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Marinus T, Foster TL, Tych KM. The application of single-molecule optical tweezers to study disease-related structural dynamics in RNA. Biochem Soc Trans 2024; 52:899-909. [PMID: 38533854 PMCID: PMC11088911 DOI: 10.1042/bst20231232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024]
Abstract
RNA, a dynamic and flexible molecule with intricate three-dimensional structures, has myriad functions in disease development. Traditional methods, such as X-ray crystallography and nuclear magnetic resonance, face limitations in capturing real-time, single-molecule dynamics crucial for understanding RNA function. This review explores the transformative potential of single-molecule force spectroscopy using optical tweezers, showcasing its capability to directly probe time-dependent structural rearrangements of individual RNA molecules. Optical tweezers offer versatility in exploring diverse conditions, with the potential to provide insights into how environmental changes, ligands and RNA-binding proteins impact RNA behaviour. By enabling real-time observations of large-scale structural dynamics, optical tweezers emerge as an invaluable tool for advancing our comprehension of RNA structure and function. Here, we showcase their application in elucidating the dynamics of RNA elements in virology, such as the pseudoknot governing ribosomal frameshifting in SARS-CoV-2.
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Affiliation(s)
- Tycho Marinus
- Chemical Biology 1, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Toshana L. Foster
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, LE12 5RD Loughborough, U.K
| | - Katarzyna M. Tych
- Chemical Biology 1, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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2
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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.
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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
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Morse M, Sefcikova J, Rouzina I, Beuning PJ, Williams M. Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates. Nucleic Acids Res 2022; 51:290-303. [PMID: 36533523 PMCID: PMC9841419 DOI: 10.1093/nar/gkac1179] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein performs several functions including binding, compacting, and packaging the ∼30 kb viral genome into the viral particle. N protein consists of two ordered domains, with the N terminal domain (NTD) primarily associated with RNA binding and the C terminal domain (CTD) primarily associated with dimerization/oligomerization, and three intrinsically disordered regions, an N-arm, a C-tail, and a linker that connects the NTD and CTD. We utilize an optical tweezers system to isolate a long single-stranded nucleic acid substrate to measure directly the binding and packaging function of N protein at a single molecule level in real time. We find that N protein binds the nucleic acid substrate with high affinity before oligomerizing and forming a highly compact structure. By comparing the activities of truncated protein variants missing the NTD, CTD, and/or linker, we attribute specific steps in this process to the structural domains of N protein, with the NTD driving initial binding to the substrate and ensuring high localized protein density that triggers interprotein interactions mediated by the CTD, which forms a compact and stable protein-nucleic acid complex suitable for packaging into the virion.
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Affiliation(s)
- Michael Morse
- Department of Physics, Northeastern University, Boston, MA, USA
| | - Jana Sefcikova
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Mark C Williams
- To whom correspondence should be addressed. Tel: +1 617 373 5705;
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Buck S, Pekarek L, Caliskan N. POTATO: Automated pipeline for batch analysis of optical tweezers data. Biophys J 2022; 121:2830-2839. [PMID: 35778838 PMCID: PMC9388390 DOI: 10.1016/j.bpj.2022.06.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/22/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
Optical tweezers are a single-molecule technique that allows probing of intra- and intermolecular interactions that govern complex biological processes involving molecular motors, protein-nucleic acid interactions, and protein/RNA folding. Recent developments in instrumentation eased and accelerated optical tweezers data acquisition, but analysis of the data remains challenging. Here, to enable high-throughput data analysis, we developed an automated python-based analysis pipeline called POTATO (practical optical tweezers analysis tool). POTATO automatically processes the high-frequency raw data generated by force-ramp experiments and identifies (un)folding events using predefined parameters. After segmentation of the force-distance trajectories at the identified (un)folding events, sections of the curve can be fitted independently to a worm-like chain and freely jointed chain models, and the work applied on the molecule can be calculated by numerical integration. Furthermore, the tool allows plotting of constant force data and fitting of the Gaussian distance distribution over time. All these features are wrapped in a user-friendly graphical interface, which allows researchers without programming knowledge to perform sophisticated data analysis.
