RNA systems. The review concludes with a description of computational studies, highlighting the impact of biomolecular simulations in elucidating the mechanistic details of various steps in the HIV-1's replication cycle.
Collapse
Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
| | - Harish Vashisth
- Department of Chemical Engineering & Bioengineering, University of New Hampshire, Durham, USA
| |
Collapse
|
2
|
Ding J, Deme J, Stagno JR, Yu P, Lea S, Wang YX. Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM. Nucleic Acids Res 2023; 51:9952-9960. [PMID: 37534568 PMCID: PMC10570017 DOI: 10.1093/nar/gkad651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/13/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023] Open
Abstract
RNA conformational heterogeneity often hampers its high-resolution structure determination, especially for large and flexible RNAs devoid of stabilizing proteins or ligands. The adenosylcobalamin riboswitch exhibits heterogeneous conformations under 1 mM Mg2+ concentration and ligand binding reduces conformational flexibility. Among all conformers, we determined one apo (5.3 Å) and four holo cryo-electron microscopy structures (overall 3.0-3.5 Å, binding pocket 2.9-3.2 Å). The holo dimers exhibit global motions of helical twisting and bending around the dimer interface. A backbone comparison of the apo and holo states reveals a large structural difference in the P6 extension position. The central strand of the binding pocket, junction 6/3, changes from an 'S'- to a 'U'-shaped conformation to accommodate ligand. Furthermore, the binding pocket can partially form under 1 mM Mg2+ and fully form under 10 mM Mg2+ within the bound-like structure in the absence of ligand. Our results not only demonstrate the stabilizing ligand-induced conformational changes in and around the binding pocket but may also provide further insight into the role of the P6 extension in ligand binding and selectivity.
Collapse
Affiliation(s)
- Jienyu Ding
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Justin C Deme
- Molecular Basis of Disease Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Jason R Stagno
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Ping Yu
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Susan M Lea
- Molecular Basis of Disease Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein–Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| |
Collapse
|
3
|
Deng J, Fang X, Huang L, Li S, Xu L, Ye K, Zhang J, Zhang K, Zhang QC. RNA structure determination: From 2D to 3D. FUNDAMENTAL RESEARCH 2023; 3:727-737. [PMID: 38933295 PMCID: PMC11197651 DOI: 10.1016/j.fmre.2023.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2024] Open
Abstract
RNA molecules serve a wide range of functions that are closely linked to their structures. The basic structural units of RNA consist of single- and double-stranded regions. In order to carry out advanced functions such as catalysis and ligand binding, certain types of RNAs can adopt higher-order structures. The analysis of RNA structures has progressed alongside advancements in structural biology techniques, but it comes with its own set of challenges and corresponding solutions. In this review, we will discuss recent advances in RNA structure analysis techniques, including structural probing methods, X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and small-angle X-ray scattering. Often, a combination of multiple techniques is employed for the integrated analysis of RNA structures. We also survey important RNA structures that have been recently determined using various techniques.
Collapse
Affiliation(s)
- Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xianyang Fang
- Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Shanshan Li
- MOE Key Laboratory for Cellular Dynamics and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Lilei Xu
- Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinsong Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| |
Collapse
|
4
|
Banna HA, Das NK, Ojha M, Koirala D. Advances in chaperone-assisted RNA crystallography using synthetic antibodies. BBA ADVANCES 2023; 4:100101. [PMID: 37655005 PMCID: PMC10466895 DOI: 10.1016/j.bbadva.2023.100101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/13/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023] Open
Abstract
RNA molecules play essential roles in many biological functions, from gene expression regulation, cellular growth, and metabolism to catalysis. They frequently fold into three-dimensional structures to perform their functions. Therefore, determining RNA structure represents a key step for understanding the structure-function relationships and developing RNA-targeted therapeutics. X-ray crystallography remains a method of choice for determining high-resolution RNA structures, but it has been challenging due to difficulties associated with RNA crystallization and phasing. Several natural and synthetic RNA binding proteins have been used to facilitate RNA crystallography. Having unique properties to help crystal packing and phasing, synthetic antibody fragments, specifically the Fabs, have emerged as promising RNA crystallization chaperones, and so far, over a dozen of RNA structures have been solved using this strategy. Nevertheless, multiple steps in this approach need to be improved, including the recombinant expression of these anti-RNA Fabs, to warrant the full potential of these synthetic Fabs as RNA crystallization chaperones. This review highlights the nuts and bolts and recent advances in the chaperone-assisted RNA crystallography approach, specifically emphasizing the Fab antibody fragments as RNA crystallization chaperones.
Collapse
Affiliation(s)
- Hasan Al Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Naba Krishna Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
| |
Collapse
|
5
|
Li S, Zhang K, Chiu W. Near-Atomic Resolution Cryo-EM Image Reconstruction of RNA. Methods Mol Biol 2023; 2568:179-192. [PMID: 36227569 DOI: 10.1007/978-1-0716-2687-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The rapid development of cryogenic electron microscopy (cryo-EM) enables the structure determination of macromolecules without the need for crystallization. Protein, protein-lipid, and protein-nucleic acid complexes can now be routinely resolved by cryo-EM single-particle analysis (SPA) to near-atomic or atomic resolution. Here we describe the structure determination of pure RNAs by SPA, from cryo-specimen preparation to data collection and 3D reconstruction. This protocol is useful to yield many cryo-EM structures of RNA, here exemplified by the Tetrahymena L-21 ScaI ribozyme at 3.1-Å resolution.
Collapse
Affiliation(s)
- Shanshan Li
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
| |
Collapse
|
6
|
Sharma S, Pisignano G, Merulla J, Catapano CV, Varani G. A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript. Nucleic Acids Res 2022; 50:11331-11343. [PMID: 36243981 DOI: 10.1093/nar/gkac875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 09/03/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Transcription of E-cadherin, a tumor suppressor that plays critical roles in cell adhesion and the epithelial-mesenchymal transition, is regulated by a promoter-associated non-coding RNA (paRNA). The sense-oriented paRNA (S-paRNA) includes a functional C/A single nucleotide polymorphism (SNP rs16260). The A-allele leads to decreased transcriptional activity and increased prostate cancer risk. The polymorphic site is known to affect binding of a microRNA-guided Argonaute 1 (AGO1) complex and recruitment of chromatin-modifying enzymes to silence the promoter. Yet the SNP is distant from the microRNA-AGO1 binding domain in both primary sequence and secondary structure, raising the question of how regulation occurs. Here we report the 3D NMR structure of the 104-nucleotide domain of the S-paRNA that encompasses the SNP and the microRNA-binding site. We show that the A to C change alters the locally dynamic and metastable structure of the S-paRNA, revealing how the single nucleotide mutation regulates the E-cadherin promoter through its effect on the non-coding RNA structure.
Collapse
Affiliation(s)
- Shrikant Sharma
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | | | - Jessica Merulla
- Institute of Oncology Research (IOR), Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland
| | - Carlo V Catapano
- Institute of Oncology Research (IOR), Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| |
Collapse
|
7
|
Dayie TK, Olenginski LT, Taiwo KM. Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs. Chem Rev 2022; 122:9357-9394. [PMID: 35442658 PMCID: PMC9136934 DOI: 10.1021/acs.chemrev.1c00845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 02/07/2023]
Abstract
RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.
