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Bohdan DR, Bujnicki JM, Baulin EF. ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment. Nucleic Acids Res 2024:gkae758. [PMID: 39258540 DOI: 10.1093/nar/gkae758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 09/12/2024] Open
Abstract
Non-coding RNAs play a major role in diverse processes in living cells with their sequence and spatial structure serving as the principal determinants of their function. Superposition of RNA 3D structures is the most accurate method for comparative analysis of RNA molecules and for inferring structure-based sequence alignments. Topology-independent superposition is particularly relevant, as evidenced by structurally similar RNAs with sequence permutations such as tRNA and Y RNA. To date, state-of-the-art methods for RNA 3D structure superposition rely on intricate heuristics, and the potential for topology-independent superposition has not been exhausted. Recently, we introduced the ARTEM method for unrestrained pairwise superposition of RNA 3D modules and now we developed it further to solve the global RNA 3D structure alignment problem. Our new tool ARTEMIS significantly outperforms state-of-the-art tools in both sequentially-ordered and topology-independent RNA 3D structure superposition. Using ARTEMIS we discovered a helical packing motif to be preserved within different backbone topology contexts across various non-coding RNAs, including multiple ribozymes and riboswitches. We anticipate that ARTEMIS will be essential for elucidating the landscape of RNA 3D folds and motifs featuring sequence permutations that thus far remained unexplored due to limitations in previous computational approaches.
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Affiliation(s)
- Davyd R Bohdan
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Eugene F Baulin
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
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2
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Zhang C, Shine M, Pyle AM, Zhang Y. US-align: universal structure alignments of proteins, nucleic acids, and macromolecular complexes. Nat Methods 2022; 19:1109-1115. [PMID: 36038728 DOI: 10.1038/s41592-022-01585-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022]
Abstract
Structure comparison and alignment are of fundamental importance in structural biology studies. We developed the first universal platform, US-align, to uniformly align monomer and complex structures of different macromolecules-proteins, RNAs and DNAs. The pipeline is built on a uniform TM-score objective function coupled with a heuristic alignment searching algorithm. Large-scale benchmarks demonstrated consistent advantages of US-align over state-of-the-art methods in pairwise and multiple structure alignments of different molecules. Detailed analyses showed that the main advantage of US-align lies in the extensive optimization of the unified objective function powered by efficient heuristic search iterations, which substantially improve the accuracy and speed of the structural alignment process. Meanwhile, the universal protocol fusing different molecular and structural types helps facilitate the heterogeneous oligomer structure comparison and template-based protein-protein and protein-RNA/DNA docking.
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Affiliation(s)
- Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Morgan Shine
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA
| | - Anna Marie Pyle
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA.,Department of Chemistry, Yale University, New Haven, CT, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. .,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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3
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Gong S, Zhang C, Zhang Y. RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. Bioinformatics 2020; 35:4459-4461. [PMID: 31161212 DOI: 10.1093/bioinformatics/btz282] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Comparison of RNA 3D structures can be used to infer functional relationship of RNA molecules. Most of the current RNA structure alignment programs are built on size-dependent scales, which complicate the interpretation of structure and functional relations. Meanwhile, the low speed prevents the programs from being applied to large-scale RNA structural database search. RESULTS We developed an open-source algorithm, RNA-align, for RNA 3D structure alignment which has the structure similarity scaled by a size-independent and statistically interpretable scoring metric. Large-scale benchmark tests show that RNA-align significantly outperforms other state-of-the-art programs in both alignment accuracy and running speed. The major advantage of RNA-align lies at the quick convergence of the heuristic alignment iterations and the coarse-grained secondary structure assignment, both of which are crucial to the speed and accuracy of RNA structure alignments. AVAILABILITY AND IMPLEMENTATION https://zhanglab.ccmb.med.umich.edu/RNA-align/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sha Gong
- School of Physics and Electronic Information, Huanggang Normal University, Huanggang, China.,Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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4
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Nguyen MN, Sim AYL, Wan Y, Madhusudhan MS, Verma C. Topology independent comparison of RNA 3D structures using the CLICK algorithm. Nucleic Acids Res 2016; 45:e5. [PMID: 27634929 PMCID: PMC5741206 DOI: 10.1093/nar/gkw819] [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: 01/21/2015] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 01/15/2023] Open
Abstract
RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions. We previously developed the algorithm CLICK to superimpose a pair of protein 3D structures by clique matching and 3D least squares fitting. In this study, we extend and optimize the CLICK algorithm to superimpose pairs of RNA 3D structures and RNA-protein complexes, independent of the associated topologies. Benchmarking Rclick on four different datasets showed that it is either comparable to or better than other structural alignment methods in terms of the extent of structural overlaps. Rclick also recognizes conformational changes between RNA structures and produces complementary alignments to maximize the extent of detectable similarity. Applying Rclick to study Ribonuclease III protein correctly aligned the RNA binding sites of RNAse III with its substrate. Rclick can be further extended to identify ligand-binding pockets in RNA. A web server is developed at http://mspc.bii.a-star.edu.sg/minhn/rclick.html.
