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Parvez F, Sangpal D, Paithankar H, Amin Z, Chugh J. Differential conformational dynamics in two type-A RNA-binding domains drive the double-stranded RNA recognition and binding. eLife 2024; 13:RP94842. [PMID: 39116184 PMCID: PMC11309768 DOI: 10.7554/elife.94842] [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: 08/10/2024] Open
Abstract
Trans-activation response (TAR) RNA-binding protein (TRBP) has emerged as a key player in the RNA interference pathway, wherein it binds to different pre-microRNAs (miRNAs) and small interfering RNAs (siRNAs), each varying in sequence and/or structure. We hypothesize that TRBP displays dynamic adaptability to accommodate heterogeneity in target RNA structures. Thus, it is crucial to ascertain the role of intrinsic and RNA-induced protein dynamics in RNA recognition and binding. We have previously elucidated the role of intrinsic and RNA-induced conformational exchange in the double-stranded RNA-binding domain 1 (dsRBD1) of TRBP in shape-dependent RNA recognition. The current study delves into the intrinsic and RNA-induced conformational dynamics of the TRBP-dsRBD2 and then compares it with the dsRBD1 study carried out previously. Remarkably, the two domains exhibit differential binding affinity to a 12-bp dsRNA owing to the presence of critical residues and structural plasticity. Furthermore, we report that dsRBD2 depicts constrained conformational plasticity when compared to dsRBD1. Although, in the presence of RNA, dsRBD2 undergoes induced conformational exchange within the designated RNA-binding regions and other residues, the amplitude of the motions remains modest when compared to those observed in dsRBD1. We propose a dynamics-driven model of the two tandem domains of TRBP, substantiating their contributions to the versatility of dsRNA recognition and binding.
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Affiliation(s)
- Firdousi Parvez
- Department of Biology, Indian Institute of Science Education and Research (IISER)PuneIndia
| | - Devika Sangpal
- Department of Biotechnology (with jointly merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune UniversityPuneIndia
| | - Harshad Paithankar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)PuneIndia
| | - Zainab Amin
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)PuneIndia
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER)PuneIndia
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Aute R, Waghela N, Deshmukh MV. Key arginine residues in R2D2 dsRBD1 and dsRBD2 lead the siRNA recognition in Drosophila melanogaster RNAi pathway. Biophys Chem 2024; 310:107247. [PMID: 38663122 DOI: 10.1016/j.bpc.2024.107247] [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: 01/17/2024] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/23/2024]
Abstract
In Drosophila melanogaster, Dcr-2:R2D2 heterodimer binds to the 21 nucleotide siRNA duplex to form the R2D2/Dcr-2 Initiator (RDI) complex, which is critical for the initiation of siRNA-induced silencing complex (RISC) assembly. During RDI complex formation, R2D2, a protein that contains three dsRNA binding domains (dsRBD), senses two aspects of the siRNA: thermodynamically more stable end (asymmetry sensing) and the 5'-phosphate (5'-P) recognition. Despite several detailed studies to date, the molecular determinants arising from R2D2 for performing these two tasks remain elusive. In this study, we have performed structural, biophysical, and biochemical characterization of R2D2 dsRBDs. We found that the solution NMR-derived structure of R2D2 dsRBD1 yielded a canonical α1-β1-β2-β3-α2 fold, wherein two arginine salt bridges provide additional stability to the R2D2 dsRBD1. Furthermore, we show that R2D2 dsRBD1 interacts with thermodynamically asymmetric siRNA duplex independent of its 5'-phosphorylation state, whereas R2D2 dsRBD2 prefers to interact with 5'-P siRNA duplex. The mutation of key arginine residues, R53 and R101, in concatenated dsRBDs of R2D2 results in a significant loss of siRNA duplex recognition. Our study deciphers the active roles of R2D2 dsRBDs by showing that dsRBD1 initiates siRNA recognition, whereas dsRBD2 senses 5'-phosphate as an authentic mark on functional siRNA.
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Affiliation(s)
- Ramdas Aute
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Nilam Waghela
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mandar V Deshmukh
- CSIR - Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, Telangana, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Srivastava A, Nagai T, Srivastava A, Miyashita O, Tama F. Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics. Int J Mol Sci 2018; 19:E3401. [PMID: 30380757 PMCID: PMC6274748 DOI: 10.3390/ijms19113401] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/20/2018] [Accepted: 10/27/2018] [Indexed: 12/13/2022] Open
Abstract
Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.
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Affiliation(s)
- Ashutosh Srivastava
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
| | - Tetsuro Nagai
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Arpita Srivastava
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
| | - Osamu Miyashita
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
| | - Florence Tama
- Institute of Transformative Bio-Molecules (WPI), Nagoya University, Nagoya, Aichi 464-8601, Japan.
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
- RIKEN-Center for Computational Science, Kobe, Hyogo 650-0047, Japan.
