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Tang M, Hwang K, Kang SH. StemP: A Fast and Deterministic Stem-Graph Approach for RNA Secondary Structure Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:3278-3291. [PMID: 37028040 DOI: 10.1109/tcbb.2023.3253049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
We propose a new deterministic methodology to predict the secondary structure of RNA sequences. What information of stem is important for structure prediction, and is it enough ? The proposed simple deterministic algorithm uses minimum stem length, Stem-Loop score, and co-existence of stems, to give good structure predictions for short RNA and tRNA sequences. The main idea is to consider all possible stem with certain stem loop energy and strength to predict RNA secondary structure. We use graph notation, where stems are represented as vertexes, and co-existence between stems as edges. This full Stem-graph presents all possible folding structure, and we pick sub-graph(s) which give the best matching energy for structure prediction. Stem-Loop score adds structure information and speeds up the computation. The proposed method can predict secondary structure even with pseudo knots. One of the strengths of this approach is the simplicity and flexibility of the algorithm, and it gives a deterministic answer. Numerical experiments are done on various sequences from Protein Data Bank and the Gutell Lab using a laptop and results take only a few seconds.
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2
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Wang X, Yu S, Lou E, Tan YL, Tan ZJ. RNA 3D Structure Prediction: Progress and Perspective. Molecules 2023; 28:5532. [PMID: 37513407 PMCID: PMC10386116 DOI: 10.3390/molecules28145532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/05/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Ribonucleic acid (RNA) molecules play vital roles in numerous important biological functions such as catalysis and gene regulation. The functions of RNAs are strongly coupled to their structures or proper structure changes, and RNA structure prediction has been paid much attention in the last two decades. Some computational models have been developed to predict RNA three-dimensional (3D) structures in silico, and these models are generally composed of predicting RNA 3D structure ensemble, evaluating near-native RNAs from the structure ensemble, and refining the identified RNAs. In this review, we will make a comprehensive overview of the recent advances in RNA 3D structure modeling, including structure ensemble prediction, evaluation, and refinement. Finally, we will emphasize some insights and perspectives in modeling RNA 3D structures.
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Affiliation(s)
- Xunxun Wang
- Department of Physics, Key Laboratory of Artificial Micro & Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Shixiong Yu
- Department of Physics, Key Laboratory of Artificial Micro & Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - En Lou
- Department of Physics, Key Laboratory of Artificial Micro & Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Lan Tan
- School of Bioengineering and Health, Wuhan Textile University, Wuhan 430200, China
- Research Center of Nonlinear Science, School of Mathematical and Physical Sciences, Wuhan Textile University, Wuhan 430200, China
| | - Zhi-Jie Tan
- Department of Physics, Key Laboratory of Artificial Micro & Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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3
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Langlois NI, Ma KY, Clark HA. Nucleic acid nanostructures for in vivo applications: The influence of morphology on biological fate. APPLIED PHYSICS REVIEWS 2023; 10:011304. [PMID: 36874908 PMCID: PMC9869343 DOI: 10.1063/5.0121820] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/12/2022] [Indexed: 05/23/2023]
Abstract
The development of programmable biomaterials for use in nanofabrication represents a major advance for the future of biomedicine and diagnostics. Recent advances in structural nanotechnology using nucleic acids have resulted in dramatic progress in our understanding of nucleic acid-based nanostructures (NANs) for use in biological applications. As the NANs become more architecturally and functionally diverse to accommodate introduction into living systems, there is a need to understand how critical design features can be controlled to impart desired performance in vivo. In this review, we survey the range of nucleic acid materials utilized as structural building blocks (DNA, RNA, and xenonucleic acids), the diversity of geometries for nanofabrication, and the strategies to functionalize these complexes. We include an assessment of the available and emerging characterization tools used to evaluate the physical, mechanical, physiochemical, and biological properties of NANs in vitro. Finally, the current understanding of the obstacles encountered along the in vivo journey is contextualized to demonstrate how morphological features of NANs influence their biological fates. We envision that this summary will aid researchers in the designing novel NAN morphologies, guide characterization efforts, and design of experiments and spark interdisciplinary collaborations to fuel advancements in programmable platforms for biological applications.