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Affiliation(s)
- Minh N Nguyen
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Adelene Y L Sim
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671
| | - Yue Wan
- Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672
| | - M S Madhusudhan
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671.,Indian Institute of Science Education and Research, Pune, India
| | - Chandra Verma
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671.,Department of Biological Sciences, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore
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5
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Gleghorn ML, Zhao J, Turner DH, Maquat LE. Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation. Nucleic Acids Res 2016; 44:8417-24. [PMID: 27288442 PMCID: PMC5041459 DOI: 10.1093/nar/gkw526] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/01/2016] [Indexed: 12/22/2022] Open
Abstract
We have solved at 1.07 Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA7, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA7 forms well-ordered crystals, whereas rA6 forms fragile crystalline-like structures, and rA5, rA8 and rA11 fail to crystallize. Our findings support studies from ∼50 years ago: one showed using spectroscopic methods that duplex formation at pH 4.5 largely starts with rA7 and begins to plateau with rA8; another proposed a so-called ‘staggered zipper’ model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP−rAMP helix base pair. Our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.
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Affiliation(s)
- Michael L Gleghorn
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Jianbo Zhao
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Douglas H Turner
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
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6
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Zahran M, Sevim Bayrak C, Elmetwaly S, Schlick T. RAG-3D: a search tool for RNA 3D substructures. Nucleic Acids Res 2015; 43:9474-88. [PMID: 26304547 PMCID: PMC4627073 DOI: 10.1093/nar/gkv823] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/03/2015] [Indexed: 01/23/2023] Open
Abstract
To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.
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Affiliation(s)
- Mai Zahran
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, NY 11201, USA
| | | | - Shereef Elmetwaly
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, New York, NY 10003, USA Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
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7
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Čech P, Hoksza D, Svozil D. MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinformatics 2015; 16:253. [PMID: 26264783 PMCID: PMC4531852 DOI: 10.1186/s12859-015-0696-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/05/2015] [Indexed: 12/03/2022] Open
Abstract
Background Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. Results In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. Conclusion To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.
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Affiliation(s)
- Petr Čech
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic
| | - David Hoksza
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic. .,Department of Software Engineering, Faculty of Mathematics and Physics, Charles University in Prague, Malostranské nám. 25, CZ-118 00, Prague, Czech Republic.
| | - Daniel Svozil
- Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, CZ-166 28, Prague, Czech Republic.
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8
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Purzycka KJ, Popenda M, Szachniuk M, Antczak M, Lukasiak P, Blazewicz J, Adamiak RW. Automated 3D RNA structure prediction using the RNAComposer method for riboswitches. Methods Enzymol 2015; 553:3-34. [PMID: 25726459 DOI: 10.1016/bs.mie.2014.10.050] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Understanding the numerous functions of RNAs depends critically on the knowledge of their three-dimensional (3D) structure. In contrast to the protein field, a much smaller number of RNA 3D structures have been assessed using X-ray crystallography, NMR spectroscopy, and cryomicroscopy. This has led to a great demand to obtain the RNA 3D structures using prediction methods. The 3D structure prediction, especially of large RNAs, still remains a significant challenge and there is still a great demand for high-resolution structure prediction methods. In this chapter, we describe RNAComposer, a method and server for the automated prediction of RNA 3D structures based on the knowledge of secondary structure. Its applications are supported by other automated servers: RNA FRABASE and RNApdbee, developed to search and analyze secondary and 3D structures. Another method, RNAlyzer, offers new way to analyze and visualize quality of RNA 3D models. Scope and limitations of RNAComposer in application for an automated prediction of riboswitches' 3D structure will be presented and discussed. Analysis of the cyclic di-GMP-II riboswitch from Clostridium acetobutylicum (PDB ID 3Q3Z) as an example allows for 3D structure prediction of related riboswitches from Clostridium difficile 4, Bacillus halodurans 1, and Thermus aquaticus Y5.1 of yet unknown structures.
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Affiliation(s)
- K J Purzycka
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - M Popenda
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland
| | - M Szachniuk
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - M Antczak
- European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - P Lukasiak
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - J Blazewicz
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - R W Adamiak
- Department of Structural Chemistry and Biology of Nucleic Acids, Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznan, Poland; European Center for Bioinformatics and Genomics, Institute of Computing Science, Poznan University of Technology, Poznan, Poland.
