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Chyży P, Kulik M, Shinobu A, Re S, Sugita Y, Trylska J. Molecular dynamics in multidimensional space explains how mutations affect the association path of neomycin to a riboswitch. Proc Natl Acad Sci U S A 2024; 121:e2317197121. [PMID: 38579011 PMCID: PMC11009640 DOI: 10.1073/pnas.2317197121] [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] [Received: 10/08/2023] [Accepted: 02/15/2024] [Indexed: 04/07/2024] Open
Abstract
Riboswitches are messenger RNA (mRNA) fragments binding specific small molecules to regulate gene expression. A synthetic N1 riboswitch, inserted into yeast mRNA controls the translation of a reporter gene in response to neomycin. However, its regulatory activity is sensitive to single-point RNA mutations, even those distant from the neomycin binding site. While the association paths of neomycin to N1 and its variants remain unknown, recent fluorescence kinetic experiments indicate a two-step process driven by conformational selection. This raises the question of which step is affected by mutations. To address this, we performed all-atom two-dimensional replica-exchange molecular dynamics simulations for N1 and U14C, U14C[Formula: see text], U15A, and A17G mutants, ensuring extensive conformational sampling of both RNA and neomycin. The obtained neomycin association and binding paths, along with multidimensional free-energy profiles, revealed a two-step binding mechanism, consisting of conformational selection and induced fit. Neomycin binds to a preformed N1 conformation upon identifying a stable upper stem and U-turn motif in the riboswitch hairpin. However, the positioning of neomycin in the binding site occurs at different RNA-neomycin distances for each mutant, which may explain their different regulatory activities. The subsequent induced fit arises from the interactions of the neomycin's N3 amino group with RNA, causing the G9 backbone to rearrange. In the A17G mutant, the critical C6-A17/G17 stacking forms at a closer RNA-neomycin distance compared to N1. These findings together with estimated binding free energies coincide with experiments and elucidate why the A17G mutation decreases and U15A enhances N1 activity in response to neomycin.
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Affiliation(s)
- Piotr Chyży
- Centre of New Technologies, University of Warsaw, 02-097Warsaw, Poland
| | - Marta Kulik
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093Warsaw, Poland
| | - Ai Shinobu
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 650-0047Kobe, Japan
| | - Suyong Re
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 650-0047Kobe, Japan
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health, and Nutrition, 567-0085Ibaraki, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 650-0047Kobe, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 351-0198Wako, Japan
- RIKEN Center for Computational Science, 650-0047Kobe, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, 02-097Warsaw, Poland
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2
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Tieng FYF, Abdullah-Zawawi MR, Md Shahri NAA, Mohamed-Hussein ZA, Lee LH, Mutalib NSA. A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools. Brief Bioinform 2023; 25:bbad421. [PMID: 38040490 PMCID: PMC10753535 DOI: 10.1093/bib/bbad421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 12/03/2023] Open
Abstract
RNA biology has risen to prominence after a remarkable discovery of diverse functions of noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions into RNA-RNA complexes via base pairing with complementary sequences in other RNAs. An interplay between RNAs is essential, as it possesses various functional roles in human cells, including genetic translation, RNA splicing, editing, ribosomal RNA maturation, RNA degradation and the regulation of metabolic pathways/riboswitches. Moreover, the pervasive transcription of the human genome allows for the discovery of novel genomic functions via RNA interactome investigation. The advancement of experimental procedures has resulted in an explosion of documented data, necessitating the development of efficient and precise computational tools and algorithms. This review provides an extensive update on RNA-RNA interaction (RRI) analysis via thermodynamic- and comparative-based RNA secondary structure prediction (RSP) and RNA-RNA interaction prediction (RIP) tools and their general functions. We also highlighted the current knowledge of RRIs and the limitations of RNA interactome mapping via experimental data. Then, the gap between RSP and RIP, the importance of RNA homologues, the relationship between pseudoknots, and RNA folding thermodynamics are discussed. It is hoped that these emerging prediction tools will deepen the understanding of RNA-associated interactions in human diseases and hasten treatment processes.