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Affiliation(s)
- Nicole I. Langlois
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
| | - Kristine Y. Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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4
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Zhou L, Wang X, Yu S, Tan YL, Tan ZJ. FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures. Biophys J 2022; 121:3381-3392. [PMID: 35978551 PMCID: PMC9515226 DOI: 10.1016/j.bpj.2022.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 11/23/2022] Open
Abstract
Knowledge of RNA three-dimensional (3D) structures is critical to understanding the important biological functions of RNAs. Although various structure prediction models have been developed, the high-accuracy predictions of RNA 3D structures are still limited to the RNAs with short lengths or with simple topology. In this work, we proposed a new model, namely FebRNA, for building RNA 3D structures through fragment assembly based on coarse-grained (CG) fragment ensembles. Specifically, FebRNA is composed of four processes: establishing the library of different types of non-redundant CG fragment ensembles regardless of the sequences, building CG 3D structure ensemble through fragment assembly, identifying top-scored CG structures through a specific CG scoring function, and rebuilding the all-atom structures from the top-scored CG ones. Extensive examination against different types of RNA structures indicates that FebRNA consistently gives the reliable predictions on RNA 3D structures, including pseudoknots, three-way junctions, four-way and five-way junctions, and RNAs in the RNA-Puzzles. FebRNA is available on the Web site: https://github.com/Tan-group/FebRNA.
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Affiliation(s)
- Li Zhou
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xunxun Wang
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Shixiong Yu
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Lan Tan
- Research Center of Nonlinear Science, School of Mathematical and Physical Sciences, Wuhan Textile University, Wuhan 430073, China.
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro & Nano-structures of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China.
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5
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Wiedemann J, Kaczor J, Milostan M, Zok T, Blazewicz J, Szachniuk M, Antczak M. RNAloops: a database of RNA multiloops. Bioinformatics 2022; 38:4200-4205. [PMID: 35809063 PMCID: PMC9438955 DOI: 10.1093/bioinformatics/btac484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/26/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Knowledge of the 3D structure of RNA supports discovering its functions and is crucial for designing drugs and modern therapeutic solutions. Thus, much attention is devoted to experimental determination and computational prediction targeting the global fold of RNA and its local substructures. The latter include multi-branched loops-functionally significant elements that highly affect the spatial shape of the entire molecule. Unfortunately, their computational modeling constitutes a weak point of structural bioinformatics. A remedy for this is in collecting these motifs and analyzing their features. RESULTS RNAloops is a self-updating database that stores multi-branched loops identified in the PDB-deposited RNA structures. A description of each loop includes angular data-planar and Euler angles computed between pairs of adjacent helices to allow studying their mutual arrangement in space. The system enables search and analysis of multiloops, presents their structure details numerically and visually, and computes data statistics. AVAILABILITY AND IMPLEMENTATION RNAloops is freely accessible at https://rnaloops.cs.put.poznan.pl. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jakub Wiedemann
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Jacek Kaczor
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Maciej Milostan
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland,Poznan Supercomputing and Networking Center, 61-131 Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland,Poznan Supercomputing and Networking Center, 61-131 Poznan, Poland
| | - Jacek Blazewicz
- Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland,Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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Amirloo B, Staroseletz Y, Yousaf S, Clarke DJ, Brown T, Aojula H, Zenkova MA, Bichenkova EV. "Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates. Nucleic Acids Res 2021; 50:651-673. [PMID: 34967410 PMCID: PMC8789077 DOI: 10.1093/nar/gkab1273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
Antisense sequence-specific knockdown of pathogenic RNA offers opportunities to find new solutions for therapeutic treatments. However, to gain a desired therapeutic effect, the multiple turnover catalysis is critical to inactivate many copies of emerging RNA sequences, which is difficult to achieve without sacrificing the sequence-specificity of cleavage. Here, engineering two or three catalytic peptides into the bulge-loop inducing molecular framework of antisense oligonucleotides achieved catalytic turnover of targeted RNA. Different supramolecular configurations revealed that cleavage of the RNA backbone upon sequence-specific hybridization with the catalyst accelerated with increase in the number of catalytic guanidinium groups, with almost complete demolition of target RNA in 24 h. Multiple sequence-specific cuts at different locations within and around the bulge-loop facilitated release of the catalyst for subsequent attacks of at least 10 further RNA substrate copies, such that delivery of only a few catalytic molecules could be sufficient to maintain knockdown of typical RNA copy numbers. We have developed fluorescent assay and kinetic simulation tools to characterise how the limited availability of different targets and catalysts had restrained catalytic reaction progress considerably, and to inform how to accelerate the catalytic destruction of shorter linear and larger RNAs even further.