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9
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Abstract
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also, abound in viral DNA packaged inside bacteriophages. RNA molecules, however, have not yet been systematically screened for the occurrence of physical knots. We have accordingly undertaken the systematic profiling of the several thousand RNA structures present in the Protein Data Bank (PDB). The search identified no more than three deeply knotted RNA molecules. These entries are rRNAs of about 3,000 nt solved by cryo-EM. Their genuine knotted state is, however, doubtful based on the detailed structural comparison with homologs of higher resolution, which are all unknotted. Compared with the case of proteins and viral DNA, the observed incidence of knots in available RNA structures is, therefore, practically negligible. This fact suggests that either evolutionary selection or thermodynamic and kinetic folding mechanisms act toward minimizing the entanglement of RNA to an extent that is unparalleled by other types of biomolecules. A possible general strategy for designing synthetic RNA sequences capable of self-tying in a twist-knot fold is finally proposed.
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10
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11
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He G, Steppi A, Laborde J, Srivastava A, Zhao P, Zhang J. RASS: a web server for RNA alignment in the joint sequence-structure space. Nucleic Acids Res 2014; 42:W377-81. [PMID: 24831547 PMCID: PMC4086137 DOI: 10.1093/nar/gku429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Comparison of ribonucleic acid (RNA) molecules is important for revealing their
evolutionary relationships, predicting their functions and predicting their
structures. Many methods have been developed for comparing RNAs using either
sequence or three-dimensional (3D) structure (backbone geometry) information.
Sequences and 3D structures contain non-overlapping sets of information that
both determine RNA functions. When comparing RNA 3D structures, both types of
information need to be taken into account. However, few methods compare RNA
structures using both sequence and 3D structure information. Recently, we have
developed a new method based on elastic shape analysis (ESA) that compares RNA
molecules by combining both sequence and 3D structure information. ESA treats
RNA structures as 3D curves with sequence information encoded on additional
coordinates so that the alignment can be performed in the joint
sequence-structure space. The similarity between two RNA molecules is quantified
by a formal distance, geodesic distance. In this study, we implement a web
server for the method, called RASS, to make it publicly available to research
community. The web server is located at http://cloud.stat.fsu.edu/RASS/.
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Affiliation(s)
- Gewen He
- Department of Computer Science, Florida State University, Tallahassee, FL 32306, USA
| | - Albert Steppi
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Jose Laborde
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Anuj Srivastava
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Peixiang Zhao
- Department of Computer Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
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12
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Rahrig RR, Petrov AI, Leontis NB, Zirbel CL. R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures. Nucleic Acids Res 2013; 41:W15-21. [PMID: 23716643 PMCID: PMC3692076 DOI: 10.1093/nar/gkt417] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The R3D Align web server provides online access to ‘RNA 3D Align’ (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.
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Affiliation(s)
- Ryan R Rahrig
- Department of Mathematics and Statistics, Ohio Northern University, Ada, OH 45810, USA.
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13
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Abstract
The 3DNA software package is a popular and versatile bioinformatics tool with capabilities to analyze, construct, and visualize three-dimensional nucleic acid structures. This article presents detailed protocols for a subset of new and popular features available in 3DNA, applicable to both individual structures and ensembles of related structures. Protocol 1 lists the set of instructions needed to download and install the software. This is followed, in Protocol 2, by the analysis of a nucleic acid structure, including the assignment of base pairs and the determination of rigid-body parameters that describe the structure and, in Protocol 3, by a description of the reconstruction of an atomic model of a structure from its rigid-body parameters. The most recent version of 3DNA, version 2.1, has new features for the analysis and manipulation of ensembles of structures, such as those deduced from nuclear magnetic resonance (NMR) measurements and molecular dynamic (MD) simulations; these features are presented in Protocols 4 and 5. In addition to the 3DNA stand-alone software package, the w3DNA web server, located at http://w3dna.rutgers.edu, provides a user-friendly interface to selected features of the software. Protocol 6 demonstrates a novel feature of the site for building models of long DNA molecules decorated with bound proteins at user-specified locations.
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Affiliation(s)
- Andrew V Colasanti
- Department of Chemistry & Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers - The State University of New Jersey.
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14
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Abstract
MOTIVATION To recognize remote relationships between RNA molecules, one must be able to align structures without regard to sequence similarity. We have implemented a method, which is swift [O(n(2))], sensitive and tolerant of large gaps and insertions. Molecules are broken into overlapping fragments, which are characterized by their memberships in a probabilistic classification based on local geometry and H-bonding descriptors. This leads to a probabilistic similarity measure that is used in a conventional dynamic programming method. RESULTS Examples are given of database searching, the detection of structural similarities, which would not be found using sequence based methods, and comparisons with a previously published approach. AVAILABILITY AND IMPLEMENTATION Source code (C and perl) and binaries for linux are freely available at www.zbh.uni-hamburg.de/fries.
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Affiliation(s)
- Tim Wiegels
- Centre for Bioinformatics, University of Hamburg, Bundesstr. 43, D-20146 Hamburg, Germany.
