1
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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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2
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Bohdan DR, Voronina VV, Bujnicki JM, Baulin EF. A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures. Nucleic Acids Res 2023; 51:8367-8382. [PMID: 37471030 PMCID: PMC10484739 DOI: 10.1093/nar/gkad605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
Understanding the 3D structure of RNA is key to understanding RNA function. RNA 3D structure is modular and can be seen as a composition of building blocks of various sizes called tertiary motifs. Currently, long-range motifs formed between distant loops and helical regions are largely less studied than the local motifs determined by the RNA secondary structure. We surveyed long-range tertiary interactions and motifs in a non-redundant set of non-coding RNA 3D structures. A new dataset of annotated LOng-RAnge RNA 3D modules (LORA) was built using an approach that does not rely on the automatic annotations of non-canonical interactions. An original algorithm, ARTEM, was developed for annotation-, sequence- and topology-independent superposition of two arbitrary RNA 3D modules. The proposed methods allowed us to identify and describe the most common long-range RNA tertiary motifs. Along with the prevalent canonical A-minor interactions, a large number of previously undescribed staple interactions were observed. The most frequent long-range motifs were found to belong to three main motif families: planar staples, tilted staples, and helical packing motifs.
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Affiliation(s)
- Davyd R Bohdan
- Department of Innovation and High Technology, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valeria V Voronina
- Department of Information Systems, Ulyanovsk State Technical University, Ulyanovsk 432027, Russia
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Eugene F Baulin
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
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3
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Ghani NSA, Emrizal R, Moffit SM, Hamdani HY, Ramlan EI, Firdaus-Raih M. GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA. Nucleic Acids Res 2022; 50:W375-W383. [PMID: 35639505 PMCID: PMC9252811 DOI: 10.1093/nar/gkac402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Accepted: 05/08/2022] [Indexed: 12/03/2022] Open
Abstract
The GrAfSS (Graph theoretical Applications for Substructure Searching) webserver is a platform to search for three-dimensional substructures of: (i) amino acid side chains in protein structures; and (ii) base arrangements in RNA structures. The webserver interfaces the functions of five different graph theoretical algorithms – ASSAM, SPRITE, IMAAAGINE, NASSAM and COGNAC – into a single substructure searching suite. Users will be able to identify whether a three-dimensional (3D) arrangement of interest, such as a ligand binding site or 3D motif, observed in a protein or RNA structure can be found in other structures available in the Protein Data Bank (PDB). The webserver also allows users to determine whether a protein or RNA structure of interest contains substructural arrangements that are similar to known motifs or 3D arrangements. These capabilities allow for the functional annotation of new structures that were either experimentally determined or computationally generated (such as the coordinates generated by AlphaFold2) and can provide further insights into the diversity or conservation of functional mechanisms of structures in the PDB. The computed substructural superpositions are visualized using integrated NGL viewers. The GrAfSS server is available at http://mfrlab.org/grafss/.
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Affiliation(s)
- Nur Syatila Ab Ghani
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Reeki Emrizal
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Sabrina Mohamed Moffit
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Hazrina Yusof Hamdani
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas 13200, Pulau Pinang, Malaysia
| | | | - Mohd Firdaus-Raih
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.,Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
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4
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Developing Community Resources for Nucleic Acid Structures. Life (Basel) 2022; 12:life12040540. [PMID: 35455031 PMCID: PMC9031032 DOI: 10.3390/life12040540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 01/14/2023] Open
Abstract
In this review, we describe the creation of the Nucleic Acid Database (NDB) at Rutgers University and how it became a testbed for the current infrastructure of the RCSB Protein Data Bank. We describe some of the special features of the NDB and how it has been used to enable research. Plans for the next phase as the Nucleic Acid Knowledgebase (NAKB) are summarized.