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Affiliation(s)
- Bahareh Amirloo
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Sameen Yousaf
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - David J Clarke
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Harmesh Aojula
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090 Novosibirsk, Russian Federation
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
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7
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Zhang D, Chen SJ, Zhou R. Modeling Noncanonical RNA Base Pairs by a Coarse-Grained IsRNA2 Model. J Phys Chem B 2021; 125:11907-11915. [PMID: 34694128 DOI: 10.1021/acs.jpcb.1c07288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncanonical base pairs contribute crucially to the three-dimensional architecture of large RNA molecules; however, how to accurately model them remains an open challenge in RNA 3D structure prediction. Here, we report a promising coarse-grained (CG) IsRNA2 model to predict noncanonical base pairs in large RNAs through molecular dynamics simulations. By introducing a five-bead per nucleotide CG representation to reserve the three interacting edges of nucleobases, IsRNA2 accurately models various base-pairing interactions, including both canonical and noncanonical base pairs. A benchmark test indicated that IsRNA2 achieves a comparable performance to the atomic model in de novo modeling of noncanonical RNA structures. In addition, IsRNA2 was able to refine the 3D structure predictions for large RNAs in RNA-puzzle challenges. Finally, the graphics processing unit acceleration was introduced to speed up the sampling efficiency in IsRNA2 for very large RNA molecules. Therefore, the CG IsRNA2 model reported here offers a reliable approach to predict the structures and dynamics of large RNAs.
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Affiliation(s)
- Dong Zhang
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Ruhong Zhou
- College of Life Sciences and Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China
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Zhou Y, Li J, Hurst T, Chen SJ. SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction. Front Mol Biosci 2021; 8:721955. [PMID: 34395533 PMCID: PMC8355595 DOI: 10.3389/fmolb.2021.721955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 11/13/2022] Open
Abstract
Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing serves as a convenient and efficient experiment technique for providing information about RNA local flexibility. The local structural information contained in SHAPE reactivity data can be used as constraints in 2D/3D structure predictions. Here, we present SHAPE predictoR (SHAPER), a web server for fast and accurate SHAPE reactivity prediction. The main purpose of the SHAPER web server is to provide a portal that uses experimental SHAPE data to refine 2D/3D RNA structure selection. Input structures for the SHAPER server can be obtained through experimental or computational modeling. The SHAPER server can accept RNA structures with single or multiple conformations, and the predicted SHAPE profile and correlation with experimental SHAPE data (if provided) for each conformation can be freely downloaded through the web portal. The SHAPER web server is available at http://rna.physics.missouri.edu/shaper/.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, United States
| | - Jun Li
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, United States
| | - Travis Hurst
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, United States
| | - Shi-Jie Chen
- Department of Physics and Astronomy, University of Missouri, Columbia, MO, United States.,Department of Biochemistry, University of Missouri, Columbia, MO, United States.,Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO, United States
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9
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Zhang D, Li J, Chen SJ. IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures. J Chem Theory Comput 2021; 17:1842-1857. [PMID: 33560836 DOI: 10.1021/acs.jctc.0c01148] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modeling structures and functions of large ribonucleic acid (RNAs) especially with complicated topologies is highly challenging due to the inefficiency of large conformational sampling and the presence of complicated tertiary interactions. To address this problem, one highly promising approach is coarse-grained modeling. Here, following an iterative simulated reference state approach to decipher the correlations between different structural parameters, we developed a potent coarse-grained RNA model named as IsRNA1 for RNA studies. Molecular dynamics simulations in the IsRNA1 can predict the native structures of small RNAs from a sequence and fold medium-sized RNAs into near-native tertiary structures with the assistance of secondary structure constraints. A large-scale benchmark test on RNA 3D structure prediction shows that IsRNA1 exhibits improved performance for relatively large RNAs of complicated topologies, such as large stem-loop structures and structures containing long-range tertiary interactions. The advantages of IsRNA1 include the consideration of the correlations between the different structural variables, the appropriate characterization of canonical base-pairing and base-stacking interactions, and the better sampling for the backbone conformations. Moreover, a blind screening protocol was developed based on IsRNA1 to identify good structural models from a pool of candidates without prior knowledge of the native structures.