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15
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Hoksza D, Svozil D. Efficient RNA pairwise structure comparison by SETTER method. Bioinformatics 2012; 28:1858-64. [DOI: 10.1093/bioinformatics/bts301] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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16
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Vanegas PL, Hudson GA, Davis AR, Kelly SC, Kirkpatrick CC, Znosko BM. RNA CoSSMos: Characterization of Secondary Structure Motifs--a searchable database of secondary structure motifs in RNA three-dimensional structures. Nucleic Acids Res 2011; 40:D439-44. [PMID: 22127861 PMCID: PMC3245015 DOI: 10.1093/nar/gkr943] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
RNA secondary structure is important for designing therapeutics, understanding protein–RNA binding and predicting tertiary structure of RNA. Several databases and downloadable programs exist that specialize in the three-dimensional (3D) structure of RNA, but none focus specifically on secondary structural motifs such as internal, bulge and hairpin loops. The RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database is a freely accessible and searchable online database and website of 3D characteristics of secondary structure motifs. To create the RNA CoSSMos database, 2156 Protein Data Bank (PDB) files were searched for internal, bulge and hairpin loops, and each loop's structural information, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions, was included in the database. False positives were defined, identified and reclassified or omitted from the database to ensure the most accurate results possible. Users can search via general PDB information, experimental parameters, sequence and specific motif and by specific structural parameters in the subquery page after the initial search. Returned results for each search can be viewed individually or a complete set can be downloaded into a spreadsheet to allow for easy comparison. The RNA CoSSMos database is automatically updated weekly and is available at http://cossmos.slu.edu.
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Affiliation(s)
- Pamela L Vanegas
- Department of Chemistry, Saint Louis University, Saint Louis, MO 63103, USA
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17
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Nguyen MN, Tan KP, Madhusudhan MS. CLICK--topology-independent comparison of biomolecular 3D structures. Nucleic Acids Res 2011; 39:W24-8. [PMID: 21602266 PMCID: PMC3125785 DOI: 10.1093/nar/gkr393] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Revised: 04/19/2011] [Accepted: 05/03/2011] [Indexed: 01/28/2023] Open
Abstract
Our server, CLICK: http://mspc.bii.a-star.edu.sg/click, is capable of superimposing the 3D structures of any pair of biomolecules (proteins, DNA, RNA, etc.). The server makes use of the Cartesian coordinates of the molecules with the option of using other structural features such as secondary structure, solvent accessible surface area and residue depth to guide the alignment. CLICK first looks for cliques of points (3-7 residues) that are structurally similar in the pair of structures to be aligned. Using these local similarities, a one-to-one equivalence is charted between the residues of the two structures. A least square fit then superimposes the two structures. Our method is especially powerful in establishing protein relationships by detecting similarities in structural subdomains, domains and topological variants. CLICK has been extensively benchmarked and compared with other popular methods for protein and RNA structural alignments. In most cases, CLICK alignments were statistically significantly better in terms of structure overlap. The method also recognizes conformational changes that may have occurred in structural domains or subdomains in one structure with respect to the other. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server.
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Affiliation(s)
- M. N. Nguyen
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Department of Biological Sciences, National University of Singapore and School of Biological Sciences, Nanyang Technological University, Singapore
| | - K. P. Tan
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Department of Biological Sciences, National University of Singapore and School of Biological Sciences, Nanyang Technological University, Singapore
| | - M. S. Madhusudhan
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Department of Biological Sciences, National University of Singapore and School of Biological Sciences, Nanyang Technological University, Singapore
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18
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Nguyen MN, Madhusudhan MS. Biological insights from topology independent comparison of protein 3D structures. Nucleic Acids Res 2011; 39:e94. [PMID: 21596786 PMCID: PMC3152366 DOI: 10.1093/nar/gkr348] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Comparing and classifying the three-dimensional (3D) structures of proteins is of crucial importance to molecular biology, from helping to determine the function of a protein to determining its evolutionary relationships. Traditionally, 3D structures are classified into groups of families that closely resemble the grouping according to their primary sequence. However, significant structural similarities exist at multiple levels between proteins that belong to these different structural families. In this study, we propose a new algorithm, CLICK, to capture such similarities. The method optimally superimposes a pair of protein structures independent of topology. Amino acid residues are represented by the Cartesian coordinates of a representative point (usually the Cα atom), side chain solvent accessibility, and secondary structure. Structural comparison is effected by matching cliques of points. CLICK was extensively benchmarked for alignment accuracy on four different sets: (i) 9537 pair-wise alignments between two structures with the same topology; (ii) 64 alignments from set (i) that were considered to constitute difficult alignment cases; (iii) 199 pair-wise alignments between proteins with similar structure but different topology; and (iv) 1275 pair-wise alignments of RNA structures. The accuracy of CLICK alignments was measured by the average structure overlap score and compared with other alignment methods, including HOMSTRAD, MUSTANG, Geometric Hashing, SALIGN, DALI, GANGSTA+, FATCAT, ARTS and SARA. On average, CLICK produces pair-wise alignments that are either comparable or statistically significantly more accurate than all of these other methods. We have used CLICK to uncover relationships between (previously) unrelated proteins. These new biological insights include: (i) detecting hinge regions in proteins where domain or sub-domains show flexibility; (ii) discovering similar small molecule binding sites from proteins of different folds and (iii) discovering topological variants of known structural/sequence motifs. Our method can generally be applied to compare any pair of molecular structures represented in Cartesian coordinates as exemplified by the RNA structure superimposition benchmark.