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Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | | | - Nur Alyaa Afifah Md Shahri
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology (INBIOSIS), UKM, Selangor 43600, Malaysia
- Department of Applied Physics, Faculty of Science and Technology, UKM, Selangor 43600, Malaysia
| | - Learn-Han Lee
- Sunway Microbiomics Centre, School of Medical and Life Sciences, Sunway University, Sunway City 47500, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia (UKM), Kuala Lumpur 56000, Malaysia
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University of Malaysia, Selangor 47500, Malaysia
- Faculty of Health Sciences, UKM, Kuala Lumpur 50300, Malaysia
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3
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Zhang M, Ding Y, Hu S, Li F, Wang Y, Zhou Y, Qi M, Ni H, Fang S, Chen Q. Transcriptomics and systems network-based molecular mechanism of herbal formula Huosu-Yangwei inhibited gastric cancer in vivo. JOURNAL OF ETHNOPHARMACOLOGY 2023:116674. [PMID: 37277085 DOI: 10.1016/j.jep.2023.116674] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/08/2023] [Accepted: 05/21/2023] [Indexed: 06/07/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The efficacy of the herbal formula Huosu-Yangwei (HSYW) in the treatment of advanced gastric cancer and chronic atrophic gastritis with precancerous lesions has been reported in clinical trials. However, the molecular mechanisms underlying its inhibition of gastric tumor are not well-understood. AIM OF THE STUDY Combined with transcriptomics and systems network-based molecular mechanism to explore the potential circRNA-miRNA-mRNA network of HSYW in the treatment of gastric cancer. MATERIALS AND METHODS Animal experiments were conducted to investigate the effect of HSYW on tumor growth in vivo. RNA sequencing (RNA-seq) was implemented to identify the differentially expressed (DE) genes. Predictive miRNA targets and mRNA were used to construct circRNA-miRNA-mRNA networks and protein-protein interaction (PPI) networks. Quantitative real-time PCR (qRT-PCR) was utilized to verify the accuracy of the proposed circRNA-miRNA-mRNA networks. Additionally, the differentially expressed target proteins between gastric cancer (GC) and normal patients were assessed using data from the TCGA (The Cancer Genome Atlas) and HPA (The Human Protein Atlas) databases. RESULTS We demonstrate HSYW significantly inhibits tumor growth of N87 cell-bearing Balb/c mice. Transcriptomic analysis revealed the existence of 119 differentially expressed (DE) circRNAs and 200 DE mRNAs between HSYW-treated and model mice. By associating predicted circRNA-miRNA pairs and miRNA-mRNA pairs, we constructed a circRNA-miRNA-mRNA (CMM) network. Furthermore, a protein-protein interaction (PPI) network was developed using the differential expressed mRNAs. Consequently, the reconstructed core CMM network and qRT-PCR validation indicated that 4 circRNAs, 5 miRNAs and 6 mRNAs could potentially serve as biomarkers to assess the therapeutic effects of HSYW-treated N87-bearing Balb/c mice. The TCGA and HPA databases also demonstrated that mRNA KLF15 and PREX1 had substantial differences between gastric cancer (GC) and healthy controls. CONCLUSIONS By combining the experimental and bioinformatics analysis, this study confirms that the circRNA_00240/hsa-miR-642a-5p/KLF15 and circRNA_07980/hsa-miR-766-3p/PREX1 pathways play critical roles in HSYW-treated gastric cancer.
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Affiliation(s)
- Mengyuan Zhang
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Yujie Ding
- School of Basic Medical Science, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Sheng Hu
- Central Laboratory, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China
| | - Fulong Li
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Yi Wang
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Yue Zhou
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Mei Qi
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - HongMei Ni
- School of Basic Medical Science, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Shengquan Fang
- Department of Gastroenterology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China.
| | - Qilong Chen
- Central Laboratory, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, 200443, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China.
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4
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Kensinger AH, Makowski JA, Pellegrene KA, Imperatore JA, Cunningham CL, Frye CJ, Lackey PE, Mihailescu MR, Evanseck JD. Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 s2m Elements Using Molecular Dynamics Simulations. ACS PHYSICAL CHEMISTRY AU 2023; 3:30-43. [PMID: 36711027 PMCID: PMC9578647 DOI: 10.1021/acsphyschemau.2c00032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/05/2022]
Abstract
The functional role of the highly conserved stem-loop II motif (s2m) in SARS-CoV and SARS-CoV-2 in the viral lifecycle remains enigmatic and an intense area of research. Structure and dynamics of the s2m are key to establishing a structure-function connection, yet a full set of atomistic resolution coordinates is not available for SARS-CoV-2 s2m. Our work constructs three-dimensional coordinates consistent with NMR solution phase data for SARS-CoV-2 s2m and provides a comparative analysis with its counterpart SARS-CoV s2m. We employed initial coordinates based on PDB ID 1XJR for SARS-CoV s2m and two models for SARS-CoV-2 s2m: one based on 1XJR in which we introduced the mutations present in SARS-CoV-2 s2m and the second based on the available SARS-CoV-2 NMR NOE data supplemented with knowledge-based methods. For each of the three systems, 3.5 μs molecular dynamics simulations were used to sample the structure and dynamics, and principal component analysis (PCA) reduced the ensembles to hierarchal conformational substates for detailed analysis. Dilute solution simulations of SARS-CoV s2m demonstrate that the GNRA-like terminal pentaloop is rigidly defined by base stacking uniquely positioned for possible kissing dimer formation. However, the SARS-CoV-2 s2m simulation did not retain the reported crystallographic SARS-CoV motifs and the terminal loop expands to a highly dynamic "nonaloop." Increased flexibility and structural disorganization are observed for the larger terminal loop, where an entropic penalty is computed to explain the experimentally observed reduction in kissing complex formation. Overall, both SARS-CoV and SARS-CoV-2 s2m elements have a similarly pronounced L-shape due to different motif interactions. Our study establishes the atomistic three-dimensional structure and uncovers dynamic differences that arise from s2m sequence changes, which sets the stage for the interrogation of different mechanistic pathways of suspected biological function.
