1
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Levintov L, Vashisth H. Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides. Biophys J 2021; 120:5060-5073. [PMID: 34710377 PMCID: PMC8633718 DOI: 10.1016/j.bpj.2021.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/17/2021] [Accepted: 10/06/2021] [Indexed: 12/14/2022] Open
Abstract
Interactions between RNA molecules and proteins are critical to many cellular processes and are implicated in various diseases. The RNA-peptide complexes are good model systems to probe the recognition mechanism of RNA by proteins. In this work, we report studies on the binding-unbinding process of a helical peptide from a viral RNA element using nonequilibrium molecular dynamics simulations. We explored the existence of various dissociation pathways with distinct free-energy profiles that reveal metastable states and distinct barriers to peptide dissociation. We also report the free-energy differences for each of the four pathways to be 96.47 ± 12.63, 96.1 ± 10.95, 91.83 ± 9.81, and 92 ± 11.32 kcal/mol. Based on the free-energy analysis, we further propose the preferred pathway and the mechanism of peptide dissociation. The preferred pathway is characterized by the formation of sequential hydrogen-bonding and salt-bridging interactions between several key arginine amino acids and the viral RNA nucleotides. Specifically, we identified one arginine amino acid (R8) of the peptide to play a significant role in the recognition mechanism of the peptide by the viral RNA molecule.
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Affiliation(s)
- Lev Levintov
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire
| | - Harish Vashisth
- Department of Chemical Engineering, University of New Hampshire, Durham, New Hampshire.
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2
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Jodder J. Regulation of pri-MIRNA processing: mechanistic insights into the miRNA homeostasis in plant. PLANT CELL REPORTS 2021; 40:783-798. [PMID: 33454802 DOI: 10.1007/s00299-020-02660-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
miRNAs in plant plays crucial role in controlling proper growth, development and fitness by modulating the expression of their target genes. Therefore to modulate the expression of any stress/development related gene specifically, it is better to modulate expression of the miRNA that can target that gene. To modulate the expression level of miRNA, it is prerequisite to uncover the underlying molecular mechanism of its biogenesis. The biogenesis pathway consists of two major steps, transcription of MIR gene to pri-MIRNA and processing of pri-MIRNA into mature miRNA via sequential cleavage steps. Both of these pathways are tightly controlled by several different factors involving structural and functional molecules. This review is mainly focused on different aspects of pri-MIRNA processing mechanism to emphasize on the fact that to modulate the level of a miRNA in the cell only over-expression or knock-down of that MIR gene is not always sufficient rather it is also crucial to take processing regulation into consideration. The data collected from the recent and relevant literatures depicts that processing regulation is controlled by several aspects like structure and size of the pri-MIRNA, presence of introns in MIR gene and their location, interaction of processing factors with the core components of processing machinery etc. These detailed information can be utilized to figure out the particular point which can be utilized to modulate the expression of the miRNA which would ultimately be beneficial for the scientist and researcher working in this field to generate protocol for engineering plant with improved yield and stress tolerance.
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Affiliation(s)
- Jayanti Jodder
- School of Biotechnology, Presidency University (Rajarhat Campus), Canal Bank 7 Road, DG Block, Action Area 1D, Newtown, Kolkata, West Bengal, 700156, India.