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Affiliation(s)
- Minh N Nguyen
- Bioinformatics Institute, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
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19
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Petrov AI, Zirbel CL, Leontis NB. WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Res 2011; 39:W50-5. [PMID: 21515634 PMCID: PMC3125732 DOI: 10.1093/nar/gkr249] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
WebFR3D is the on-line version of ‘Find RNA 3D’ (FR3D), a program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate and compare RNA 3D structural motifs. WebFR3D provides on-line access to the central features of FR3D, including geometric and symbolic search modes, without need for installing programs or downloading and maintaining 3D structure data locally. In geometric search mode, WebFR3D finds all motifs similar to a user-specified query structure. In symbolic search mode, WebFR3D finds all sets of nucleotides making user-specified interactions. In both modes, users can specify sequence, sequence–continuity, base pairing, base-stacking and other constraints on nucleotides and their interactions. WebFR3D can be used to locate hairpin, internal or junction loops, list all base pairs or other interactions, or find instances of recurrent RNA 3D motifs (such as sarcin–ricin and kink-turn internal loops or T- and GNRA hairpin loops) in any PDB file or across a whole set of 3D structure files. The output page provides facilities for comparing the instances returned by the search by superposition of the 3D structures and the alignment of their sequences annotated with pairwise interactions. WebFR3D is available at http://rna.bgsu.edu/webfr3d.
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Affiliation(s)
- Anton I Petrov
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, USA
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20
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Capriotti E, Norambuena T, Marti-Renom MA, Melo F. All-atom knowledge-based potential for RNA structure prediction and assessment. ACTA ACUST UNITED AC 2011; 27:1086-93. [PMID: 21349865 DOI: 10.1093/bioinformatics/btr093] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
MOTIVATION Over the recent years, the vision that RNA simply serves as information transfer molecule has dramatically changed. The study of the sequence/structure/function relationships in RNA is becoming more important. As a direct consequence, the total number of experimentally solved RNA structures has dramatically increased and new computer tools for predicting RNA structure from sequence are rapidly emerging. Therefore, new and accurate methods for assessing the accuracy of RNA structure models are clearly needed. RESULTS Here, we introduce an all-atom knowledge-based potential for the assessment of RNA three-dimensional (3D) structures. We have benchmarked our new potential, called Ribonucleic Acids Statistical Potential (RASP), with two different decoy datasets composed of near-native RNA structures. In one of the benchmark sets, RASP was able to rank the closest model to the X-ray structure as the best and within the top 10 models for ∼93 and ∼95% of decoys, respectively. The average correlation coefficient between model accuracy, calculated as the root mean square deviation and global distance test-total score (GDT-TS) measures of C3' atoms, and the RASP score was 0.85 and 0.89, respectively. Based on a recently released benchmark dataset that contains hundreds of 3D models for 32 RNA motifs with non-canonical base pairs, RASP scoring function compared favorably to ROSETTA FARFAR force field in the selection of accurate models. Finally, using the self-splicing group I intron and the stem-loop IIIc from hepatitis C virus internal ribosome entry site as test cases, we show that RASP is able to discriminate between known structure-destabilizing mutations and compensatory mutations. AVAILABILITY RASP can be readily applied to assess all-atom or coarse-grained RNA structures and thus should be of interest to both developers and end-users of RNA structure prediction methods. The computer software and knowledge-based potentials are freely available at http://melolab.org/supmat.html. CONTACT fmelo@bio.puc.cl; mmarti@cipf.es SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emidio Capriotti
- Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Principe Felipe, 46012 Valencia, Spain
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21
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Wang CW, Chen KT, Lu CL. iPARTS: an improved tool of pairwise alignment of RNA tertiary structures. Nucleic Acids Res 2010; 38:W340-7. [PMID: 20507908 PMCID: PMC2896121 DOI: 10.1093/nar/gkq483] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nucleotides on a 2D axis using their two pseudo-torsion angles η and θ. Next, we apply the affinity propagation clustering algorithm to this η-θ plot to obtain an SA of 23-nt conformations. We finally use this SA to transform RNA 3D structures into 1D sequences of SA letters and continue to utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. iPARTS takes as input two RNA 3D structures in the PDB format and outputs their global alignment (for determining overall structural similarity), semiglobal alignments (for detecting structural motifs or substructures), local alignments (for finding locally similar substructures) and normalized local structural alignments (for identifying more similar local substructures without non-similar internal fragments), with graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online at http://bioalgorithm.life.nctu.edu.tw/iPARTS/.