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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Chiliveri SC, Deshmukh MV. Chemical shift assignments of DRB4 (1-153), a dsRNA binding protein in A. thaliana RNAi pathway. BIOMOLECULAR NMR ASSIGNMENTS 2015; 9:253-256. [PMID: 25281003 DOI: 10.1007/s12104-014-9585-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 09/29/2014] [Indexed: 06/03/2023]
Abstract
RNA interference (RNAi) is a conserved biological response to dsRNA and regulates the expression of protein-coding genes to mediate resistance to both endogenous parasitic and exogenous pathogenic nucleic acids. In RNAi pathway, dsRNA binding proteins assists Dicer at various stages of RNAi. In plants, DRB4, is a multidomain protein containing two dsRNA binding domains that recognizes the long exogenous/endogenous dsRNA and presents it to Ribonuclease enzyme, Dicer like 4, resulting in the production of 21 nt small interfering RNA. Here, we report nearly complete backbone and sidechain chemical shift assignments of N-terminus of DRB4 (1-153, ~18 kDa), containing both double stranded RNA binding domains and the linker.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- CSIR-Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Mandar V Deshmukh
- CSIR-Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad, 500007, Telangana, India.
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Heyam A, Lagos D, Plevin M. Dissecting the roles of TRBP and PACT in double-stranded RNA recognition and processing of noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2015; 6:271-89. [PMID: 25630541 PMCID: PMC7169789 DOI: 10.1002/wrna.1272] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 12/27/2022]
Abstract
HIV TAR RNA-binding protein (TRBP) and Protein Activator of PKR (PACT) are double-stranded (ds) RNA-binding proteins that participate in both small regulatory RNA biogenesis and the response to viral dsRNA. Despite considerable progress toward understanding the structure-function relationship of TRBP and PACT, their specific roles in these seemingly distinct cellular pathways remain unclear. Both proteins are composed of three copies of the double-stranded RNA-binding domain, two of which interact with dsRNA, while the C-terminal copy mediates protein-protein interactions. PACT and TRBP are found in a complex with the endonuclease Dicer and facilitate processing of immature microRNAs. Their precise contribution to the Dicing step has not yet been defined: possibilities include precursor recruitment, rearrangement of dsRNA within the complex, loading the processed microRNA into the RNA-induced silencing complex, and distinguishing different classes of small dsRNA. TRBP and PACT also interact with the viral dsRNA sensors retinoic acid-inducible gene I (RIG-I) and double-stranded RNA-activated protein kinase (PKR). Current models suggest that PACT enables RIG-I to detect a wider range of viral dsRNAs, while TRBP and PACT exert opposing regulatory effects on PKR. Here, the evidence that implicates TRBP and PACT in regulatory RNA processing and viral dsRNA sensing is reviewed and discussed in the context of their molecular structure. The broader implications of a link between microRNA biogenesis and the innate antiviral response pathway are also considered.
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MESH Headings
- Amino Acid Sequence
- Carboxypeptidases/chemistry
- Carboxypeptidases/metabolism
- Carboxypeptidases/physiology
- Models, Genetic
- Models, Molecular
- Molecular Sequence Data
- Protein Structure, Tertiary
- RNA, Double-Stranded/chemistry
- RNA, Double-Stranded/immunology
- RNA, Double-Stranded/metabolism
- RNA, Untranslated/metabolism
- RNA, Viral/chemistry
- RNA, Viral/immunology
- RNA, Viral/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/physiology
- Ribonuclease III/chemistry
- Ribonuclease III/metabolism
- Ribonuclease III/physiology
- Structure-Activity Relationship
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Affiliation(s)
- Alex Heyam
- Department of Biology, University of York, York, UK
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Gleghorn ML, Maquat LE. 'Black sheep' that don't leave the double-stranded RNA-binding domain fold. Trends Biochem Sci 2014; 39:328-40. [PMID: 24954387 DOI: 10.1016/j.tibs.2014.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/19/2014] [Accepted: 05/19/2014] [Indexed: 12/28/2022]
Abstract
The canonical double-stranded RNA (dsRNA)-binding domain (dsRBD) is composed of an α1-β1-β2-β3-α2 secondary structure that folds in three dimensions to recognize dsRNA. Recently, structural and functional studies of divergent dsRBDs revealed adaptations that include intra- and/or intermolecular protein interactions, sometimes in the absence of detectable dsRNA-binding ability. We describe here how discrete dsRBD components can accommodate pronounced amino-acid sequence changes while maintaining the core fold. We exemplify the growing importance of divergent dsRBDs in mRNA decay by discussing Dicer, Staufen (STAU)1 and 2, trans-activation responsive RNA-binding protein (TARBP)2, protein activator of protein kinase RNA-activated (PKR) (PACT), DiGeorge syndrome critical region (DGCR)8, DEAH box helicase proteins (DHX) 9 and 30, and dsRBD-like fold-containing proteins that have ribosome-related functions. We also elaborate on the computational limitations to discovering yet-to-be-identified divergent dsRBDs.
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Affiliation(s)
- Michael L Gleghorn
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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