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Affiliation(s)
- Adam H. Kensinger
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Joseph A. Makowski
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Kendy A. Pellegrene
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Joshua A. Imperatore
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Caylee L. Cunningham
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Caleb J. Frye
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Patrick E. Lackey
- Department
of Biochemistry and Chemistry, Westminster
College, New Wilmington, Pennsylvania16172, United States
| | - Mihaela Rita Mihailescu
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
| | - Jeffrey D. Evanseck
- Department
of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania15282, United States
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5
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Shine M, Harris SE, Pellegrene KA, Kensinger AH, Mihailescu MR, Evanseck JD, Lackey PE. Uridylation of the histone mRNA stem-loop weakens binding interactions with SLBP while maintaining interactions with 3'hExo. RNA Biol 2023; 20:469-481. [PMID: 37516934 PMCID: PMC10388802 DOI: 10.1080/15476286.2023.2171760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/03/2022] [Accepted: 01/19/2023] [Indexed: 07/31/2023] Open
Abstract
Histone mRNA degradation is controlled by the unique 3' stem-loop of histone mRNA and the stem-loop binding protein (SLBP). As part of this process, the 3' stem-loop is trimmed by the histone-specific 3' exonuclease (3'hExo) and uridylated by the terminal uridylyl transferase 7 (TUT7), creating partially degraded intermediates with short uridylations. The role of these uridylations in degradation is not fully understood. Our work examines changes in the stability of the ternary complex created by trimming and uridylation of the stem-loop to better understand the role of this process in the histone mRNA life cycle. In this study, we used fluorescence polarization and electrophoretic mobility shift assays to demonstrate that both SLBP and 3'hExo can bind to uridylated and partially degraded stem-loop intermediates, although with lower affinity. We further characterized this complex by performing 1-µs molecular dynamics simulations using the AMBER force field and Nanoscale Molecular Dynamics (NAMD). These simulations show that while uridylation helps maintain the overall shape of the stem-loop, the combination of uridylation and dephosphorylation of the TPNK motif in SLBP disrupts key RNA-protein interactions. They also demonstrate that uridylation allows 3'hExo to maintain contact with the stem-loop after partial degradation and plays a role in disrupting key base pairs in partially degraded histone mRNA intermediates. Together, these experiments and simulations suggest that trimming by 3'hExo, uridylation, and SLBP dephosphorylation weakens both RNA-protein interactions and the stem-loop itself. Our results further elucidate the role of uridylation and SLBP dephosphorylation in the early stages of histone mRNA degradation.
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Affiliation(s)
- Morgan Shine
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, PA, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Sarah E Harris
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, PA, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kendy A Pellegrene
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Adam H Kensinger
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Mihaela Rita Mihailescu
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Jeffrey D Evanseck
- Department of Chemistry and Biochemistry and Center for Computational Sciences, Duquesne University, Pittsburgh, PA, USA
| | - Patrick E Lackey
- Department of Biochemistry and Chemistry, Westminster College, New Wilmington, PA, USA
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6
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Jana SK, Harikrishna S, Sudhakar S, El-Khoury R, Pradeepkumar PI, Damha MJ. Nucleoside Analogues with a Seven-Membered Sugar Ring: Synthesis and Structural Compatibility in DNA-RNA Hybrids. J Org Chem 2022; 87:2367-2379. [PMID: 35133166 DOI: 10.1021/acs.joc.1c02254] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we describe results on the pairing properties of synthetic DNA and RNA oligonucleotides that contain nucleotide analogues with a 7-membered sugar ring (oxepane nucleotides). Specifically, we describe the stereoselective synthesis of a set of three oxepane thymine nucleosides (OxT), their conversion to phosphoramidite derivatives, and their use in solid-phase synthesis to yield chimeric OxT-DNA and OxT-RNA strands. The different regioisomeric OxT phosphoramidites allowed for positional variations of the phosphate bridge and assessment of duplex stability when the oxepane nucleotides were incorporated in dsDNA, dsRNA, and DNA-RNA hybrids. Little to no destabilization was observed when two of the three regioisomeric OxT units were incorporated in the DNA strand of DNA-RNA hybrids, a remarkable result considering the dramatically different structure of oxepanes in comparison to 2'-deoxynucleosides. Extensive molecular modeling and dynamics studies further revealed the various structural features responsible for the tolerance of both OxT modifications in DNA-RNA duplexes, such as base-base stacking and sugar-phosphate H-bond interactions. These studies suggest that oxepane nucleotide analogues may find applications in synthetic biology, where synthetic oligonucleotides can be used to create new tools for biotechnology and medicine.
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Affiliation(s)
- Sunit Kumar Jana
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - S Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Roberto El-Khoury
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
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7
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3D Modeling of Non-coding RNA Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:281-317. [DOI: 10.1007/978-3-031-08356-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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8
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Chyży P, Kulik M, Re S, Sugita Y, Trylska J. Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection. Front Mol Biosci 2021; 8:633130. [PMID: 33708793 PMCID: PMC7942488 DOI: 10.3389/fmolb.2021.633130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Short, structured fragments of non-coding mRNA may act as molecular switches upon binding specific ligands, regulating the translation of proteins encoded downstream this mRNA sequence. One switch, called riboswitch N1, is regulated by aminoglycosides such as neomycin. Nucleobase mutations in the apical loop, although distant from the binding pocket, significantly affect neomycin affinity and riboswitch regulatory efficiency. To explain this influence, we conducted molecular dynamics simulations using generalized replica exchange with solute tempering (gREST). Translation assay of a reporter protein in a yeast system shows that mutating A17 to G in the riboswitch apical loop reduces 6-fold the translation regulation efficiency of the mutant. Indeed, simulations of the unbound riboswitch show that G17 frequently stacks with base 7, while base 8 is stabilized towards the binding site in a way that it may interfere with the conformational selection mechanism and decrease riboswitch regulatory activity. In the riboswitch complexes, this single-point A to G mutation disrupts a strong hydrogen bond between nucleotides 5 and 17 and, instead, a new hydrogen bond between residue 17 and neomycin is created. This change forces neomycin to occupy a slightly shifted position in the binding pocket, which increases neomycin flexibility. Our simulations of the U14C mutation suggest that the riboswitch complex with neomycin is more stable if cytosine 14 is protonated. A hydrogen bond between the RNA phosphate and protonated cytosine appears as the stabilizing factor. Also, based on the cell-free translation assay and isothermal titration calorimetry experiments, mutations of nucleotides 14 and 15 affect only slightly the riboswitch ability to bind the ligand and its activity. Indeed, the simulation of the unbound U15A mutant suggests conformations preformed for ligand binding, which may explain slightly higher regulatory activity of this mutant. Overall, our results corroborate the in vivo and in vitro experiments on the N1 riboswitch-neomycin system, detail the relationship between nucleobase mutations and RNA dynamics, and reveal the conformations playing the major role in the conformational selection mechanism.