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3
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Rojas AML, Drusin SI, Chorostecki U, Mateos JL, Moro B, Bologna NG, Bresso EG, Schapire A, Rasia RM, Moreno DM, Palatnik JF. Identification of key sequence features required for microRNA biogenesis in plants. Nat Commun 2020; 11:5320. [PMID: 33087730 PMCID: PMC7577975 DOI: 10.1038/s41467-020-19129-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/24/2020] [Indexed: 01/23/2023] Open
Abstract
MicroRNAs (miRNAs) are endogenous small RNAs of ∼21 nt that regulate multiple biological pathways in multicellular organisms. They derive from longer transcripts that harbor an imperfect stem-loop structure. In plants, the ribonuclease type III DICER-LIKE1 assisted by accessory proteins cleaves the precursor to release the mature miRNA. Numerous studies highlight the role of the precursor secondary structure during plant miRNA biogenesis; however, little is known about the relevance of the precursor sequence. Here, we analyzed the sequence composition of plant miRNA primary transcripts and found specifically located sequence biases. We show that changes in the identity of specific nucleotides can increase or abolish miRNA biogenesis. Most conspicuously, our analysis revealed that the identity of the nucleotides at unpaired positions of the precursor plays a crucial role during miRNA biogenesis in Arabidopsis. The secondary structure of miRNA precursor sequences is known to affect processing by DICER-like proteins. Here Rojas et al. show that additional sequence features also play a regulatory role in plants with nucleotide identity at unpaired positions substantially impacting processing efficiency.
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Affiliation(s)
- Arantxa M L Rojas
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Salvador I Drusin
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Área Física, Departamento de Química-Física, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Santa Fe, Argentina
| | - Uciel Chorostecki
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Barcelona Supercomputing Centre (BSC-CNS), Barcelona, (08034), Spain.,Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology, Barcelona, (08028), Spain
| | - Julieta L Mateos
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-UBA, Buenos Aires, (1428), Argentina
| | - Belén Moro
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, (08193), Spain
| | - Nicolas G Bologna
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, (08193), Spain
| | - Edgardo G Bresso
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Arnaldo Schapire
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Rodolfo M Rasia
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Santa Fe, Argentina
| | - Diego M Moreno
- Instituto de Química de Rosario (CONICET-UNR), Suipacha 570, S2002LRK, Rosario, Santa Fe, Argentina.,Área Química General e Inorgánica, Departamento de Química-Física, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Santa Fe, Argentina
| | - Javier F Palatnik
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, 2000, Argentina. .,Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, 2000, Argentina.
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4
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Study of the role of Mg 2+ in dsRNA processing mechanism by bacterial RNase III through QM/MM simulations. J Biol Inorg Chem 2019; 25:89-98. [PMID: 31754801 DOI: 10.1007/s00775-019-01741-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/06/2019] [Indexed: 12/28/2022]
Abstract
The ribonuclease III (RNase III) cleaves dsRNA in specific positions generating mature RNAs. RNase III enzymes play important roles in RNA processing, post-transcriptional gene expression, and defense against viral infection. The enzyme's active site contains Mg2+ ions bound by a network of acidic residues and water molecules, but there is a lack of information about their specific roles. In this work, multiple steered molecular dynamics simulations at QM/MM level were performed to explore the hydrolysis reaction carried out by the enzyme. Free energy profiles modifying the features of the active site are obtained and the role of Mg2+ ions, the solvent molecules and the residues of the active site are discussed in detail. Our results show that Mg2+ ions carry out different roles in the hydrolysis process positioning the substrate for the attack from a coordinated nucleophile and activating it to perform hydrolysis reaction, cleaving the dsRNA backbone in a SN2 substitution. In addition, water molecules present in the active site lower the energy barrier of the process. RNase III hydrolyzes dsRNA to generate mature RNAs. For this purpose, its active site contains Mg2+ which has an important role during the reaction. Results show that the Mg2+ activates the solvent molecule that produces the nucleophilic attack and the surrounding waters contribute significantly to the hydrolysis process.