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5
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Hong X, Zheng J, Xie J, Tong X, Liu X, Song Q, Liu S, Liu S. RR3DD: an RNA global structure-based RNA three-dimensional structural classification database. RNA Biol 2021; 18:738-746. [PMID: 34663179 DOI: 10.1080/15476286.2021.1989200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The three-dimensional (3D) structure of RNA usually plays an important role in the recognition with RNA-binding protein. Along with the discovering of RNAs, several RNA databases are developed to study the functions of RNA based on sequence, secondary structure, local 3D structural motif and global structure. Based on RNA function and structure, different RNAs are classified and stored in SCOR and DARTS, respectively. The classification of RNA structures is useful in RNA structure prediction and function annotation. However, the SCOR and DARTS are not updated any more. In this study, we present an RNA classification database RR3DD based on RNA fold with the global 3D structural similarity. The RR3DD includes 13,601 RNA chains from PDB and mmCIF format structures which are classified into 780 RNA folds. The RNA chains from PDB and mmCIF format structures are aligned and clustered into 675 and 220 RNA folds, respectively. By analysing the RNA structure in RR3DD, we find that there are 11 clusters with more than 50 members. These clusters include rRNAs, riboswitches, tRNAs and so on. By mapping RR3DD into Rfam, we found that some RNAs without annotation by Rfam can be annotated through structural alignment. For example, we analysed tRNAs and found that tRNA were successfully grouped in RR3DD for which Rfam did not classify them into one family. Finally, we provide a web interface of RR3DD offering functions of browsing RR3DD, annotating RNA 3D structure and finding templates for RNA homology modelling.
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Affiliation(s)
- Xu Hong
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Jinfang Zheng
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Xie
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoxue Tong
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Xudong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Song
- Key Laboratory of Fermentation Engineering (Ministry of Education, Hubei University of Technology, Wuhan, China
| | - Sen Liu
- Key Laboratory of Fermentation Engineering (Ministry of Education, Hubei University of Technology, Wuhan, China
| | - Shiyong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, China
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6
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Baulin EF. Features and Functions of the A-Minor Motif, the Most Common Motif in RNA Structure. BIOCHEMISTRY (MOSCOW) 2021; 86:952-961. [PMID: 34488572 DOI: 10.1134/s000629792108006x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A-minor motifs are RNA tertiary structure motifs that generally involve a canonical base pair and an adenine base forming hydrogen bonds with the minor groove of the base pair. Such motifs are among the most common tertiary interactions in known RNA structures, comparable in number with the non-canonical base pairs. They are often found in functionally important regions of non-coding RNAs and, in particular, play a central role in protein synthesis. Here, we review local variations of the A-minor geometry and discuss difficulties associated with their annotation, as well as various structural contexts and common A-minor co-motifs, and diverse functions of A-minors in various processes in a living cell.
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Affiliation(s)
- Eugene F Baulin
- Institute of Mathematical Problems of Biology RAS - the Branch of Keldysh Institute of Applied Mathematics of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
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7
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Emrizal R, Hamdani HY, Firdaus-Raih M. Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures. Int J Mol Sci 2021; 22:ijms22168553. [PMID: 34445259 PMCID: PMC8395288 DOI: 10.3390/ijms22168553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 12/12/2022] Open
Abstract
The increasing number and complexity of structures containing RNA chains in the Protein Data Bank (PDB) have led to the need for automated structure annotation methods to replace or complement expert visual curation. This is especially true when searching for tertiary base motifs and substructures. Such base arrangements and motifs have diverse roles that range from contributions to structural stability to more direct involvement in the molecule's functions, such as the sites for ligand binding and catalytic activity. We review the utility of computational approaches in annotating RNA tertiary base motifs in a dataset of PDB structures, particularly the use of graph theoretical algorithms that can search for such base motifs and annotate them or find and annotate clusters of hydrogen-bond-connected bases. We also demonstrate how such graph theoretical algorithms can be integrated into a workflow that allows for functional analysis and comparisons of base arrangements and sub-structures, such as those involved in ligand binding. The capacity to carry out such automatic curations has led to the discovery of novel motifs and can give new context to known motifs as well as enable the rapid compilation of RNA 3D motifs into a database.
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Affiliation(s)
- Reeki Emrizal
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi 43600, Selangor, Malaysia;
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi 43600, Selangor, Malaysia
| | - Hazrina Yusof Hamdani
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas 13200, Pulau Pinang, Malaysia
- Correspondence: (H.Y.H.); (M.F.-R.)
| | - Mohd Firdaus-Raih
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi 43600, Selangor, Malaysia;
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi 43600, Selangor, Malaysia
- Correspondence: (H.Y.H.); (M.F.-R.)