Collapse
Affiliation(s)
- Theodore K. Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kehinde M. Taiwo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
8
|
Guan X, Wang Y, Shao W, Li Z, Huang S, Zhang D. S2Snet: deep learning for low molecular weight RNA identification with nanopore. Brief Bioinform 2022; 23:6562681. [DOI: 10.1093/bib/bbac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Ribonucleic acid (RNA) is a pivotal nucleic acid that plays a crucial role in regulating many biological activities. Recently, one study utilized a machine learning algorithm to automatically classify RNA structural events generated by a Mycobacterium smegmatis porin A nanopore trap. Although it can achieve desirable classification results, compared with deep learning (DL) methods, this classic machine learning requires domain knowledge to manually extract features, which is sophisticated, labor-intensive and time-consuming. Meanwhile, the generated original RNA structural events are not strictly equal in length, which is incompatible with the input requirements of DL models. To alleviate this issue, we propose a sequence-to-sequence (S2S) module that transforms the unequal length sequence (UELS) to the equal length sequence. Furthermore, to automatically extract features from the RNA structural events, we propose a sequence-to-sequence neural network based on DL. In addition, we add an attention mechanism to capture vital information for classification, such as dwell time and blockage amplitude. Through quantitative and qualitative analysis, the experimental results have achieved about a 2% performance increase (accuracy) compared to the previous method. The proposed method can also be applied to other nanopore platforms, such as the famous Oxford nanopore. It is worth noting that the proposed method is not only aimed at pursuing state-of-the-art performance but also provides an overall idea to process nanopore data with UELS.
Collapse
Affiliation(s)
- Xiaoyu Guan
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Wei Shao
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| | - Zhongnian Li
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| |
Collapse
|
9
|
Ma H, Jia X, Zhang K, Su Z. Cryo-EM advances in RNA structure determination. Signal Transduct Target Ther 2022; 7:58. [PMID: 35197441 PMCID: PMC8864457 DOI: 10.1038/s41392-022-00916-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 02/08/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) has emerged as an unprecedented tool to resolve protein structures at atomic resolution. Structural insights of biological samples not accessible by conventional X-ray crystallography and NMR can be explored with cryo-EM because measurements are carried out under near-native crystal-free conditions, and large protein complexes with conformational and compositional heterogeneity are readily resolved. RNA has remained underexplored in cryo-EM, despite its essential role in various biological processes. This review highlights current challenges and recent progress in using cryo-EM single-particle analysis to determine protein-free RNA structures, enabled by improvement in sample preparation and integration of multiple structural and biochemical methods.
Collapse
Affiliation(s)
- Haiyun Ma
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, China
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, China.
| |
Collapse
|
10
|
Holmes JB, Liu V, Caulkins BG, Hilario E, Ghosh RK, Drago VN, Young RP, Romero JA, Gill AD, Bogie PM, Paulino J, Wang X, Riviere G, Bosken YK, Struppe J, Hassan A, Guidoulianov J, Perrone B, Mentink-Vigier F, Chang CEA, Long JR, Hooley RJ, Mueser TC, Dunn MF, Mueller LJ. Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate. Proc Natl Acad Sci U S A 2022; 119:e2109235119. [PMID: 34996869 PMCID: PMC8764694 DOI: 10.1073/pnas.2109235119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 02/07/2023] Open
Abstract
NMR-assisted crystallography-the integrated application of solid-state NMR, X-ray crystallography, and first-principles computational chemistry-holds significant promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in enzyme active sites, including hydrogen atom locations and tautomeric equilibria, NMR crystallography offers insight into both structure and chemical dynamics. Here, this integrated approach is used to characterize the tryptophan synthase α-aminoacrylate intermediate, a defining species for pyridoxal-5'-phosphate-dependent enzymes that catalyze β-elimination and replacement reactions. For this intermediate, NMR-assisted crystallography is able to identify the protonation states of the ionizable sites on the cofactor, substrate, and catalytic side chains as well as the location and orientation of crystallographic waters within the active site. Most notable is the water molecule immediately adjacent to the substrate β-carbon, which serves as a hydrogen bond donor to the ε-amino group of the acid-base catalytic residue βLys87. From this analysis, a detailed three-dimensional picture of structure and reactivity emerges, highlighting the fate of the L-serine hydroxyl leaving group and the reaction pathway back to the preceding transition state. Reaction of the α-aminoacrylate intermediate with benzimidazole, an isostere of the natural substrate indole, shows benzimidazole bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the benzimidazole position, indole is positioned with C3 in contact with the α-aminoacrylate Cβ and aligned for nucleophilic attack. Here, the chemically detailed, three-dimensional structure from NMR-assisted crystallography is key to understanding why benzimidazole does not react, while indole does.
Collapse
Affiliation(s)
- Jacob B Holmes
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Viktoriia Liu
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Bethany G Caulkins
- Department of Chemistry, University of California, Riverside, CA 92521
- W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711
| | - Eduardo Hilario
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Rittik K Ghosh
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Victoria N Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606
| | - Robert P Young
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Jennifer A Romero
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Adam D Gill
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Paul M Bogie
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Joana Paulino
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310
| | - Xiaoling Wang
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310
| | - Gwladys Riviere
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, National High Magnetic Field Laboratory, University of Florida, Gainesville, FL 32610
| | - Yuliana K Bosken
- Department of Biochemistry, University of California, Riverside, CA 92521
| | | | - Alia Hassan
- Bruker Switzerland AG 8117 Fällanden, Switzerland
| | | | | | | | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Joanna R Long
- Department of Biochemistry and Molecular Biology, McKnight Brain Institute, National High Magnetic Field Laboratory, University of Florida, Gainesville, FL 32610
| | - Richard J Hooley
- Department of Chemistry, University of California, Riverside, CA 92521
- Department of Biochemistry, University of California, Riverside, CA 92521
| | - Timothy C Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606
| | - Michael F Dunn
- Department of Biochemistry, University of California, Riverside, CA 92521;
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, CA 92521;
| |
Collapse
|
11
|
Dagenais P, Desjardins G, Legault P. An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme. Nucleic Acids Res 2021; 49:11959-11973. [PMID: 34718697 PMCID: PMC8599749 DOI: 10.1093/nar/gkab963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.
Collapse
Affiliation(s)
- Pierre Dagenais
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Geneviève Desjardins
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Pascale Legault
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| |
Collapse
|
12
|
Blakemore RJ, Burnett C, Swanson C, Kharytonchyk S, Telesnitsky A, Munro JB. Stability and conformation of the dimeric HIV-1 genomic RNA 5'UTR. Biophys J 2021; 120:4874-4890. [PMID: 34529947 PMCID: PMC8595565 DOI: 10.1016/j.bpj.2021.09.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/13/2021] [Accepted: 09/08/2021] [Indexed: 12/20/2022] Open
Abstract
During HIV-1 assembly, the viral Gag polyprotein specifically selects the dimeric RNA genome for packaging into new virions. The 5′ untranslated region (5′UTR) of the dimeric genome may adopt a conformation that is optimal for recognition by Gag. Further conformational rearrangement of the 5′UTR, promoted by the nucleocapsid (NC) domain of Gag, is predicted during virus maturation. Two 5′UTR dimer conformations, the kissing dimer (KD) and the extended dimer (ED), have been identified in vitro, which differ in the extent of intermolecular basepairing. Whether 5′UTRs from different HIV-1 strains with distinct sequences have access to the same dimer conformations has not been determined. Here, we applied fluorescence cross-correlation spectroscopy and single-molecule Förster resonance energy transfer imaging to demonstrate that 5′UTRs from two different HIV-1 subtypes form (KDs) with divergent stabilities. We further show that both 5′UTRs convert to a stable dimer in the presence of the viral NC protein, adopting a conformation consistent with extensive intermolecular contacts. These results support a unified model in which the genomes of diverse HIV-1 strains adopt an ED conformation.