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Affiliation(s)
- Piotr Chyży
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Marta Kulik
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Suyong Re
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Yuji Sugita
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,RIKEN Cluster for Pioneering Research (CPR), Wako, Japan.,RIKEN Center for Computational Science, Kobe, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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9
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Gorb L, Pekh A, Nyporko A, Ilchenko M, Golius A, Zubatiuk T, Zubatyuk R, Dubey I, Hovorun DM, Leszczynski J. Effect of Microenvironment on the Geometrical Structure of d(A)5 d(T)5 and d(G)5 d(C)5 DNA Mini-Helixes and the Dickerson Dodecamer: A Density Functional Theory Study. J Phys Chem B 2020; 124:9343-9353. [DOI: 10.1021/acs.jpcb.0c06154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Leonid Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Anatolii Pekh
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv 03022, Ukraine
| | - Alexey Nyporko
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv 03022, Ukraine
| | - Mykola Ilchenko
- Department of Synthetic Bioregulators, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
| | - Anastasiia Golius
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Tetiana Zubatiuk
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Roman Zubatyuk
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
| | - Igor Dubey
- Department of Synthetic Bioregulators, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Vul. Zabolotnogo, Kyiv 03143, Ukraine
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, P.O. Box 17910, 1325 Lynch Street, Jackson, Mississippi 39217, United States
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10
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Jasiński M, Miszkiewicz J, Feig M, Trylska J. Thermal Stability of Peptide Nucleic Acid Complexes. J Phys Chem B 2019; 123:8168-8177. [PMID: 31491077 DOI: 10.1021/acs.jpcb.9b05168] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptide nucleic acid (PNA) is a neutral nucleic acid analogue that base pairs with itself and natural nucleic acids. PNA-nucleic acid complexes are more thermally stable than the corresponding complexes of natural nucleic acids. In addition, PNA is biostable and thus used in many antisense and antigene applications to block functional RNA or DNA via sequence-specific interactions. We have recently developed force field parameters for molecular dynamics (MD) simulations of PNA and PNA-involving duplexes with natural nucleic acids. In this work, we provide the first application of this force field to biologically relevant PNA sequences and their complexes with RNA. We investigated thermal stabilities of short PNA-PNA, PNA-RNA, and RNA-RNA duplexes using UV-monitored thermal denaturation experiments and MD simulations at ambient and elevated temperatures. The simulations show a two-state melting transition and reproduce the thermal stability from melting experiments, with PNA-PNA being the most and RNA-RNA the least stable. The PNA-PNA duplex also displays the highest activation energy for melting. The atomistic details of unfolding of PNA duplexes suggest that all PNA-PNA bases melt concomitantly, whereas the RNA-RNA and PNA-RNA are destabilized from the termini toward the central part of the duplexes.
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Affiliation(s)
| | | | - Michael Feig
- Department of Biochemistry and Molecular Biology , Michigan State University , 603 Wilson Road , East Lansing , Michigan 48824 , United States
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11
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Kulik M, Mori T, Sugita Y, Trylska J. Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides. Nucleic Acids Res 2019; 46:9960-9970. [PMID: 30239867 PMCID: PMC6212780 DOI: 10.1093/nar/gky833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/07/2018] [Indexed: 01/14/2023] Open
Abstract
A synthetic riboswitch N1, inserted into the 5'-untranslated mRNA region of yeast, regulates gene expression upon binding ribostamycin and neomycin. Interestingly, a similar aminoglycoside, paromomycin, differing from neomycin by only one substituent (amino versus hydroxyl), also binds to the N1 riboswitch, but without affecting gene expression, despite NMR evidence that the N1 riboswitch binds all aminoglycosides in a similar way. Here, to explore the details of structural dynamics of the aminoglycoside-N1 riboswitch complexes, we applied all-atom molecular dynamics (MD) and temperature replica-exchange MD simulations in explicit solvent. Indeed, we found that ribostamycin and neomycin affect riboswitch dynamics similarly but paromomycin allows for more flexibility because its complex lacks the contact between the distinctive 6' hydroxyl group and the G9 phosphate. Instead, a transient hydrogen bond of 6'-OH with A17 is formed, which partially diminishes interactions between the bulge and apical loop of the riboswitch, likely contributing to riboswitch inactivity. In many ways, the paromomycin complex mimics the conformations, interactions, and Na+ distribution of the free riboswitch. The MD-derived interaction network helps understand why riboswitch activity depends on aminoglycoside type, whereas for another aminoglycoside-binding site, aminoacyl-tRNA site in 16S rRNA, activity is not discriminatory.