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8
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Regulation of Glycine Cleavage and Detoxification by a Highly Conserved Glycine Riboswitch in Burkholderia spp. Curr Microbiol 2021; 78:2943-2955. [PMID: 34076709 DOI: 10.1007/s00284-021-02550-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 05/21/2021] [Indexed: 10/21/2022]
Abstract
The glycine riboswitch is a known regulatory element that is unique in having two aptamers that are joined by a linker region. In this study, we investigated a glycine riboswitch located in the 5' untranslated region of a glycine cleavage system homolog (gcvTHP) in Burkholderia spp. Structure prediction using the sequence generated a model with a glycine binding pocket composed of base-triple interactions (G62-A64-A86 and G65-U84-C85) that are supported by A/G minor interactions (A17-C60-G88 and G16-C61-G87, respectively) and two ribose-zipper motifs (C11-G12 interacting with A248-A247 and C153-U154 interacting with A79-A78) which had not been previously reported. The capacity of the riboswitch to bind to glycine was experimentally validated by native gel assays and the crucial role of interactions that make up the glycine binding pocket were proven by mutations of A17U and G16C which resulted in conformational differences that may lead to dysfunction. Using glycine supplemented minimal media, we were able to prove that the expression of the gcvTHP genes found downstream of the riboswitch responded to the glycine concentrations introduced thus confirming the role of this highly conserved Burkholderia riboswitch and its associated genes as a putative glycine detoxification system in Burkholderia spp.
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9
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Soulé A, Reinharz V, Sarrazin-Gendron R, Denise A, Waldispühl J. Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs. PLoS Comput Biol 2021; 17:e1008990. [PMID: 34048427 PMCID: PMC8191989 DOI: 10.1371/journal.pcbi.1008990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/10/2021] [Accepted: 04/22/2021] [Indexed: 11/25/2022] Open
Abstract
RNA tertiary structure is crucial to its many non-coding molecular functions. RNA architecture is shaped by its secondary structure composed of stems, stacked canonical base pairs, enclosing loops. While stems are precisely captured by free-energy models, loops composed of non-canonical base pairs are not. Nor are distant interactions linking together those secondary structure elements (SSEs). Databases of conserved 3D geometries (a.k.a. modules) not captured by energetic models are leveraged for structure prediction and design, but the computational complexity has limited their study to local elements, loops. Representing the RNA structure as a graph has recently allowed to expend this work to pairs of SSEs, uncovering a hierarchical organization of these 3D modules, at great computational cost. Systematically capturing recurrent patterns on a large scale is a main challenge in the study of RNA structures. In this paper, we present an efficient algorithm to compute maximal isomorphisms in edge colored graphs. We extend this algorithm to a framework well suited to identify RNA modules, and fast enough to considerably generalize previous approaches. To exhibit the versatility of our framework, we first reproduce results identifying all common modules spanning more than 2 SSEs, in a few hours instead of weeks. The efficiency of our new algorithm is demonstrated by computing the maximal modules between any pair of entire RNA in the non-redundant corpus of known RNA 3D structures. We observe that the biggest modules our method uncovers compose large shared sub-structure spanning hundreds of nucleotides and base pairs between the ribosomes of Thermus thermophilus, Escherichia Coli, and Pseudomonas aeruginosa. Ribonucleic Acids (RNAs) are performing a broad range of essential molecular functions in cells, many of which rely on intricate folding properties of the molecule. Watson-Crick and Wobble base pairs form early, stack onto each other to create stems connected by loops, which are themselves stabilized by more sophisticated base interaction patterns. These networks are essential to shape RNA 3D structures but unfortunately still poorly understood. Here, we undertake the task to build a catalog of base interaction networks occurring in multiple structures. However, a pairwise comparison of all RNA structures is computationally heavy. Therefore, we devise an algorithm leveraging intrinsic properties of RNA base interaction networks that enables us to quickly mine full databases of 3D structures. Compared to previous methods, our techniques bring the total running time of the analysis from months to hours while performing more general searches. The data collected though this work will benefit molecular evolution studies and serve in structure prediction tools.
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Affiliation(s)
- Antoine Soulé
- School of Computer Science, McGill University, Montréal, Canada
- LiX, École Polytechnique, Paris, France
| | - Vladimir Reinharz
- Department of Computer Science, Université du Québec à Montréal, Montréal, Canada
| | | | - Alain Denise
- Laboratoire de recherche en informatique, Université Paris-Saclay - CNRS, Orsay, France
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay - CEA - CNRS, Gif-sur-Yvette, France
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, Montréal, Canada
- * E-mail:
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10
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Identification of Structural Motifs Using Networks of Hydrogen-Bonded Base Interactions in RNA Crystallographic Structures. CRYSTALS 2019. [DOI: 10.3390/cryst9110550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA structural motifs can be identified using methods that analyze base–base interactions and the conformation of a structure’s backbone; however, these approaches do not necessarily take into consideration the hydrogen bonds that connect the bases or the networks of inter-connected hydrogen-bonded bases that are found in RNA structures. Large clusters of RNA bases that are tightly inter-connected by a network of hydrogen bonds are expected to be stable and relatively rigid substructures. Such base arrangements could therefore be present as structural motifs in RNA structures, especially when there is a requirement for a highly stable support platform or substructure to ensure the correct folding and spatial maintenance of functional sites that partake in catalysis or binding interactions. In order to test this hypothesis, we conducted a search in available RNA crystallographic structures in the Protein Data Bank database using queries that searched for profiles of bases inter-connected by hydrogen bonds. This method of searching does not require to have prior knowledge of the arrangement being searched. Our search results identified two clusters of six bases that are inter-connected by a network of hydrogen bonds. These arrangements of base sextuples have never been previously reported, thus making this the first report that proposes them as novel RNA tertiary motifs.