Collapse
Affiliation(s)
- Robert J Blakemore
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and School of Graduate Biomedical Sciences, Boston, Massachusetts; Graduate Program in Molecular Microbiology, Tufts University Graduate School of Biomedical Sciences, Boston, Massachusetts
| | - Cleo Burnett
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Canessa Swanson
- Department of Chemistry and Biochemistry, University of Maryland Baltimore Country, Baltimore, Maryland
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and School of Graduate Biomedical Sciences, Boston, Massachusetts; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts.
| |
Collapse
|
13
|
Olenginski LT, Taiwo KM, LeBlanc RM, Dayie TK. Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies. Molecules 2021; 26:molecules26185581. [PMID: 34577051 PMCID: PMC8466439 DOI: 10.3390/molecules26185581] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 01/19/2023] Open
Abstract
RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.
Collapse
Affiliation(s)
- Lukasz T. Olenginski
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
| | - Kehinde M. Taiwo
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
| | - Regan M. LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
- Vertex Pharmaceuticals, 50 Northern Avenue, Boston, MA 02210, USA
| | - Theodore K. Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; (L.T.O.); (K.M.T.); (R.M.L.)
- Correspondence: ; Tel.: +1-301-405-3165
| |
Collapse
|
14
|
Zhang K, Zheludev IN, Hagey RJ, Haslecker R, Hou YJ, Kretsch R, Pintilie GD, Rangan R, Kladwang W, Li S, Wu MTP, Pham EA, Bernardin-Souibgui C, Baric RS, Sheahan TP, D'Souza V, Glenn JS, Chiu W, Das R. Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome. Nat Struct Mol Biol 2021; 28:747-754. [PMID: 34426697 PMCID: PMC8848339 DOI: 10.1038/s41594-021-00653-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023]
Abstract
Drug discovery campaigns against COVID-19 are beginning to target the SARS-CoV-2 RNA genome. The highly conserved frameshift stimulation element (FSE), required for balanced expression of viral proteins, is a particularly attractive SARS-CoV-2 RNA target. Here we present a 6.9 Å resolution cryo-EM structure of the FSE (88 nucleotides, ~28 kDa), validated through an RNA nanostructure tagging method. The tertiary structure presents a topologically complex fold in which the 5' end is threaded through a ring formed inside a three-stem pseudoknot. Guided by this structure, we develop antisense oligonucleotides that impair FSE function in frameshifting assays and knock down SARS-CoV-2 virus replication in A549-ACE2 cells at 100 nM concentration.
Collapse
Affiliation(s)
- Kaiming Zhang
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ivan N Zheludev
- Department of Biochemistry Stanford University, Stanford, CA, USA
| | - Rachel J Hagey
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Raphael Haslecker
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Grigore D Pintilie
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Wipapat Kladwang
- Department of Biochemistry Stanford University, Stanford, CA, USA
| | - Shanshan Li
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Marie Teng-Pei Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Edward A Pham
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Claire Bernardin-Souibgui
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P Sheahan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Victoria D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jeffrey S Glenn
- Departments of Medicine (Division of Gastroenterology and Hepatology) and Microbiology & Immunology, Stanford School of Medicine, Stanford, CA, USA.
- Palo Alto Veterans Administration, Palo Alto, CA, USA.
| | - Wah Chiu
- Departments of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
- Biophysics Program, Stanford University, Stanford, CA, USA.
- CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
| | - Rhiju Das
- Department of Biochemistry Stanford University, Stanford, CA, USA.
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
| |
Collapse
|
15
|
Wang Y, Guan X, Zhang S, Liu Y, Wang S, Fan P, Du X, Yan S, Zhang P, Chen HY, Li W, Zhang D, Huang S. Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A. Nat Commun 2021; 12:3368. [PMID: 34099723 PMCID: PMC8185011 DOI: 10.1038/s41467-021-23764-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
Folding of RNA can produce elaborate tertiary structures, corresponding to their diverse roles in the regulation of biological activities. Direct observation of RNA structures at high resolution in their native form however remains a challenge. The large vestibule and the narrow constriction of a Mycobacterium smegmatis porin A (MspA) suggests a sensing mode called nanopore trapping/translocation, which clearly distinguishes between microRNA, small interfering RNA (siRNA), transfer RNA (tRNA) and 5 S ribosomal RNA (rRNA). To further profit from the acquired event characteristics, a custom machine learning algorithm is developed. Events from measurements with a mixture of RNA analytes can be automatically classified, reporting a general accuracy of ~93.4%. tRNAs, which possess a unique tertiary structure, report a highly distinguishable sensing feature, different from all other RNA types tested in this study. With this strategy, tRNAs from different sources are measured and a high structural conservation across different species is observed in single molecule.
Collapse
MESH Headings
- Machine Learning
- MicroRNAs/chemistry
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Dynamics Simulation
- Molecular Weight
- Mycobacterium smegmatis/genetics
- Mycobacterium smegmatis/metabolism
- Nanopores
- Nucleic Acid Conformation
- Porins/chemistry
- Porins/genetics
- Porins/metabolism
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA Folding
- RNA Transport
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
Collapse
Affiliation(s)
- Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xiaoyu Guan
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yao Liu
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Sha Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Wenfei Li
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, China
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| |
Collapse
|
16
|
Soni K, Kempf G, Manalastas-Cantos K, Hendricks A, Flemming D, Guizetti J, Simon B, Frischknecht F, Svergun DI, Wild K, Sinning I. Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation. Commun Biol 2021; 4:600. [PMID: 34017052 PMCID: PMC8137916 DOI: 10.1038/s42003-021-02132-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/22/2021] [Indexed: 12/25/2022] Open
Abstract
The eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. The canonical Alu domain consists of the SRP9/14 protein heterodimer and a tRNA-like folded Alu RNA that adopts a strictly 'closed' conformation involving a loop-loop pseudoknot. Here, we study the structure of the Alu domain from Plasmodium falciparum (PfAlu), a divergent apicomplexan protozoan that causes human malaria. Using NMR, SAXS and cryo-EM analyses, we show that, in contrast to its prokaryotic and eukaryotic counterparts, the PfAlu domain adopts an 'open' Y-shaped conformation. We show that cytoplasmic P. falciparum ribosomes are non-discriminative and recognize both the open PfAlu and closed human Alu domains with nanomolar affinity. In contrast, human ribosomes do not provide high affinity binding sites for either of the Alu domains. Our analyses extend the structural database of Alu domains to the protozoan species and reveal species-specific differences in the recognition of SRP Alu domains by ribosomes.
Collapse
Affiliation(s)
- Komal Soni
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Georg Kempf
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | | | - Astrid Hendricks
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Dirk Flemming
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Julien Guizetti
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Bernd Simon
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Klemens Wild
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany.
| |
Collapse
|
17
|
Torabi SF, Chen YL, Zhang K, Wang J, DeGregorio SJ, Vaidya AT, Su Z, Pabit SA, Chiu W, Pollack L, Steitz JA. Structural analyses of an RNA stability element interacting with poly(A). Proc Natl Acad Sci U S A 2021; 118:e2026656118. [PMID: 33785601 PMCID: PMC8040590 DOI: 10.1073/pnas.2026656118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cis-acting RNA elements are crucial for the regulation of polyadenylated RNA stability. The element for nuclear expression (ENE) contains a U-rich internal loop flanked by short helices. An ENE stabilizes RNA by sequestering the poly(A) tail via formation of a triplex structure that inhibits a rapid deadenylation-dependent decay pathway. Structure-based bioinformatic studies identified numerous ENE-like elements in evolutionarily diverse genomes, including a subclass containing two ENE motifs separated by a short double-helical region (double ENEs [dENEs]). Here, the structure of a dENE derived from a rice transposable element (TWIFB1) before and after poly(A) binding (∼24 kDa and ∼33 kDa, respectively) is investigated. We combine biochemical structure probing, small angle X-ray scattering (SAXS), and cryo-electron microscopy (cryo-EM) to investigate the dENE structure and its local and global structural changes upon poly(A) binding. Our data reveal 1) the directionality of poly(A) binding to the dENE, and 2) that the dENE-poly(A) interaction involves a motif that protects the 3'-most seven adenylates of the poly(A). Furthermore, we demonstrate that the dENE does not undergo a dramatic global conformational change upon poly(A) binding. These findings are consistent with the recently solved crystal structure of a dENE+poly(A) complex [S.-F. Torabi et al., Science 371, eabe6523 (2021)]. Identification of additional modes of poly(A)-RNA interaction opens new venues for better understanding of poly(A) tail biology.