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Affiliation(s)
- Chih-Wei Wang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan, R.O.C
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22
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Popenda M, Szachniuk M, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics 2010; 11:231. [PMID: 20459631 PMCID: PMC2873543 DOI: 10.1186/1471-2105-11-231] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 05/06/2010] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. DESCRIPTION RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. CONCLUSIONS RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.
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Affiliation(s)
- Mariusz Popenda
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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23
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Laing C, Jung S, Iqbal A, Schlick T. Tertiary motifs revealed in analyses of higher-order RNA junctions. J Mol Biol 2009; 393:67-82. [PMID: 19660472 DOI: 10.1016/j.jmb.2009.07.089] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/29/2009] [Accepted: 07/29/2009] [Indexed: 12/22/2022]
Abstract
RNA junctions are secondary-structure elements formed when three or more helices come together. They are present in diverse RNA molecules with various fundamental functions in the cell. To better understand the intricate architecture of three-dimensional (3D) RNAs, we analyze currently solved 3D RNA junctions in terms of base-pair interactions and 3D configurations. First, we study base-pair interaction diagrams for solved RNA junctions with 5 to 10 helices and discuss common features. Second, we compare these higher-order junctions to those containing 3 or 4 helices and identify global motif patterns such as coaxial stacking and parallel and perpendicular helical configurations. These analyses show that higher-order junctions organize their helical components in parallel and helical configurations similar to lower-order junctions. Their sub-junctions also resemble local helical configurations found in three- and four-way junctions and are stabilized by similar long-range interaction preferences such as A-minor interactions. Furthermore, loop regions within junctions are high in adenine but low in cytosine, and in agreement with previous studies, we suggest that coaxial stacking between helices likely forms when the common single-stranded loop is small in size; however, other factors such as stacking interactions involving noncanonical base pairs and proteins can greatly determine or disrupt coaxial stacking. Finally, we introduce the ribo-base interactions: when combined with the along-groove packing motif, these ribo-base interactions form novel motifs involved in perpendicular helix-helix interactions. Overall, these analyses suggest recurrent tertiary motifs that stabilize junction architecture, pack helices, and help form helical configurations that occur as sub-elements of larger junction networks. The frequent occurrence of similar helical motifs suggest nature's finite and perhaps limited repertoire of RNA helical conformation preferences. More generally, studies of RNA junctions and tertiary building blocks can ultimately help in the difficult task of RNA 3D structure prediction.
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Affiliation(s)
- Christian Laing
- Department of Chemistry, New York University, 251 Mercer Street, New York, NY 10012, USA
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24
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Capriotti E, Marti-Renom MA. SARA: a server for function annotation of RNA structures. Nucleic Acids Res 2009; 37:W260-5. [PMID: 19483098 PMCID: PMC2703911 DOI: 10.1093/nar/gkp433] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Recent interest in non-coding RNA transcripts has resulted in a rapid increase of deposited RNA structures in the Protein Data Bank. However, a characterization and functional classification of the RNA structure and function space have only been partially addressed. Here, we introduce the SARA program for pair-wise alignment of RNA structures as a web server for structure-based RNA function assignment. The SARA server relies on the SARA program, which aligns two RNA structures based on a unit-vector root-mean-square approach. The likely accuracy of the SARA alignments is assessed by three different P-values estimating the statistical significance of the sequence, secondary structure and tertiary structure identity scores, respectively. Our benchmarks, which relied on a set of 419 RNA structures with known SCOR structural class, indicate that at a negative logarithm of mean P-value higher or equal than 2.5, SARA can assign the correct or a similar SCOR class to 81.4% and 95.3% of the benchmark set, respectively. The SARA server is freely accessible via the World Wide Web at http://sgu.bioinfo.cipf.es/services/SARA/.
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Affiliation(s)
- Emidio Capriotti
- Structural Genomics Unit, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
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25
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Lai CE, Tsai MY, Liu YC, Wang CW, Chen KT, Lu CL. FASTR3D: a fast and accurate search tool for similar RNA 3D structures. Nucleic Acids Res 2009; 37:W287-95. [PMID: 19435878 PMCID: PMC2703968 DOI: 10.1093/nar/gkp330] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
FASTR3D is a web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs. Currently, it allows the user to input three types of queries: (i) a PDB code of an RNA tertiary structure (default), optionally with specified residue range, (ii) an RNA secondary structure, optionally with primary sequence, in the dot-bracket notation and (iii) an RNA primary sequence in the FASTA format. In addition, the user can run FASTR3D with specifying additional filtering options: (i) the released date of RNA structures in the PDB database, and (ii) the experimental methods used to determine RNA structures and their least resolutions. In the output page, FASTR3D will show the user-queried RNA molecule, as well as user-specified options, followed by a detailed list of identified structurally similar RNAs. Particularly, when queried with RNA tertiary structures, FASTR3D provides a graphical display to show the structural superposition of the query structure and each of identified structures. FASTR3D is now available online at http://bioalgorithm.life.nctu.edu.tw/FASTR3D/.