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11
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Reinharz V, Soulé A, Westhof E, Waldispühl J, Denise A. Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families. Nucleic Acids Res 2019; 46:3841-3851. [PMID: 29608773 PMCID: PMC5934684 DOI: 10.1093/nar/gky197] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/22/2018] [Indexed: 11/14/2022] Open
Abstract
The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to assemble into sophisticated interaction networks, which are used to create complex 3D substructures. These interaction networks are essential to shape the 3D architecture of the molecule, and also to provide the key elements to carry molecular functions such as protein or ligand binding. They are made of organised sets of long-range tertiary interactions which connect distinct secondary structure elements in 3D structures. Here, we present a de novo data-driven approach to extract automatically from large data sets of full RNA 3D structures the recurrent interaction networks (RINs). Our methodology enables us for the first time to detect the interaction networks connecting distinct components of the RNA structure, highlighting their diversity and conservation through non-related functional RNAs. We use a graphical model to perform pairwise comparisons of all RNA structures available and to extract RINs and modules. Our analysis yields a complete catalog of RNA 3D structures available in the Protein Data Bank and reveals the intricate hierarchical organization of the RNA interaction networks and modules. We assembled our results in an online database (http://carnaval.lri.fr) which will be regularly updated. Within the site, a tool allows users with a novel RNA structure to detect automatically whether the novel structure contains previously observed RINs.
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Affiliation(s)
- Vladimir Reinharz
- Department of Computer Science, Ben-Gurion University of the Negev, P.O.B. 653 Beer-Sheva, 84105, Israel.,School of Computer Science, McGill University, 3480 University, Montreal, Quebec H3A 0E9, Canada
| | - Antoine Soulé
- School of Computer Science, McGill University, 3480 University, Montreal, Quebec H3A 0E9, Canada.,LIX, École Polytechnique, CNRS, Inria, Palaiseau 91120, France
| | - Eric Westhof
- ARN, Université de Strasbourg, IBMC-CNRS, 15 rue René Descartes, Strasbourg Cedex 67084, France
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, 3480 University, Montreal, Quebec H3A 0E9, Canada
| | - Alain Denise
- LRI, Université Paris-Sud, CNRS, Université Paris-Saclay, Bâtiment 650, Orsay cedex 91405, France.,I2BC, Université Paris-Sud, CNRS, CEA, Université Paris-Saclay, Bâtiment 400, Orsay cedex 91405, France
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12
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Abriata LA. Structural database resources for biological macromolecules. Brief Bioinform 2017; 18:659-669. [PMID: 27273290 DOI: 10.1093/bib/bbw049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 12/30/2022] Open
Abstract
This Briefing reviews the widely used, currently active, up-to-date databases derived from the worldwide Protein Data Bank (PDB) to facilitate browsing, finding and exploring its entries. These databases contain visualization and analysis tools tailored to specific kinds of molecules and interactions, often including also complex metrics precomputed by experts or external programs, and connections to sequence and functional annotation databases. Importantly, updates of most of these databases involves steps of curation and error checks based on specific expertise about the subject molecules or interactions, and removal of sequence redundancy, both leading to better data sets for mining studies compared with the full list of raw PDB entries. The article presents the databases in groups such as those aimed to facilitate browsing through PDB entries, their molecules and their general information, those built to link protein structure with sequence and dynamics, those specific for transmembrane proteins, nucleic acids, interactions of biomacromolecules with each other and with small molecules or metal ions, and those concerning specific structural features or specific protein families. A few webservers directly connected to active databases, and a few databases that have been discontinued but would be important to have back, are also briefly commented on. Along the Briefing, sample cases where these databases have been used to aid structural studies or advance our knowledge about biological macromolecules are referenced. A few specific examples are also given where using these databases is easier and more informative than using raw PDB data.
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