Collapse
Affiliation(s)
- Seyed-Fakhreddin Torabi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536
- HHMI, Yale University School of Medicine, New Haven, CT 06536
| | - Yen-Lin Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Kaiming Zhang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- James H. Clark Center, Stanford University, Stanford, CA 94305
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536
| | - Suzanne J DeGregorio
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536
- HHMI, Yale University School of Medicine, New Haven, CT 06536
| | - Anand T Vaidya
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536
- HHMI, Yale University School of Medicine, New Haven, CT 06536
- Tata Institute of Fundamental Research Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, 10 500046 Hyderabad, India
| | - Zhaoming Su
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- James H. Clark Center, Stanford University, Stanford, CA 94305
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA 94305;
- James H. Clark Center, Stanford University, Stanford, CA 94305
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853;
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06536;
- HHMI, Yale University School of Medicine, New Haven, CT 06536
| |
Collapse
|
18
|
Identification of a Novel Cis-Acting Regulator of HIV-1 Genome Packaging. Int J Mol Sci 2021; 22:ijms22073435. [PMID: 33810482 PMCID: PMC8036536 DOI: 10.3390/ijms22073435] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/17/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) uptakes homo-dimerized viral RNA genome into its own particle. A cis-acting viral RNA segment responsible for this event, termed packaging signal (psi), is located at the 5′-end of the viral genome. Although the psi segment exhibits nucleotide variation in nature, its effects on the psi function largely remain unknown. Here we show that a psi sequence from an HIV-1 regional variant, subtype D, has a lower packaging ability compared with that from another regional variant, HIV-1 subtype B, despite maintaining similar genome dimerization activities. A series of molecular genetic investigations narrowed down the responsible element of the selective attenuation to the two sequential nucleotides at positions 226 and 227 in the psi segment. Molecular dynamics simulations predicted that the dinucleotide substitution alters structural dynamics, fold, and hydrogen-bond networks primarily of the psi-SL2 element that contains the binding interface of viral nucleocapsid protein for the genome packaging. In contrast, such structural changes were minimal within the SL1 element involved in genome dimerization. These results suggest that the psi 226/227 dinucleotide pair functions as a cis-acting regulator to control the psi structure to selectively tune the efficiency of packaging, but not dimerization of highly variable HIV-1 genomes.
Collapse
|
19
|
Krupkin M, Jackson LN, Ha B, Puglisi EV. Advances in understanding the initiation of HIV-1 reverse transcription. Curr Opin Struct Biol 2020; 65:175-183. [PMID: 32916568 PMCID: PMC9973426 DOI: 10.1016/j.sbi.2020.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/12/2020] [Accepted: 07/21/2020] [Indexed: 01/18/2023]
Abstract
Many viruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Human Immunodeficiency Virus (HIV), use RNA as their genetic material. How viruses harness RNA structure and RNA-protein interactions to control their replication remains obscure. Recent advances in the characterization of HIV-1 reverse transcriptase, the enzyme that converts its single-stranded RNA genome into a double-stranded DNA copy, reveal how the reverse transcription complex evolves during initiation. Here we highlight these advances in HIV-1 structural biology and discuss how they are furthering our understanding of HIV and related ribonucleoprotein complexes implicated in viral disease.
Collapse
Affiliation(s)
- Miri Krupkin
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lynnette Nthenya Jackson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Betty Ha
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elisabetta Viani Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
20
|
Chang JY, Cui Z, Yang K, Huang J, Minary P, Zhang J. Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities. RNA (NEW YORK, N.Y.) 2020; 26:1755-1766. [PMID: 32826323 PMCID: PMC7668250 DOI: 10.1261/rna.071100.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/15/2020] [Indexed: 06/11/2023]
Abstract
Ribonucleic acids (RNAs) play essential roles in living cells. Many of them fold into defined three-dimensional (3D) structures to perform functions. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have enabled structure determinations of RNA to atomic resolutions. However, most RNA molecules are structurally flexible, limiting the resolution of their structures solved by cryo-EM. In modeling these molecules, several computational methods are limited by the requirement of massive computational resources and/or the low efficiency in exploring large-scale structural variations. Here we use hierarchical natural move Monte Carlo (HNMMC), which takes advantage of collective motions for groups of nucleic acid residues, to refine RNA structures into their cryo-EM maps, preserving atomic details in the models. After validating the method on a simulated density map of tRNA, we applied it to objectively obtain the model of the folding intermediate for the specificity domain of ribonuclease P from Bacillus subtilis and refine a flexible ribosomal RNA (rRNA) expansion segment from the Mycobacterium tuberculosis (Mtb) ribosome in different conformational states. Finally, we used HNMMC to model atomic details and flexibility for two distinct conformations of the complete genomic RNA (gRNA) inside MS2, a single-stranded RNA virus, revealing multiple pathways for its capsid assembly.
Collapse
Affiliation(s)
- Jeng-Yih Chang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, College Station, Texas 77843, USA
| | - Zhicheng Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, College Station, Texas 77843, USA
| | - Kailu Yang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, College Station, Texas 77843, USA
| | - Jianhua Huang
- Department of Statistics, Texas A&M University, College Station, Texas 77843, USA
| | - Peter Minary
- Department of Computer Science, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, College Station, Texas 77843, USA
| |
Collapse
|
21
|
Atherton J, Hummel JJA, Olieric N, Locke J, Peña A, Rosenfeld SS, Steinmetz MO, Hoogenraad CC, Moores CA. The mechanism of kinesin inhibition by kinesin-binding protein. eLife 2020; 9:e61481. [PMID: 33252036 PMCID: PMC7746232 DOI: 10.7554/elife.61481] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/28/2020] [Indexed: 12/25/2022] Open
Abstract
Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of intracellular cargo distribution. Kinesin-binding protein (KBP) interacts with a subset of kinesins via their motor domains, inhibits their microtubule (MT) attachment, and blocks their cellular function. However, its mechanisms of inhibition and selectivity have been unclear. Here we use cryo-electron microscopy to reveal the structure of KBP and of a KBP-kinesin motor domain complex. KBP is a tetratricopeptide repeat-containing, right-handed α-solenoid that sequesters the kinesin motor domain's tubulin-binding surface, structurally distorting the motor domain and sterically blocking its MT attachment. KBP uses its α-solenoid concave face and edge loops to bind the kinesin motor domain, and selected structure-guided mutations disrupt KBP inhibition of kinesin transport in cells. The KBP-interacting motor domain surface contains motifs exclusively conserved in KBP-interacting kinesins, suggesting a basis for kinesin selectivity.