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Affiliation(s)
- Chin-En Lai
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan
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26
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Apostolico A, Ciriello G, Guerra C, Heitsch CE, Hsiao C, Williams LD. Finding 3D motifs in ribosomal RNA structures. Nucleic Acids Res 2009; 37:e29. [PMID: 19158187 PMCID: PMC2651809 DOI: 10.1093/nar/gkn1044] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The identification of small structural motifs and their organization into larger subassemblies is of fundamental interest in the analysis, prediction and design of 3D structures of large RNAs. This problem has been studied only sparsely, as most of the existing work is limited to the characterization and discovery of motifs in RNA secondary structures. We present a novel geometric method for the characterization and identification of structural motifs in 3D rRNA molecules. This method enables the efficient recognition of known 3D motifs, such as tetraloops, E-loops, kink-turns and others. Furthermore, it provides a new way of characterizing complex 3D motifs, notably junctions, that have been defined and identified in the secondary structure but have not been analyzed and classified in three dimensions. We demonstrate the relevance and utility of our approach by applying it to the Haloarcula marismortui large ribosomal unit. Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author.
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Affiliation(s)
- Alberto Apostolico
- College of Computing, Georgia Institute of Technology, Atlanta, GA 30332-0280, USA
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27
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Abstract
MOTIVATION The recent discovery of tiny RNA molecules such as microRNAs and small interfering RNA are transforming the view of RNA as a simple information transfer molecule. Similar to proteins, the native three-dimensional structure of RNA determines its biological activity. Therefore, classifying the current structural space is paramount for functionally annotating RNA molecules. The increasing numbers of RNA structures deposited in the PDB requires more accurate, automatic and benchmarked methods for RNA structure comparison. In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach. The algorithm has been implemented in the SARA program, which results in RNA structure pairwise alignments and their statistical significance. RESULTS The SARA program has been implemented to be of general applicability even when no secondary structure can be calculated from the RNA structures. A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in inverted approximately 6% extra alignments with at least 50% structurally superposed nucleotides and base pairs. A first attempt to perform RNA automatic functional annotation based on structure alignments indicates that SARA can correctly assign the deepest SCOR classification to >60% of the query structures. AVAILABILITY The SARA program is freely available through a World Wide Web server http://sgu.bioinfo.cipf.es/services/SARA/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Emidio Capriotti
- Bioinformatics and Genomics Department, Structural Genomics Unit, Centro de Investigación Príncipe Felipe, Valencia, Spain
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28
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Clote P. Introduction to special issue on RNA. J Math Biol 2008; 56:3-13. [PMID: 17938928 DOI: 10.1007/s00285-007-0130-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this introduction to the special issue on RNA, we provide a brief overview of some of the novel and exciting biological discoveries concerning diverse roles played by RNA, and subsequently we give a rapid summary of some algorithmic aspects of RNA structure and alignment. Each of the contributions to this special issue is briefly described.
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Affiliation(s)
- Peter Clote
- Biology Department, Courtesy Appointment in Computer Science Department, Boston College, Chestnut Hill, MA 02467, USA.
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29
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Chang YF, Huang YL, Lu CL. SARSA: a web tool for structural alignment of RNA using a structural alphabet. Nucleic Acids Res 2008; 36:W19-24. [PMID: 18502774 PMCID: PMC2447761 DOI: 10.1093/nar/gkn327] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
SARSA is a web tool that can be used to align two or more RNA tertiary structures. The basic idea behind SARSA is that we use the vector quantization approach to derive a structural alphabet (SA) of 23 nucleotide conformations, via which we transform RNA 3D structures into 1D sequences of SA letters and then utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. In SARSA, we provide two RNA structural alignment tools, PARTS for pairwise alignment of RNA tertiary structures and MARTS for multiple alignment of RNA tertiary structures. Particularly in PARTS, we have implemented four kinds of pairwise alignments for a variety of practical applications: (i) global alignment for comparing whole structural similarity, (ii) semiglobal alignment for detecting structural motifs, (iii) local alignment for finding locally similar substructures and (iv) normalized local alignment for eliminating the mosaic effect of local alignment. Both tools in SARSA take as input RNA 3D structures in the PDB format and in their outputs provide graphical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA molecules. SARSA is available online at http://bioalgorithm.life.nctu.edu.tw/SARSA/.
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Affiliation(s)
- Yen-Fu Chang
- Institute of Bioinformatics, National Chioa Tung University, Department of Computer Science, National Tsing Hua University, Hsinchu 300, Taiwan
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30
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Lu XJ, Olson WK. 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat Protoc 2008; 3:1213-27. [PMID: 18600227 PMCID: PMC3065354 DOI: 10.1038/nprot.2008.104] [Citation(s) in RCA: 486] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We present a set of protocols showing how to use the 3DNA suite of programs to analyze, rebuild and visualize three-dimensional nucleic-acid structures. The software determines a wide range of conformational parameters, including the identities and rigid-body parameters of interacting bases and base-pair steps, the nucleotides comprising helical fragments, the area of overlap of stacked bases and so on. The reconstruction of three-dimensional structure takes advantage of rigorously defined rigid-body parameters, producing rectangular block representations of the nucleic-acid bases and base pairs and all-atom models with approximate sugar-phosphate backbones. The visualization components create vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The utility programs use geometric variables to control the view and scale of an object, for comparison of related structures. The commands run in seconds even for large structures. The software and related information are available at http://3dna.rutgers.edu/.