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Affiliation(s)
- Stefan Buck
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Lukas Pekarek
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany; Medical Faculty, Julius-Maximilians University Würzburg, Würzburg, Germany.
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Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch. Nat Commun 2021; 12:7166. [PMID: 34887415 PMCID: PMC8660796 DOI: 10.1038/s41467-021-27400-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/12/2021] [Indexed: 12/21/2022] Open
Abstract
Programmed –1 ribosomal frameshifting (PRF) in cardioviruses is activated by the 2A protein, a multi-functional virulence factor that also inhibits cap-dependent translational initiation. Here we present the X-ray crystal structure of 2A and show that it selectively binds to a pseudoknot-like conformation of the PRF stimulatory RNA element in the viral genome. Using optical tweezers, we demonstrate that 2A stabilises this RNA element, likely explaining the increase in PRF efficiency in the presence of 2A. Next, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a cryo-EM structure of 2A bound to initiated 70S ribosomes. Multiple copies of 2A bind to the 16S rRNA where they may compete for binding with initiation and elongation factors. Together, these results define the structural basis for RNA recognition by 2A, show how 2A-mediated stabilisation of an RNA pseudoknot promotes PRF, and reveal how 2A accumulation may shut down translation during virus infection. Many RNA viruses employ programmed –1 ribosomal frameshifting (PRF) to expand their coding capacity and optimize production of viral proteins. Here, the authors report structural and biophysical analysis of protein 2A from a cardiovirus, with insights into the mechanism of its PRF-stimulatory function.
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Wang Y, Guo C, Wang X, Xu L, Li R, Wang J. The Zinc Content of HIV-1 NCp7 Affects Its Selectivity for Packaging Signal and Affinity for Stem-Loop 3. Viruses 2021; 13:v13101922. [PMID: 34696351 PMCID: PMC8540335 DOI: 10.3390/v13101922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022] Open
Abstract
The nucleocapsid (NC) protein of human immunodeficiency (HIV) is a small, highly basic protein containing two CCHC zinc-finger motifs, which is cleaved from the NC domain of the Gag polyprotein during virus maturation. We previously reported that recombinant HIV-1 Gag and NCp7 overexpressed in an E. coli host contains two and one zinc ions, respectively, and Gag exhibited much higher selectivity for packaging signal (Psi) and affinity for the stem-loop (SL)-3 of Psi than NCp7. In this study, we prepared NCp7 containing 0 (0NCp7), 1 (NCp7) or 2 (2NCp7) zinc ions, and compared their secondary structure, Psi-selectivity and SL3-affinity. Along with the decrease of the zinc content, less ordered conformations were detected. Compared to NCp7, 2NCp7 exhibited a much higher Psi-selectivity and SL3-affinity, similar to Gag, whereas 0NCp7 exhibited a lower Psi-selectivity and SL3-affinity, similar to the H23&H44K double mutant of NCp7, indicating that the different RNA-binding property of Gag NC domain and the mature NCp7 may be resulted, at least partially, from their different zinc content. This study will be helpful to elucidate the critical roles that zinc played in the viral life cycle, and benefit further investigations of the functional switch from the NC domain of Gag to the mature NCp7.
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Affiliation(s)
- Ying Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China; (Y.W.); (X.W.); (L.X.); (R.L.)
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
| | - Chao Guo
- College of Basic Medical Sciences, Shanxi Medical University, Taiyuan 030001, China;
| | - Xing Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China; (Y.W.); (X.W.); (L.X.); (R.L.)
| | - Lianmei Xu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China; (Y.W.); (X.W.); (L.X.); (R.L.)
| | - Rui Li
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China; (Y.W.); (X.W.); (L.X.); (R.L.)
| | - Jinzhong Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, China; (Y.W.); (X.W.); (L.X.); (R.L.)