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Affiliation(s)
- Marta Kulik
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | | | - Yuji Sugita
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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12
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Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana. Sci Rep 2019; 9:4197. [PMID: 30862893 PMCID: PMC6414600 DOI: 10.1038/s41598-019-40875-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/19/2019] [Indexed: 01/03/2023] Open
Abstract
Riboswitches are RNA sensors that affect post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch class is the most widespread riboswitch occurring in all three domains of life. Even though it controls different genes involved in the synthesis or transport of thiamine and its phosphorylated derivatives in bacteria, archaea, fungi, and plants, the TPP aptamer has a conserved structure. In this study, we aimed at understanding differences in the structural dynamics of TPP riboswitches from Escherichia coli and Arabidopsis thaliana, based on their crystallographic structures (TPPswec and TPPswat, respectively) and dynamics in aqueous solution, both in apo and holo states. A combination of Molecular Dynamics Simulations and Network Analysis empowered to find out slight differences in the dynamical behavior of TPP riboswitches, although relevant for their dynamics in bacteria and plants species. Our results suggest that distinct interactions in the microenvironment surrounding nucleotide U36 of TPPswec (and U35 in TPPswat) are related to different responses to TPP. The network analysis showed that minor structural differences in the aptamer enable enhanced intramolecular communication in the presence of TPP in TPPswec, but not in TPPswat. TPP riboswitches of plants present subtler and slower regulation mechanisms than bacteria do.
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13
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Bottaro S, Bussi G, Pinamonti G, Reißer S, Boomsma W, Lindorff-Larsen K. Barnaba: software for analysis of nucleic acid structures and trajectories. RNA (NEW YORK, N.Y.) 2019; 25:219-231. [PMID: 30420522 PMCID: PMC6348988 DOI: 10.1261/rna.067678.118] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 11/06/2018] [Indexed: 06/09/2023]
Abstract
RNA molecules are highly dynamic systems characterized by a complex interplay between sequence, structure, dynamics, and function. Molecular simulations can potentially provide powerful insights into the nature of these relationships. The analysis of structures and molecular trajectories of nucleic acids can be nontrivial because it requires processing very high-dimensional data that are not easy to visualize and interpret. Here we introduce Barnaba, a Python library aimed at facilitating the analysis of nucleic acid structures and molecular simulations. The software consists of a variety of analysis tools that allow the user to (i) calculate distances between three-dimensional structures using different metrics, (ii) back-calculate experimental data from three-dimensional structures, (iii) perform cluster analysis and dimensionality reductions, (iv) search three-dimensional motifs in PDB structures and trajectories, and (v) construct elastic network models for nucleic acids and nucleic acids-protein complexes. In addition, Barnaba makes it possible to calculate torsion angles, pucker conformations, and to detect base-pairing/base-stacking interactions. Barnaba produces graphics that conveniently visualize both extended secondary structure and dynamics for a set of molecular conformations. The software is available as a command-line tool as well as a library, and supports a variety of file formats such as PDB, dcd, and xtc files. Source code, documentation, and examples are freely available at https://github.com/srnas/barnaba under GNU GPLv3 license.
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Affiliation(s)
- Sandro Bottaro
- Structural Biology and NMR Laboratory and Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
- International School for Advanced Studies, 34136 Trieste, Italy
| | - Giovanni Bussi
- International School for Advanced Studies, 34136 Trieste, Italy
| | - Giovanni Pinamonti
- International School for Advanced Studies, 34136 Trieste, Italy
- Department of Mathematics and Computer Science, Freie Universität, 14195 Berlin, Germany
| | - Sabine Reißer
- International School for Advanced Studies, 34136 Trieste, Italy
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Copenhagen 2200, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory and Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
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14
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Leonarski F, Jasiński M, Trylska J. Thermodynamics of the fourU RNA thermal switch derived from molecular dynamics simulations and spectroscopic techniques. Biochimie 2018; 156:22-32. [PMID: 30244136 DOI: 10.1016/j.biochi.2018.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
Abstract
Bacterial 5' untranslated regions of mRNA, termed thermal switches or thermometers, change their structure in response to temperature change. This structural change provides for the regulation of gene expression. One of such thermal switches, called fourU, is present in the Salmonella species. Mutations of fourU were found to abrogate its regulatory properties. We investigated the thermodynamics of the fourU fragment responsible for its structural changes. All-atom molecular dynamics simulations at various temperatures and spectroscopic experiments in solution were performed for the wild-type fourU and its mutants. We found that the U11C and A8C mutations stabilize the fourU structure in comparison to the wild-type fourU, and the double-point G14A/C25U mutant has the most destabilizing effect on the fourU hairpin 2 responsible for temperature sensing. The G14A/C25U mutant is also the easiest to strand-invade by a complementary oligonucleotide as indicated by fluorescence spectroscopy experiments.
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Affiliation(s)
- Filip Leonarski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Maciej Jasiński
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
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15
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Kulczycka-Mierzejewska K, Sadlej J, Trylska J. Molecular dynamics simulations suggest why the A2058G mutation in 23S RNA results in bacterial resistance against clindamycin. J Mol Model 2018; 24:191. [PMID: 29971530 PMCID: PMC6028897 DOI: 10.1007/s00894-018-3689-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/22/2018] [Indexed: 01/15/2023]
Abstract
Clindamycin, a lincosamide antibiotic, binds to 23S ribosomal RNA and inhibits protein synthesis. The A2058G mutation in 23S RNA results in bacterial resistance to clindamycin. To understand the influence of this mutation on short-range interactions of clindamycin with 23S RNA, we carried out full-atom molecular dynamics simulations of a ribosome fragment containing clindamycin binding site. We compared the dynamical behavior of this fragment simulated with and without the A2058G mutation. Molecular dynamics simulations suggest that clindamycin in the native ribosomal binding site is more internally flexible than in the A2058G mutant. Only in the native ribosome fragment did we observe intramolecular conformational change of clindamycin around its C7-N1-C10-C11 dihedral. In the mutant, G2058 makes more stable hydrogen bonds with clindamycin hindering its conformational freedom in the ribosome-bound state. Clindamycin binding site is located in the entrance to the tunnel through which the newly synthesized polypeptide leaves the ribosome. We observed that in the native ribosome fragment, clindamycin blocks the passage in the tunnel entrance, whereas in the mutated fragment the aperture is undisturbed due to a different mode of binding of clindamycin in the mutant. Restricted conformational freedom of clindamycin in a position not blocking the tunnel entrance in the A2058G mutant could explain the molecular mechanism of bacterial resistance against clindamycin occurring in this mutant.