Collapse
Affiliation(s)
- Joseph Atherton
- Randall Centre for Cell and Molecular Biophysics, King’s CollegeLondonUnited Kingdom
- Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondonUnited Kingdom
| | - Jessica JA Hummel
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Natacha Olieric
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer InstitutVilligen PSISwitzerland
| | - Julia Locke
- Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondonUnited Kingdom
| | - Alejandro Peña
- Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondonUnited Kingdom
| | | | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer InstitutVilligen PSISwitzerland
- University of Basel, BiozentrumBaselSwitzerland
| | - Casper C Hoogenraad
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Birkbeck, University of LondonLondonUnited Kingdom
| |
Collapse
|
22
|
Abstract
The structural and regulatory elements in therapeutically relevant RNAs offer many opportunities for targeting by small molecules, yet fundamental understanding of what drives selectivity in small molecule:RNA recognition has been a recurrent challenge. In particular, RNAs tend to be more dynamic and offer less chemical functionality than proteins, and biologically active ligands must compete with the highly abundant and highly structured RNA of the ribosome. Indeed, the only small molecule drug targeting RNA other than the ribosome was just approved in August 2020, and our recent survey of the literature revealed fewer than 150 reported chemical probes that target non-ribosomal RNA in biological systems. This Feature outlines our efforts to improve small molecule targeting strategies and gain fundamental insights into small molecule:RNA recognition by analyzing patterns in both RNA-biased small molecule chemical space and RNA topological space privileged for differentiation. First, we synthesized libraries based on RNA binding scaffolds that allowed us to reveal general principles in small molecule:recognition and to ask precise chemical questions about drivers of affinity and selectivity. Elaboration of these scaffolds has led to recognition of medicinally relevant RNA targets, including viral and long noncoding RNA structures. More globally, we identified physicochemical, structural, and spatial properties of biologically active RNA ligands that are distinct from those of protein-targeted ligands, and we have provided the dataset and associated analytical tools as part of a publicly available online platform to facilitate RNA ligand discovery. At the same time, we used pattern recognition protocols to identify RNA topologies that can be differentially recognized by small molecules and have elaborated this technique to visualize conformational changes in RNA secondary structure. These fundamental insights into the drivers of RNA recognition in vitro have led to functional targeting of RNA structures in biological systems. We hope that these initial guiding principles, as well as the approaches and assays developed in their pursuit, will enable rapid progress toward the development of RNA-targeted chemical probes and ultimately new therapeutic approaches to a wide range of deadly human diseases.
Collapse
Affiliation(s)
- Amanda E Hargrove
- Department of Chemistry, Duke University, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
| |
Collapse
|
23
|
Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
|
24
|
Li B, Cao Y, Westhof E, Miao Z. Advances in RNA 3D Structure Modeling Using Experimental Data. Front Genet 2020; 11:574485. [PMID: 33193680 PMCID: PMC7649352 DOI: 10.3389/fgene.2020.574485] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/02/2020] [Indexed: 12/26/2022] Open
Abstract
RNA is a unique bio-macromolecule that can both record genetic information and perform biological functions in a variety of molecular processes, including transcription, splicing, translation, and even regulating protein function. RNAs adopt specific three-dimensional conformations to enable their functions. Experimental determination of high-resolution RNA structures using x-ray crystallography is both laborious and demands expertise, thus, hindering our comprehension of RNA structural biology. The computational modeling of RNA structure was a milestone in the birth of bioinformatics. Although computational modeling has been greatly improved over the last decade showing many successful cases, the accuracy of such computational modeling is not only length-dependent but also varies according to the complexity of the structure. To increase credibility, various experimental data were integrated into computational modeling. In this review, we summarize the experiments that can be integrated into RNA structure modeling as well as the computational methods based on these experimental data. We also demonstrate how computational modeling can help the experimental determination of RNA structure. We highlight the recent advances in computational modeling which can offer reliable structure models using high-throughput experimental data.
Collapse
Affiliation(s)
- Bing Li
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Eric Westhof
- Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| |
Collapse
|
25
|
Boyd PS, Brown JB, Brown JD, Catazaro J, Chaudry I, Ding P, Dong X, Marchant J, O’Hern CT, Singh K, Swanson C, Summers MF, Yasin S. NMR Studies of Retroviral Genome Packaging. Viruses 2020; 12:v12101115. [PMID: 33008123 PMCID: PMC7599994 DOI: 10.3390/v12101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/03/2022] Open
Abstract
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
Collapse
|
26
|
Zhang K, Zheludev IN, Hagey RJ, Wu MTP, Haslecker R, Hou YJ, Kretsch R, Pintilie GD, Rangan R, Kladwang W, Li S, Pham EA, Bernardin-Souibgui C, Baric RS, Sheahan TP, D Souza V, Glenn JS, Chiu W, Das R. Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32743589 DOI: 10.1101/2020.07.18.209270] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Drug discovery campaigns against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are beginning to target the viral RNA genome 1, 2 . The frameshift stimulation element (FSE) of the SARS-CoV-2 genome is required for balanced expression of essential viral proteins and is highly conserved, making it a potential candidate for antiviral targeting by small molecules and oligonucleotides 3-6 . To aid global efforts focusing on SARS-CoV-2 frameshifting, we report exploratory results from frameshifting and cellular replication experiments with locked nucleic acid (LNA) antisense oligonucleotides (ASOs), which support the FSE as a therapeutic target but highlight difficulties in achieving strong inactivation. To understand current limitations, we applied cryogenic electron microscopy (cryo-EM) and the Ribosolve 7 pipeline to determine a three-dimensional structure of the SARS-CoV-2 FSE, validated through an RNA nanostructure tagging method. This is the smallest macromolecule (88 nt; 28 kDa) resolved by single-particle cryo-EM at subnanometer resolution to date. The tertiary structure model, defined to an estimated accuracy of 5.9 Å, presents a topologically complex fold in which the 5' end threads through a ring formed inside a three-stem pseudoknot. Our results suggest an updated model for SARS-CoV-2 frameshifting as well as binding sites that may be targeted by next generation ASOs and small molecules.
Collapse
|
27
|
Identification of the initial nucleocapsid recognition element in the HIV-1 RNA packaging signal. Proc Natl Acad Sci U S A 2020; 117:17737-17746. [PMID: 32647061 PMCID: PMC7395439 DOI: 10.1073/pnas.2008519117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding the molecular determinants of retroviral genome packaging is important for drug discovery and development of vectors for gene delivery. We show that the HIV-1 leader, which contains the RNA elements necessary for genome packaging, binds approximately two dozen copies of the cognate NC protein with affinities ranging from ∼40 nM to 1.4 µM. Binding to the four highest-affinity “initial” binding sites occurs with endothermic energetics attributed to NC-induced localized RNA melting. Mutations that stabilize these sites inhibit NC binding in vitro and RNA packaging in transfected cells. A small-molecule inhibitor of RNA packaging binds specifically to the initial NC binding sites and stabilizes the RNA structure. Our findings identify a potential RNA Achilles’ heel for HIV therapeutic development. Selective packaging of the HIV-1 genome during virus assembly is mediated by interactions between the dimeric 5ʹ-leader of the unspliced viral RNA and the nucleocapsid (NC) domains of a small number of assembling viral Gag polyproteins. Here, we show that the dimeric 5′-leader contains more than two dozen NC binding sites with affinities ranging from 40 nM to 1.4 μM, and that all high-affinity sites (Kd ≲ 400 nM) reside within a ∼150-nt region of the leader sufficient to promote RNA packaging (core encapsidation signal, ΨCES). The four initial binding sites with highest affinity reside near two symmetrically equivalent three-way junction structures. Unlike the other high-affinity sites, which bind NC with exothermic energetics, binding to these sites occurs endothermically due to concomitant unwinding of a weakly base-paired [UUUU]:[GGAG] helical element. Mutations that stabilize base pairing within this element eliminate NC binding to this site and severely impair RNA packaging into virus-like particles. NMR studies reveal that a recently discovered small-molecule inhibitor of HIV-1 RNA packaging that appears to function by stabilizing the structure of the leader binds directly to the [UUUU]:[GGAG] helix. Our findings suggest a sequential NC binding mechanism for Gag-genome assembly and identify a potential RNA Achilles’ heel to which HIV therapeutics may be targeted.