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Affiliation(s)
- Xiang-Jun Lu
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers-The State University of New Jersey, Piscataway, New Jersey 08854-8087, USA.
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31
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Popenda M, Blazewicz M, Szachniuk M, Adamiak RW. RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Res 2007; 36:D386-91. [PMID: 17921499 PMCID: PMC2238875 DOI: 10.1093/nar/gkm786] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling. The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a ‘dot-bracket’ notation. The algorithm searching for the requested 3D RNA fragments is very efficient. As of August 2007, the database contains: (i) RNA sequences and secondary structures, in the ‘dot-bracket’ notation, derived from 1065 protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom coordinates of unmodified and modified nucleotide residues occurring in RNA structures, (iii) calculated RNA torsion angles and sugar pucker parameters and (iv) information about base pairs. Advanced query involves filters sensitive to: modified residue contents, experimental method used and limits of conformational parameters. The output list of query-matching RNA fragments gives access to their coordinates in the PDB-format files, ready for direct download and visualization, conformational parameters and information about base pairs. The RNA FRABASE is automatically, monthly updated and is freely accessible at http://rnafrabase.ibch.poznan.pl (mirror at http://cerber.cs.put.poznan.pl/rnadb).
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Affiliation(s)
- Mariusz Popenda
- Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
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32
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Ferrè F, Ponty Y, Lorenz WA, Clote P. DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. Nucleic Acids Res 2007; 35:W659-68. [PMID: 17567620 PMCID: PMC1933154 DOI: 10.1093/nar/gkm334] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
DIAL (dihedral alignment) is a web server that provides public access to a new dynamic programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing an alignment that accounts for (i) pseudo-dihedral and/or dihedral angle similarity, (ii) nucleotide sequence similarity and (iii) nucleotide base-pairing similarity. DIAL provides access to three alignment algorithms: global (Needleman–Wunsch), local (Smith–Waterman) and semiglobal (modified to yield motif search). Suboptimal alignments are optionally returned, and also Boltzmann pair probabilities Pr(ai,bj) for aligned positions ai , bj from the optimal alignment. If a non-zero suboptimal alignment score ratio is entered, then the semiglobal alignment algorithm may be used to detect structurally similar occurrences of a user-specified 3D motif. The query motif may be contiguous in the linear chain or fragmented in a number of noncontiguous regions. The DIAL web server provides graphical output which allows the user to view, rotate and enlarge the 3D superposition for the optimal (and suboptimal) alignment of query to target. Although graphical output is available for all three algorithms, the semiglobal motif search may be of most interest in attempts to identify RNA motifs. DIAL is available at http://bioinformatics.bc.edu/clotelab/DIAL.
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Affiliation(s)
- F. Ferrè
- Harvard Medical School, Children's Hospital, Hematology/Oncology Department, Boston, MA 02115 and Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Y. Ponty
- Harvard Medical School, Children's Hospital, Hematology/Oncology Department, Boston, MA 02115 and Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - W. A. Lorenz
- Harvard Medical School, Children's Hospital, Hematology/Oncology Department, Boston, MA 02115 and Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
| | - Peter Clote
- Harvard Medical School, Children's Hospital, Hematology/Oncology Department, Boston, MA 02115 and Department of Biology, Boston College, Chestnut Hill, MA 02467, USA
- *To whom correspondence should be addressed. +1 617 552 1332+1 617 552 2011
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33
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Abstract
Since the discovery of interferon 50 years ago a great deal of progress has been made in understanding how interferons work and how and why they are induced. Key factors in interferon induction are the interferon regulatory factors (IRF). In this review of IRF we aim to show you not only the historical side of the IRF but also the integral, anti-viral and hematopoetic roles of these transcription factors, as well as the sometimes surprising and even forgotten roles that these proteins play, not only in interferon signaling but throughout the immune system and the body as a whole. Further research will no doubt expand the repertoire of these multifunctional proteins even more.
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Affiliation(s)
- A. Paun
- The Division of Viral Oncology at the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins School of Medicine Baltimore, Maryland 21231
| | - P.M. Pitha
- The Division of Viral Oncology at the Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins School of Medicine Baltimore, Maryland 21231
- Department of Molecular Biology and Genetics, The Johns Hopkins School of Medicine Baltimore, Maryland 21231
- *Corresponding author: Phone: +1 410 955 8871, Fax: +1 410 955 0840,
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