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Affiliation(s)
- Katarzyna Kulczycka-Mierzejewska
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Joanna Sadlej
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-093 Warsaw, Poland
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16
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Jasiński M, Feig M, Trylska J. Improved Force Fields for Peptide Nucleic Acids with Optimized Backbone Torsion Parameters. J Chem Theory Comput 2018; 14:3603-3620. [PMID: 29791152 DOI: 10.1021/acs.jctc.8b00291] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide nucleic acids are promising nucleic acid analogs for antisense therapies as they can form stable duplex and triplex structures with DNA and RNA. Computational studies of PNA-containing duplexes and triplexes are an important component for guiding their design, yet existing force fields have not been well validated and parametrized with modern computational capabilities. We present updated CHARMM and Amber force fields for PNA that greatly improve the stability of simulated PNA-containing duplexes and triplexes in comparison with experimental structures and allow such systems to be studied on microsecond time scales. The force field modifications focus on reparametrized PNA backbone torsion angles to match high-level quantum mechanics reference energies for a model compound. The microsecond simulations of PNA-PNA, PNA-DNA, PNA-RNA, and PNA-DNA-PNA complexes also allowed a comprehensive analysis of hydration and ion interactions with such systems.
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Affiliation(s)
- Maciej Jasiński
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States.,Centre of New Technologies , University of Warsaw , Warsaw , Poland
| | - Michael Feig
- Department of Biochemistry and Molecular Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joanna Trylska
- Centre of New Technologies , University of Warsaw , Warsaw , Poland
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17
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Wojciechowska M, Dudek M, Trylska J. Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA. Biopolymers 2018; 109:e23116. [PMID: 29570767 DOI: 10.1002/bip.23116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/24/2018] [Accepted: 02/27/2018] [Indexed: 01/13/2023]
Abstract
A fragment of E. coli 16S rRNA formed by nucleotides 500 to 545 is termed helix 18. Nucleotides 505-507 and 524-526 form a pseudo-knot and its distortion affects ribosome function. Helix 18 isolated from the ribosome context is thus an interesting fragment to investigate the structural properties and folding of RNA with pseudo-knots. With all-atom molecular dynamics simulations, spectroscopic and gel electrophoresis experiments, we investigated thermodynamics of helix 18, with a focus on its pseudo-knot. In solution studies at ambient conditions we observed dimerization of helix 18. We proposed that the loop, containing nucleotides forming the pseudo-knot, interacts with another monomer of helix 18. The native dimer is difficult to break but introducing mutations in the pseudo-knot indeed assured a monomeric form of helix 18. Molecular dynamics simulations at 310 K confirmed the stability of the pseudo-knot but at elevated temperatures this pseudo-knot was the first part of helix 18 to lose the hydrogen bond pattern. To further determine helix 18 stability, we analyzed the interactions of helix 18 with short oligomers complementary to a nucleotide stretch containing the pseudo-knot. The formation of higher-order structures by helix 18 impacts hybridization efficiency of peptide nucleic acid and 2'-O methyl RNA oligomers.
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Affiliation(s)
- Monika Wojciechowska
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland
| | - Marta Dudek
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland.,School of Molecular Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, Warsaw, 02-106, Poland.,First Faculty of Medicine, Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, Warsaw, 02-091, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland
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18
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Jasiński M, Kulik M, Wojciechowska M, Stolarski R, Trylska J. Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site. PLoS One 2018; 13:e0191138. [PMID: 29351348 PMCID: PMC5774723 DOI: 10.1371/journal.pone.0191138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022] Open
Abstract
Synthetic oligonucleotides targeting functional regions of the prokaryotic rRNA could be promising antimicrobial agents. Indeed, such oligonucleotides were proven to inhibit bacterial growth. 2’-O-methylated (2’-O-Me) oligoribonucleotides with a sequence complementary to the decoding site in 16S rRNA were reported as inhibitors of bacterial translation. However, the binding mode and structures of the formed complexes, as well as the level of selectivity of the oligonucleotides between the prokaryotic and eukaryotic target, were not determined. We have analyzed three 2’-O-Me oligoribonucleotides designed to hybridize with the models of the prokaryotic rRNA containing two neighboring aminoglycoside binding pockets. One pocket is the paromomycin/kanamycin binding site corresponding to the decoding site in the small ribosomal subunit and the other one is the close-by hygromycin B binding site whose dynamics has not been previously reported. Molecular dynamics (MD) simulations, as well as isothermal titration calorimetry, gel electrophoresis and spectroscopic studies have shown that the eukaryotic rRNA model is less conformationally stable (in terms of hydrogen bonds and stacking interactions) than the corresponding prokaryotic one. In MD simulations of the eukaryotic construct, the nucleotide U1498, which plays an important role in correct positioning of mRNA during translation, is flexible and spontaneously flips out into the solvent. In solution studies, the 2’-O-Me oligoribonucleotides did not interact with the double stranded rRNA models but all formed stable complexes with the single-stranded prokaryotic target. 2’-O-Me oligoribonucleotides with one and two mismatches bound less tightly to the eukaryotic target. This shows that at least three mismatches between the 2’-O-Me oligoribonucleotide and eukaryotic rRNA are required to ensure target selectivity. The results also suggest that, in the ribosome environment, the strand invasion is the preferred binding mode of 2’-O-Me oligoribonucleotides targeting the aminoglycoside binding sites in 16S rRNA.