Collapse
|
28
|
Kappel K, Zhang K, Su Z, Watkins AM, Kladwang W, Li S, Pintilie G, Topkar VV, Rangan R, Zheludev IN, Yesselman JD, Chiu W, Das R. Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nat Methods 2020; 17:699-707. [PMID: 32616928 PMCID: PMC7386730 DOI: 10.1038/s41592-020-0878-9] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 05/20/2020] [Indexed: 02/05/2023]
Abstract
The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable subnanometer-resolution coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. This hybrid 'Ribosolve' pipeline detects and falsifies homologies and conformational rearrangements in 11 previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length Vibrio cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and the computer-designed ATP-TTR-3 aptamer with and without AMP. Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput.
Collapse
Affiliation(s)
- Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Kaiming Zhang
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Zhaoming Su
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Sichuan, China
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Shanshan Li
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Grigore Pintilie
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Ved V Topkar
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Ivan N Zheludev
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Joseph D Yesselman
- Department of Biochemistry, Stanford University, Stanford, CA, USA
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Wah Chiu
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, USA.
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA.
- Department of Biochemistry, Stanford University, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
| |
Collapse
|
29
|
Nam H, Becette O, LeBlanc RM, Oh D, Case DA, Dayie TK. Deleterious effects of carbon-carbon dipolar coupling on RNA NMR dynamics. JOURNAL OF BIOMOLECULAR NMR 2020; 74:321-331. [PMID: 32363430 DOI: 10.1007/s10858-020-00315-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/18/2020] [Indexed: 06/11/2023]
Abstract
Many regulatory RNAs undergo dynamic exchanges that are crucial for their biological functions and NMR spectroscopy is a versatile tool for monitoring dynamic motions of biomolecules. Meaningful information on biomolecular dynamics requires an accurate measurement of relaxation parameters such as longitudinal (R1) rates, transverse (R2) rates and heteronuclear Overhauser effect (hNOE). However, earlier studies have shown that the large 13C-13C interactions complicate analysis of the carbon relaxation parameters. To investigate the effect of 13C-13C interactions on RNA dynamic studies, we performed relaxation measurements on various RNA samples with different labeling patterns and compared these measurements with the computational simulations. For uniformly labeled samples, contributions of the neighboring carbon to R1 measurements were observed. These contributions increased with increasing magnetic field and overall correlation time ([Formula: see text]) for R1 rates, necessitating more careful analysis for uniformly labeled large RNAs. In addition, the hNOE measurements were also affected by the adjacent carbon nuclei. Unlike R1 rates, R1ρ rates showed relatively good agreement between uniformly- and site-selectively labeled samples, suggesting no dramatic effect from their attached carbon, in agreement with previous observations. Overall, having more accurate rate measurements avoids complex analysis and will be a key for interpreting 13C relaxation rates for molecular motion that can provide valuable insights into cellular molecular recognition events.
Collapse
Affiliation(s)
- Hyeyeon Nam
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Owen Becette
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Regan M LeBlanc
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Daniel Oh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Theodore K Dayie
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
| |
Collapse
|
30
|
Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 2020; 25:molecules25122881. [PMID: 32585844 PMCID: PMC7357161 DOI: 10.3390/molecules25122881] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.
Collapse
|
31
|
Ultra-thermostable RNA nanoparticles for solubilizing and high-yield loading of paclitaxel for breast cancer therapy. Nat Commun 2020; 11:972. [PMID: 32080195 PMCID: PMC7033104 DOI: 10.1038/s41467-020-14780-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 01/24/2020] [Indexed: 11/17/2022] Open
Abstract
Paclitaxel is widely used in cancer treatments, but poor water-solubility and toxicity raise serious concerns. Here we report an RNA four-way junction nanoparticle with ultra-thermodynamic stability to solubilize and load paclitaxel for targeted cancer therapy. Each RNA nanoparticle covalently loads twenty-four paclitaxel molecules as a prodrug. The RNA-paclitaxel complex is structurally rigid and stable, demonstrated by the sub-nanometer resolution imaging of cryo-EM. Using RNA nanoparticles as carriers increases the water-solubility of paclitaxel by 32,000-fold. Intravenous injections of RNA-paclitaxel nanoparticles with specific cancer-targeting ligand dramatically inhibit breast cancer growth, with nearly undetectable toxicity and immune responses in mice. No fatalities are observed at a paclitaxel dose equal to the reported LD50. The use of ultra-thermostable RNA nanoparticles to deliver chemical prodrugs addresses issues with RNA unfolding and nanoparticle dissociation after high-density drug loading. This finding provides a stable nano-platform for chemo-drug delivery as well as an efficient method to solubilize hydrophobic drugs. Although paclitaxel is widely used as a chemotherapy, it suffers from poor solubility and toxicity issues. Here, the authors develop thermostable RNA nanoparticles and report the RNA-paclitaxel complex to display improved stability, drug loading capacity and solubility for improved targeted cancer therapy and reduced immune responses.
Collapse
|
32
|
Yeates TO, Agdanowski MP, Liu Y. Development of imaging scaffolds for cryo-electron microscopy. Curr Opin Struct Biol 2020; 60:142-149. [PMID: 32066085 DOI: 10.1016/j.sbi.2020.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/14/2022]
Abstract
Following recent hardware and software developments, single particle cryo-electron microscopy (cryo-EM) has become one of the most popular structural biology tools. Many targets, such as viruses, large protein complexes and oligomeric membrane proteins, have been resolved to atomic resolution using single-particle cryo-EM, which relies on the accurate assignment of particle location and orientation from intrinsically noisy projection images. The same image processing procedures are more challenging for smaller proteins due to their lower signal-to-noise ratios. Consequently, though most cellular proteins are less than 50kDa, so far it has been possible to solve cryo-EM structures near that size range for only a few favorable cases. Here we highlight some of the challenges and recent efforts to break through this lower size limit by engineering large scaffolds to rigidly display multiple small proteins for imaging. Future design efforts are noted.
Collapse
Affiliation(s)
- Todd O Yeates
- UCLA Department of Chemistry and Biochemistry, United States; UCLA-DOE Institute for Genomics and Proteomics, United States; UCLA Molecular Biology Institute, United States.
| | | | - Yuxi Liu
- UCLA Department of Chemistry and Biochemistry, United States; UCLA Molecular Biology Institute, United States
| |
Collapse
|
33
|
Geraets JA, Pothula KR, Schröder GF. Integrating cryo-EM and NMR data. Curr Opin Struct Biol 2020; 61:173-181. [PMID: 32028106 DOI: 10.1016/j.sbi.2020.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 01/06/2023]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) is increasingly used as a technique to determine the atomic structure of challenging biological systems. Recent advances in microscope engineering, electron detection, and image processing have allowed the structural determination of bigger and more flexible targets than possible with the complementary techniques X-ray crystallography and NMR spectroscopy. However, there exist many biological targets for which atomic resolution cannot be currently achieved with cryo-EM, making unambiguous determination of the protein structure impossible. Although determining the structure of large biological systems using solely NMR is often difficult, highly complementary experimental atomic-level data for each molecule can be derived from the spectra, and used in combination with cryo-EM data. We review here strategies with which both techniques can be synergistically combined, in order to reach detail and understanding unattainable by each technique acting alone; and the types of biological systems for which such an approach would be desirable.
Collapse
Affiliation(s)
- James A Geraets
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Karunakar R Pothula
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany; Physics Department, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| |
Collapse
|
34
|
Kim DN, Thiel BC, Mrozowich T, Hennelly SP, Hofacker IL, Patel TR, Sanbonmatsu KY. Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution. Nat Commun 2020; 11:148. [PMID: 31919376 PMCID: PMC6952434 DOI: 10.1038/s41467-019-13942-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/09/2019] [Indexed: 02/08/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) constitute a significant fraction of the transcriptome, playing important roles in development and disease. However, our understanding of structure-function relationships for this emerging class of RNAs has been limited to secondary structures. Here, we report the 3-D atomistic structural study of epigenetic lncRNA, Braveheart (Bvht), and its complex with CNBP (Cellular Nucleic acid Binding Protein). Using small angle X-ray scattering (SAXS), we elucidate the ensemble of Bvht RNA conformations in solution, revealing that Bvht lncRNA has a well-defined, albeit flexible 3-D structure that is remodeled upon CNBP binding. Our study suggests that CNBP binding requires multiple domains of Bvht and the RHT/AGIL RNA motif. We show that RHT/AGIL, previously shown to interact with CNBP, contains a highly flexible loop surrounded by more ordered helices. As one of the largest RNA-only 3-D studies, the work lays the foundation for future structural studies of lncRNA-protein complexes.