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5
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Zhao L, Suarez IP, Gauto DF, Rasia RM, Wang J. The key role of electrostatic interactions in the induced folding in RNA recognition by DCL1-A. Phys Chem Chem Phys 2019; 20:9376-9388. [PMID: 29565070 DOI: 10.1039/c7cp07889g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The intrinsically disordered protein domain DCL1-A is the first report of a complete double stranded RNA binding domain folding upon binding. DCL1-A recognizes the dsRNA by acquiring a well-folded structure after engagement with its interaction partner. Despite the structural characterization of the interaction complex underlying the recognition of dsRNA has been established, the dynamics of disorder-to-order transitions in the binding process remains elusive. Here we have developed a coarse-grained structure-based model with consideration of electrostatic interactions to explore the mechanism of the coupled folding and binding. Our approach led to remarkable agreements with both experimental and theoretical results. We quantified the global binding-folding landscape, which indicates a synergistic binding induced folding mechanism. We further investigated the effect of electrostatic interactions in this coupled folding and binding process. It reveals that non-native electrostatic interactions dominate the initial stage of the recognition. Our results help improve our understanding of the induced folding of the IDP DCL1-A upon binding to dsRNA. Such methods developed here can be applied for further explorations of the dynamics of coupled folding and binding systems.
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Affiliation(s)
- Lingci Zhao
- College of Physics, Jilin University, Changchun, Jilin 130012, People's Republic of China and State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
| | - Irina P Suarez
- Instituto de Biología Molecular y Celular de Rosario, 27 de Febrero 210 bis, predio CCT, 2000 Rosario, Argentina
| | - Diego F Gauto
- Instituto de Biología Molecular y Celular de Rosario, 27 de Febrero 210 bis, predio CCT, 2000 Rosario, Argentina
| | - Rodolfo M Rasia
- Instituto de Biología Molecular y Celular de Rosario, 27 de Febrero 210 bis, predio CCT, 2000 Rosario, Argentina
| | - Jin Wang
- College of Physics, Jilin University, Changchun, Jilin 130012, People's Republic of China and State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China and Department of Chemistry and Physics, State University of New York, Stony Brook, NY 11794-3400, USA.
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6
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Discovering Structural Motifs in miRNA Precursors from the Viridiplantae Kingdom. Molecules 2018; 23:molecules23061367. [PMID: 29882777 PMCID: PMC6100135 DOI: 10.3390/molecules23061367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 11/17/2022] Open
Abstract
A small non-coding molecule of microRNA (19–24 nt) controls almost every biological process, including cellular and physiological, of various organisms’ lives. The amount of microRNA (miRNA) produced within an organism is highly correlated to the organism’s key processes, and determines whether the system works properly or not. A crucial factor in plant biogenesis of miRNA is the Dicer Like 1 (DCL1) enzyme. Its responsibility is to perform the cleavages in the miRNA maturation process. Despite everything we already know about the last phase of plant miRNA creation, recognition of miRNA by DCL1 in pre-miRNA structures of plants remains an enigma. Herein, we present a bioinformatic procedure we have followed to discover structure patterns that could guide DCL1 to perform a cleavage in front of or behind an miRNA:miRNA* duplex. The patterns in the closest vicinity of microRNA are searched, within pre-miRNA sequences, as well as secondary and tertiary structures. The dataset consists of structures of plant pre-miRNA from the Viridiplantae kingdom. The results confirm our previous observations based on Arabidopsis thaliana precursor analysis. Hereby, our hypothesis was tested on pre-miRNAs, collected from the miRBase database to show secondary structure patterns of small symmetric internal loops 1-1 and 2-2 at a 1–10 nt distance from the miRNA:miRNA* duplex.
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7
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 336] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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8
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Suárez IP, Gauto DF, Hails G, Mascali FC, Crespo R, Zhao L, Wang J, Rasia RM. Conformational sampling of the intrinsically disordered dsRBD-1 domain from Arabidopsis thaliana DCL1. Phys Chem Chem Phys 2018; 20:11237-11246. [DOI: 10.1039/c7cp07908g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Partial folding and stability of DCL1-dsRBD1.
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Affiliation(s)
- Irina P. Suárez
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Diego F. Gauto
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Guillermo Hails
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Florencia C. Mascali
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Roberta Crespo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Lingzi Zhao
- College of Physics
- Jilin University
- Jilin
- China
| | - Jin Wang
- State University of New York at Stony Brook
- USA
| | - Rodolfo M. Rasia
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
- Área Biofísica
- Facultad de Ciencias Bioquímicas y Farmacéuticas
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