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Affiliation(s)
- Maciej Jasiński
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
| | - Marta Kulik
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | | | - Ryszard Stolarski
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- * E-mail:
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19
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Yesudhas D, Anwar MA, Panneerselvam S, Kim HK, Choi S. Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation. FEBS Open Bio 2017; 7:1750-1767. [PMID: 29123983 PMCID: PMC5666385 DOI: 10.1002/2211-5463.12316] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 11/29/2022] Open
Abstract
Transcription factors (TFs) are gene expression regulators that bind to DNA in a sequence‐specific manner and determine the functional characteristics of the gene. It is worthwhile to study the unique characteristics of such specific TF‐binding pattern in DNA. Sox2 recognizes a 6‐ to 7‐base pair consensus DNA sequence; the central four bases of the binding site are highly conserved, whereas the two to three flanking bases are variable. Here, we attempted to analyze the binding affinity and specificity of the Sox2 protein for distinct DNA sequence patterns via steered molecular dynamics, in which a pulling force is employed to dissociate Sox2 from Sox2–DNA during simulation to study the behavior of a complex under nonequilibrium conditions. The simulation results revealed that the first two stacking bases of the binding pattern have an exclusive impact on the binding affinity, with the corresponding mutant complexes showing greater binding and longer dissociation time than the experimental complexes do. In contrast, mutation of the conserved bases tends to reduce the affinity, and mutation of the complete conserved region disrupts the binding. It might pave the way to identify the most likely binding pattern recognized by Sox2 based on the affinity of each configuration. The α2‐helix of Sox2 was found to be the key player in the Sox2–DNA association. The characterization of Sox2's binding patterns for the target genes in the genome helps in understanding of its regulatory functions.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology Ajou University Suwon Korea
| | | | | | - Han-Kyul Kim
- Department of Molecular Science and Technology Ajou University Suwon Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology Ajou University Suwon Korea
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20
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Kulik M, Markowska-Zagrajek A, Wojciechowska M, Grzela R, Wituła T, Trylska J. Helix 69 of Escherichia coli 23S ribosomal RNA as a peptide nucleic acid target. Biochimie 2017; 138:32-42. [PMID: 28396015 DOI: 10.1016/j.biochi.2017.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 03/03/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
Abstract
A fragment of 23S ribosomal RNA (nucleotides 1906-1924 in E. coli), termed Helix 69, forms a hairpin that is essential for ribosome function. Helix 69 forms a conformationally flexible inter-subunit connection with helix 44 of 16S ribosomal RNA, and the nucleotide A1913 of Helix 69 influences decoding accuracy. Nucleotides U1911 and U1917 are post-transcriptionally modified with pseudouridines (Ψ) and U1915 with 3-methyl-Ψ. We investigated Helix 69 as a target for a complementary synthetic oligonucleotide - peptide nucleic acid (PNA). We determined thermodynamic properties of Helix 69 and its complexes with PNA and tested the performance of PNA targeted at Helix 69 in inhibiting translation in cell-free extracts and growth of E. coli cells. First, we examined the interactions of a PNA oligomer complementary to the G1907-A1919 fragment of Helix 69 with the sequences corresponding to human and bacterial species (with or without pseudouridine modifications). PNA invades the Helix 69 hairpin creating stable complexes and PNA binding to the pseudouridylated bacterial sequence is stronger than to Helix 69 without any modifications. Second, we confirmed the binding of PNA to 23S rRNA and 70S ribosomes. Third, we verified the efficiency of translation inhibition of these PNA oligomers in the cell-free translation/transcription E. coli system, which were in a similar range as tetracycline. Next, we confirmed that PNA conjugated to the (KFF)3K transporter peptide inhibited E. coli growth in micromolar concentrations. Overall, targeting Helix 69 with PNA or other sequence-specific oligomers could be a promising way to inhibit bacterial translation.
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Affiliation(s)
- Marta Kulik
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland; Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Agnieszka Markowska-Zagrajek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland; Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Monika Wojciechowska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Renata Grzela
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Tomasz Wituła
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
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21
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Dudek M, Trylska J. Molecular Dynamics Simulations of l-RNA Involving Homo- and Heterochiral Complexes. J Chem Theory Comput 2017; 13:1244-1253. [DOI: 10.1021/acs.jctc.6b01075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Marta Dudek
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
- Institute
of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego
5a, 02-106 Warsaw, Poland
- Department
of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Joanna Trylska
- Centre
of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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22
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Thoduka SG, Zaleski PA, Dąbrowska Z, Równicki M, Stróżecka J, Górska A, Olejniczak M, Trylska J. Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides. Biopolymers 2017; 107. [PMID: 27858985 DOI: 10.1002/bip.23004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/06/2016] [Accepted: 11/10/2016] [Indexed: 01/15/2023]
Abstract
The bacterial ribosome has many functional ribosomal RNA (rRNA) sites. We have computationally analyzed the rRNA regions involved in the interactions between the 30S and 50S subunits. Various properties of rRNA such as solvent accessibility, opening energy, hydrogen bonding pattern, van der Waals energy, thermodynamic stability were determined. Based on these properties we selected rRNA targets for hybridization with complementary 2'-O-methyl oligoribonucleotides (2'-OMe RNAs). Further, the inhibition efficiencies of the designed ribosome-interfering 2'-OMe RNAs were tested using a β-galactosidase assay in a translation system based on the E. coli extract. Several of the oligonucleotides displayed IC50 values below 1 μM, which were in a similar range as those determined for known ribosome inhibitors, tetracycline and pactamycin. The calculated opening and van der Waals stacking energies of the rRNA targets correlated best with the inhibitory efficiencies of 2'-OMe RNAs. Moreover, the binding affinities of several oligonucleotides to both 70S ribosomes and isolated 30S and 50S subunits were measured using a double-filter retention assay. Further, we applied heat-shock chemical transformation to introduce 2'-OMe RNAs to E. coli cells and verify inhibition of bacterial growth. We observed high correlation between IC50 in the cell-free extract and bacterial growth inhibition. Overall, the results suggest that the computational analysis of potential rRNA targets within the conformationally dynamic regions of inter-subunit bridges can help design efficient antisense oligomers to probe the ribosome function.