Collapse
Affiliation(s)
- Doo Nam Kim
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Bernhard C Thiel
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Tyler Mrozowich
- Alberta RNA Research & Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Scott P Hennelly
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
- New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Trushar R Patel
- Alberta RNA Research & Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada.
| | - Karissa Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
- New Mexico Consortium, Los Alamos, New Mexico, USA.
| |
Collapse
|
35
|
Zhang K, Li S, Kappel K, Pintilie G, Su Z, Mou TC, Schmid MF, Das R, Chiu W. Cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution. Nat Commun 2019; 10:5511. [PMID: 31796736 PMCID: PMC6890682 DOI: 10.1038/s41467-019-13494-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/03/2019] [Indexed: 01/17/2023] Open
Abstract
Specimens below 50 kDa have generally been considered too small to be analyzed by single-particle cryo-electron microscopy (cryo-EM). The high flexibility of pure RNAs makes it difficult to obtain high-resolution structures by cryo-EM. In bacteria, riboswitches regulate sulfur metabolism through binding to the S-adenosylmethionine (SAM) ligand and offer compelling targets for new antibiotics. SAM-I, SAM-I/IV, and SAM-IV are the three most commonly found SAM riboswitches, but the structure of SAM-IV is still unknown. Here, we report the structures of apo and SAM-bound SAM-IV riboswitches (119-nt, ~40 kDa) to 3.7 Å and 4.1 Å resolution, respectively, using cryo-EM. The structures illustrate homologies in the ligand-binding core but distinct peripheral tertiary contacts in SAM-IV compared to SAM-I and SAM-I/IV. Our results demonstrate the feasibility of resolving small RNAs with enough detail to enable detection of their ligand-binding pockets and suggest that cryo-EM could play a role in structure-assisted drug design for RNA.
Collapse
Affiliation(s)
- Kaiming Zhang
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Shanshan Li
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, 94305, USA
| | - Grigore Pintilie
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Zhaoming Su
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Tung-Chung Mou
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT, 59812, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Department of Physics, Stanford University, Stanford, CA, 94305, USA.
| | - Wah Chiu
- Department of Bioengineering, and James H. Clark Center, Stanford University, Stanford, CA, 94305, USA.
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA.
| |
Collapse
|
36
|
Li S, Su Z, Lehmann J, Stamatopoulou V, Giarimoglou N, Henderson FE, Fan L, Pintilie GD, Zhang K, Chen M, Ludtke SJ, Wang YX, Stathopoulos C, Chiu W, Zhang J. Structural basis of amino acid surveillance by higher-order tRNA-mRNA interactions. Nat Struct Mol Biol 2019; 26:1094-1105. [PMID: 31740854 PMCID: PMC6899168 DOI: 10.1038/s41594-019-0326-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022]
Abstract
Amino acid availability in Gram-positive bacteria is monitored by T-box riboswitches. T-boxes directly bind tRNAs, assess their aminoacylation state, and regulate the transcription or translation of downstream genes to maintain nutritional homeostasis. Here, we report cocrystal and cryo-EM structures of Geobacillus kaustophilus and Bacillus subtilis T-box-tRNA complexes, detailing their multivalent, exquisitely selective interactions. The T-box forms a U-shaped molecular vise that clamps the tRNA, captures its 3' end using an elaborate 'discriminator' structure, and interrogates its aminoacylation state using a steric filter fashioned from a wobble base pair. In the absence of aminoacylation, T-boxes clutch tRNAs and form a continuously stacked central spine, permitting transcriptional readthrough or translation initiation. A modeled aminoacyl disrupts tRNA-T-box stacking, severing the central spine and blocking gene expression. Our data establish a universal mechanism of amino acid sensing on tRNAs and gene regulation by T-box riboswitches and exemplify how higher-order RNA-RNA interactions achieve multivalency and specificity.
Collapse
Affiliation(s)
- Shuang Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Zhaoming Su
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Jean Lehmann
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Campus Paris-Saclay, Gif-sur-Yvette, France
| | | | - Nikoleta Giarimoglou
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
| | - Frances E Henderson
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Lixin Fan
- Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Grigore D Pintilie
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Kaiming Zhang
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA
| | - Muyuan Chen
- Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Steven J Ludtke
- Verna Marrs and McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yun-Xing Wang
- Small-Angle X-ray Scattering Core Facility, Center for Cancer Research of the National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA.,Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | | | - Wah Chiu
- Department of Bioengineering and Department of Microbiology and Immunology, James H. Clark Center, Stanford University, Stanford, CA, USA. .,Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, Stanford University, Stanford, CA, USA.
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
| |
Collapse
|
37
|
Marchant J, Summers MF, Johnson BA. Assigning NMR spectra of RNA, peptides and small organic molecules using molecular network visualization software. JOURNAL OF BIOMOLECULAR NMR 2019; 73:525-529. [PMID: 31325088 PMCID: PMC6859155 DOI: 10.1007/s10858-019-00271-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
NMR assignment typically involves analysis of peaks across multiple NMR spectra. Chemical shifts of peaks are measured before being assigned to atoms using a variety of methods. These approaches quickly become complicated by overlap, ambiguity, and the complexity of correlating assignments among multiple spectra. Here we propose an alternative approach in which a network of linked peak-boxes is generated at the predicted positions of peaks across all spectra. These peak-boxes correlate known relationships and can be matched to the observed spectra. The method is illustrated with RNA, but a variety of molecular types should be readily tractable with this approach.
Collapse
Affiliation(s)
- Jan Marchant
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
- Howard Hughes Medical Institute, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
| |
Collapse
|
38
|
Freidhoff P, Bruist MF. In silico survey of the central conserved regions in viroids of the Pospiviroidae family for conserved asymmetric loop structures. RNA (NEW YORK, N.Y.) 2019; 25:985-1003. [PMID: 31123078 PMCID: PMC6633198 DOI: 10.1261/rna.070409.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/14/2019] [Indexed: 06/01/2023]
Abstract
Viroids are the smallest replicative pathogens, consisting of RNA circles (∼300 nucleotides) that require host machinery to replicate. Structural RNA elements recruit these host factors. Currently, many of these structural elements and the nature of their interactions are unknown. All Pospiviroidae have homology in the central conserved region (CCR). The CCR of potato spindle tuber viroid (PSTVd) contains a sarcin/ricin domain (SRD), the only viroid structural element with an unequivocal replication role. We assumed that every member of this family uses this region to recruit host factors, and that each CCR has an SRD-like asymmetric loop within it. Potential SRD or SRD-like motifs were sought in the CCR of each Pospiviroidae member as follows. Motif location in each CCR was predicted with MUSCLE alignment and Vienna RNAfold. Viroid-specific models of SRD-like motifs were built by superimposing noncanonical base pairs and nucleotides on a model of an SRD. The RNA geometry search engine FR3D was then used to find nucleotide groups close to the geometry suggested by this superimposition. Atomic resolution structures were assembled using the molecular visualization program Chimera, and the stability of each motif was assessed with molecular dynamics (MD). Some models required a protonated cytosine. To be stable within a cell, the pKa of that cytosine must be shifted up. Constant pH-replica exchange MD analysis showed such a shift in the proposed structures. These data show that every Pospiviroidae member could form a motif that resembles an SRD in its CCR, and imply there could be undiscovered mimics of other RNA domains.