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, China
- Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin 300457, China
- Correspondence:
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Arista-Romero M, Pujals S, Albertazzi L. Towards a Quantitative Single Particle Characterization by Super Resolution Microscopy: From Virus Structures to Antivirals Design. Front Bioeng Biotechnol 2021; 9:647874. [PMID: 33842446 PMCID: PMC8033170 DOI: 10.3389/fbioe.2021.647874] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
In the last year the COVID19 pandemic clearly illustrated the potential threat that viruses pose to our society. The characterization of viral structures and the identification of key proteins involved in each step of the cycle of infection are crucial to develop treatments. However, the small size of viruses, invisible under conventional fluorescence microscopy, make it difficult to study the organization of protein clusters within the viral particle. The applications of super-resolution microscopy have skyrocketed in the last years, converting this group into one of the leading techniques to characterize viruses and study the viral infection in cells, breaking the diffraction limit by achieving resolutions up to 10 nm using conventional probes such as fluorescent dyes and proteins. There are several super-resolution methods available and the selection of the right one it is crucial to study in detail all the steps involved in the viral infection, quantifying and creating models of infection for relevant viruses such as HIV-1, Influenza, herpesvirus or SARS-CoV-1. Here we review the use of super-resolution microscopy (SRM) to study all steps involved in the viral infection and antiviral design. In light of the threat of new viruses, these studies could inspire future assays to unveil the viral mechanism of emerging viruses and further develop successful antivirals against them.
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Affiliation(s)
- Maria Arista-Romero
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Silvia Pujals
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
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Introduction to Special Issue "The 11th International Retroviral Nucleocapsid and Assembly Symposium". Viruses 2020; 12:v12111243. [PMID: 33142691 PMCID: PMC7692159 DOI: 10.3390/v12111243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 11/24/2022] Open
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Guo C, Yao X, Wang K, Wang J, Wang Y. Comparison of HIV-1 Gag and NCp7 in their selectivity for package signal, affinity for stem-loop 3, and Zn 2+ content. Biochimie 2020; 179:135-145. [PMID: 32987107 DOI: 10.1016/j.biochi.2020.09.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 11/17/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) Gag recognizes viral packaging signal (Psi) specifically via its nucleocapsid (NC) domain, resulting in the encapsidation of two copies of genomic RNA (gRNA) into the viral particle. The NCp7, which is cleaved from Gag during viral maturation, is a nucleic acid chaperone, coating and protecting the gRNA. In this study, an RT-qPCR-based approach was developed to quantitatively compare the Psi-selectivity of Gag and NCp7 in the presence of bacterial or 293T total RNAs. The binding affinity of Gag and NCp7 to the stem-loop (SL) 3 of Psi was also compared using surface plasmon resonance. We found that Gag selected more Psi-RNA than NCp7 from both E. coli BL21 (DE3) and in vitro binding reactions, and Gag bound to SL3-RNA with a higher affinity than NCp7. Moreover, Gag contained two Zn2+ whereas NCp7 contained one. The N-terminal zinc-finger motif of NCp7 lost most of its Zn2+-binding activity. Deletion of N-terminal amino acids 1-11 of NCp7 resulted in increased Psi-selectivity, SL3-affinity and Zn2+ content. These results indicated that Zn2+ coordination of Gag is critical for Psi-binding and selection. Removal of Zn2+ from the first zinc-finger motif during or after Gag cleavage to generate mature NCp7 might serve as a switch to regulate the functions of Gag NC domain and mature NCp7. Our study will be helpful to elucidate the important roles that Zn2+ plays in the viral life cycle, and may benefit further investigations of the function of HIV-1 Gag and NCp7.
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Affiliation(s)
- Chao Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China
| | - Xiaohong Yao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China
| | - Kangkang Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China
| | - Jinzhong Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin, 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin, 300457, China.
| | - Ying Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin, 300457, China; Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin, 300457, China; Tianjin Key Laboratory of Microbial Functional Genomics, 23 Hongda Street, TEDA, Tianjin, 300457, China.
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