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Affiliation(s)
- Sapna G Thoduka
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
| | - Paul A Zaleski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, 61-614, Poland
| | - Zofia Dąbrowska
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
| | - Marcin Równicki
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, Warsaw, 02-097, Poland
| | - Joanna Stróżecka
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, 61-614, Poland
| | - Anna Górska
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
| | - Mikołaj Olejniczak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, Poznań, 61-614, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland
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23
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Górska A, Markowska-Zagrajek A, Równicki M, Trylska J. Scanning of 16S Ribosomal RNA for Peptide Nucleic Acid Targets. J Phys Chem B 2016; 120:8369-78. [PMID: 27105576 DOI: 10.1021/acs.jpcb.6b02081] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have designed a protocol and server to aid in the search for putative binding sites in 16S rRNA that could be targeted by peptide nucleic acid oligomers. Various features of 16S rRNA were considered to score its regions as potential targets for sequence-specific binding that could result in inhibition of ribosome function. Specifically, apart from the functional importance of a particular rRNA region, we calculated its accessibility, flexibility, energetics of strand invasion by an oligomer, as well as similarity to human rRNA. To determine 16S rRNA flexibility in the ribosome context, we performed all-atom molecular dynamics simulations of the 30S subunit in explicit solvent. We proposed a few 16S RNA target sites, and one of them was tested experimentally to verify inhibition of bacterial growth by a peptide nucleic acid oligomer.
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Affiliation(s)
- Anna Górska
- Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland
| | - Agnieszka Markowska-Zagrajek
- Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland.,Department of Biology, University of Warsaw , Miecznikowa 1, 02-096 Warsaw, Poland
| | - Marcin Równicki
- Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland.,College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences , Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland
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24
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Voltz K, Léonard J, Touceda PT, Conyard J, Chaker Z, Dejaegere A, Godet J, Mély Y, Haacke S, Stote RH. Quantitative sampling of conformational heterogeneity of a DNA hairpin using molecular dynamics simulations and ultrafast fluorescence spectroscopy. Nucleic Acids Res 2016; 44:3408-19. [PMID: 26896800 PMCID: PMC4838372 DOI: 10.1093/nar/gkw077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 01/29/2016] [Indexed: 01/22/2023] Open
Abstract
Molecular dynamics (MD) simulations and time resolved fluorescence (TRF) spectroscopy were combined to quantitatively describe the conformational landscape of the DNA primary binding sequence (PBS) of the HIV-1 genome, a short hairpin targeted by retroviral nucleocapsid proteins implicated in the viral reverse transcription. Three 2-aminopurine (2AP) labeled PBS constructs were studied. For each variant, the complete distribution of fluorescence lifetimes covering 5 orders of magnitude in timescale was measured and the populations of conformers experimentally observed to undergo static quenching were quantified. A binary quantification permitted the comparison of populations from experimental lifetime amplitudes to populations of aromatically stacked 2AP conformers obtained from simulation. Both populations agreed well, supporting the general assumption that quenching of 2AP fluorescence results from pi-stacking interactions with neighboring nucleobases and demonstrating the success of the proposed methodology for the combined analysis of TRF and MD data. Cluster analysis of the latter further identified predominant conformations that were consistent with the fluorescence decay times and amplitudes, providing a structure-based rationalization for the wide range of fluorescence lifetimes. Finally, the simulations provided evidence of local structural perturbations induced by 2AP. The approach presented is a general tool to investigate fine structural heterogeneity in nucleic acid and nucleoprotein assemblies.
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Affiliation(s)
- Karine Voltz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Jérémie Léonard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Patricia Tourón Touceda
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Jamie Conyard
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Ziyad Chaker
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Annick Dejaegere
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Julien Godet
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch Cedex, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch Cedex, France
| | - Stefan Haacke
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, CNRS UMR 7504, Université de Strasbourg, Strasbourg, France
| | - Roland H Stote
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de Santé et de Recherche Médicale (INSERM) U964, Centre National de Recherche Scientifique (CNRS) UMR 7104, Université de Strasbourg, 67404 Illkirch, France
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25
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Anwar MA, Yesudhas D, Shah M, Choi S. Structural and conformational insights into SOX2/OCT4-bound enhancer DNA: a computational perspective. RSC Adv 2016. [DOI: 10.1039/c6ra15176k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The roles of SOX2 and OCT4 are critical in stem cell maintenance either in the context of iPSCs generation or cancer stem cell growth; therefore, it is imperative to study their cooperative binding and SOX2/OCT4-induced DNA conformational switching.
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Affiliation(s)
- Muhammad Ayaz Anwar
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| | - Dhanusha Yesudhas
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| | - Masaud Shah
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
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