Collapse
Affiliation(s)
- Paul Freidhoff
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, USA
| | - Michael F Bruist
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
39
|
Wamhoff EC, Banal JL, Bricker WP, Shepherd TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming Structured DNA Assemblies to Probe Biophysical Processes. Annu Rev Biophys 2019; 48:395-419. [PMID: 31084582 PMCID: PMC7035826 DOI: 10.1146/annurev-biophys-052118-115259] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade.
Collapse
Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - William P Bricker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Tyson R Shepherd
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Molly F Parsons
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Rémi Veneziano
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew B Stone
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Hyungmin Jun
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Xiao Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| |
Collapse
|
40
|
Zhang H, Keane SC. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1541. [PMID: 31025514 PMCID: PMC7169810 DOI: 10.1002/wrna.1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high-resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
41
|
Computational modeling of RNA 3D structure based on experimental data. Biosci Rep 2019; 39:BSR20180430. [PMID: 30670629 PMCID: PMC6367127 DOI: 10.1042/bsr20180430] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 01/02/2023] Open
Abstract
RNA molecules are master regulators of cells. They are involved in a variety of molecular processes: they transmit genetic information, sense cellular signals and communicate responses, and even catalyze chemical reactions. As in the case of proteins, RNA function is dictated by its structure and by its ability to adopt different conformations, which in turn is encoded in the sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore the majority of known RNAs remain structurally uncharacterized. To address this problem, predictive computational methods were developed based on the accumulated knowledge of RNA structures determined so far, the physical basis of the RNA folding, and taking into account evolutionary considerations, such as conservation of functionally important motifs. However, all theoretical methods suffer from various limitations, and they are generally unable to accurately predict structures for RNA sequences longer than 100-nt residues unless aided by additional experimental data. In this article, we review experimental methods that can generate data usable by computational methods, as well as computational approaches for RNA structure prediction that can utilize data from experimental analyses. We outline methods and data types that can be potentially useful for RNA 3D structure modeling but are not commonly used by the existing software, suggesting directions for future development.
Collapse
|
42
|
Strickland M, Catazaro J, Rajasekaran R, Strub MP, O'Hern C, Bermejo GA, Summers MF, Marchant J, Tjandra N. Long-Range RNA Structural Information via a Paramagnetically Tagged Reporter Protein. J Am Chem Soc 2019; 141:1430-1434. [PMID: 30652860 DOI: 10.1021/jacs.8b11384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
NMR has provided a wealth of structural and dynamical information for RNA molecules of up to ∼50 nucleotides, but its application to larger RNAs has been hampered in part by difficulties establishing global structural features. A potential solution involves measurement of NMR perturbations after site-specific paramagnetic labeling. Although the approach works well for proteins, the inability to place the label at specific sites has prevented its application to larger RNAs transcribed in vitro. Here, we present a strategy in which RNA loop residues are modified to promote binding to a paramagnetically tagged reporter protein. Lanthanide-induced pseudocontact shifts are demonstrated for a 232-nucleotide RNA bound to tagged derivatives of the spliceosomal U1A RNA-binding domain. Further, the method is validated with a 36-nucleotide RNA for which measured NMR values agreed with predictions based on the previously known protein and RNA structures. The ability to readily insert U1A binding sites into ubiquitous hairpin and/or loop structures should make this approach broadly applicable for the atomic-level study of large RNAs.
Collapse
Affiliation(s)
- Madeleine Strickland
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | | | - Rohith Rajasekaran
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Marie-Paule Strub
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | | | - Guillermo A Bermejo
- Office of Intramural Research, Center for Information Technology, National Institutes of Health , Bethesda , Maryland 20892 , United States
| | | | | | - Nico Tjandra
- Laboratory of Structural Biophysics, Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| |
Collapse
|
43
|
Schroeder SJ. Challenges and approaches to predicting RNA with multiple functional structures. RNA (NEW YORK, N.Y.) 2018; 24:1615-1624. [PMID: 30143552 PMCID: PMC6239171 DOI: 10.1261/rna.067827.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The revolution in sequencing technology demands new tools to interpret the genetic code. As in vivo transcriptome-wide chemical probing techniques advance, new challenges emerge in the RNA folding problem. The emphasis on one sequence folding into a single minimum free energy structure is fading as a new focus develops on generating RNA structural ensembles and identifying functional structural features in ensembles. This review describes an efficient combinatorially complete method and three free energy minimization approaches to predicting RNA structures with more than one functional fold, as well as two methods for analysis of a thermodynamics-based Boltzmann ensemble of structures. The review then highlights two examples of viral RNA 3'-UTR regions that fold into more than one conformation and have been characterized by single molecule fluorescence energy resonance transfer or NMR spectroscopy. These examples highlight the different approaches and challenges in predicting structure and function from sequence for RNA with multiple biological roles and folds. More well-defined examples and new metrics for measuring differences in RNA structures will guide future improvements in prediction of RNA structure and function from sequence.
Collapse
Affiliation(s)
- Susan J Schroeder
- Department of Chemistry and Biochemistry, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, USA
| |
Collapse
|
44
|
Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
Collapse
Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
| |
Collapse
|
45
|
Kappel K, Das R. Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking. Structure 2018; 27:140-151.e5. [PMID: 30416038 DOI: 10.1016/j.str.2018.10.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/27/2018] [Accepted: 10/05/2018] [Indexed: 10/27/2022]
Abstract
RNA-protein complexes underlie numerous cellular processes including translation, splicing, and posttranscriptional regulation of gene expression. The structures of these complexes are crucial to their functions but often elude high-resolution structure determination. Computational methods are needed that can integrate low-resolution data for RNA-protein complexes while modeling de novo the large conformational changes of RNA components upon complex formation. To address this challenge, we describe RNP-denovo, a Rosetta method to simultaneously fold-and-dock RNA to a protein surface. On a benchmark set of diverse RNA-protein complexes not solvable with prior strategies, RNP-denovo consistently sampled native-like structures with better than nucleotide resolution. We revisited three past blind modeling challenges involving the spliceosome, telomerase, and a methyltransferase-ribosomal RNA complex in which previous methods gave poor results. When coupled with the same sparse FRET, crosslinking, and functional data used previously, RNP-denovo gave models with significantly improved accuracy. These results open a route to modeling global folds of RNA-protein complexes from low-resolution data.
Collapse
Affiliation(s)
- Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Physics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
46
|
Denny SK, Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ. High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. Cell 2018; 174:377-390.e20. [PMID: 29961580 PMCID: PMC6053692 DOI: 10.1016/j.cell.2018.05.038] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/07/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022]
Abstract
RNAs fold into defined tertiary structures to function in critical biological processes. While quantitative models can predict RNA secondary structure stability, we are still unable to predict the thermodynamic stability of RNA tertiary structure. Here, we probe conformational preferences of diverse RNA two-way junctions to develop a predictive model for the formation of RNA tertiary structure. We quantitatively measured tertiary assembly energetics of >1,000 of RNA junctions inserted in multiple structural scaffolds to generate a "thermodynamic fingerprint" for each junction. Thermodynamic fingerprints enabled comparison of junction conformational preferences, revealing principles for how sequence influences 3-dimensional conformations. Utilizing fingerprints of junctions with known crystal structures, we generated ensembles for related junctions that predicted their thermodynamic effects on assembly formation. This work reveals sequence-structure-energetic relationships in RNA, demonstrates the capacity for diverse compensation strategies within tertiary structures, and provides a path to quantitative modeling of RNA folding energetics based on "ensemble modularity."
Collapse
Affiliation(s)
| | - Namita Bisaria
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph David Yesselman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
| | - William James Greenleaf
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| |
Collapse
|