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Affiliation(s)
- Dong Zhang
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Jun Li
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
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Abstract
Novel RNA motif design is of great practical importance for technology and medicine. Increasingly, computational design plays an important role in such efforts. Our coarse-grained RAG (RNA-As-Graphs) framework offers strategies for enumerating the universe of RNA 2D folds, selecting "RNA-like" candidates for design, and determining sequences that fold onto these candidates. In RAG, RNA secondary structures are represented as tree or dual graphs. Graphs with known RNA structures are called "existing", and the others are labeled "hypothetical". By using simplified features for RNA graphs, we have clustered the hypothetical graphs into "RNA-like" and "non-RNA-like" groups and proposed RNA-like graphs as candidates for design. Here, we propose a new way of designing graph features by using Fiedler vectors. The new features reflect graph shapes better, and they lead to a more clustered organization of existing graphs. We show significant increases in K-means clustering accuracy by using the new features (e.g., up to 95% and 98% accuracy for tree and dual graphs, respectively). In addition, we propose a scoring model for top graph candidate selection. This scoring model allows users to set a threshold for candidates, and it incorporates weighing of existing graphs based on their corresponding number of known RNAs. We include a list of top scored RNA-like candidates, which we hope will stimulate future novel RNA design.
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Affiliation(s)
- Qiyao Zhu
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
| | - Tamar Schlick
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, United States
- Department of Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200062, P. R. China
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Perret G, Boschetti E. Aptamer-Based Affinity Chromatography for Protein Extraction and Purification. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 174:93-139. [PMID: 31485702 DOI: 10.1007/10_2019_106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Aptamers are oligonucleotide molecules able to recognize very specifically proteins. Among the possible applications, aptamers have been used for affinity chromatography with effective results and advantages over most advanced protein separation technologies. This chapter first discusses the context of the affinity chromatography with aptamer ligands. With the adaptation of SELEX, the chemical modifications of aptamers to comply with the covalent coupling and the separation process are then extensively presented. A focus is then made about the most important applications for protein separation with real-life examples and the comparison with immunoaffinity chromatography. In spite of well-advanced demonstrations and the extraordinary potential developments, a significant optimization work is still due to deserve large-scale applications with all necessary validations. Graphical Abstract Aptamer-protein complexes by X-ray crystallography.
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Watkins AM, Rangan R, Das R. FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds. Structure 2020; 28:963-976.e6. [PMID: 32531203 PMCID: PMC7415647 DOI: 10.1016/j.str.2020.05.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 04/27/2020] [Accepted: 05/20/2020] [Indexed: 01/01/2023]
Abstract
Predicting RNA three-dimensional structures from sequence could accelerate understanding of the growing number of RNA molecules being discovered across biology. Rosetta's Fragment Assembly of RNA with Full-Atom Refinement (FARFAR) has shown promise in community-wide blind RNA-Puzzle trials, but lack of a systematic and automated benchmark has left unclear what limits FARFAR performance. Here, we benchmark FARFAR2, an algorithm integrating RNA-Puzzle-inspired innovations with updated fragment libraries and helix modeling. In 16 of 21 RNA-Puzzles revisited without experimental data or expert intervention, FARFAR2 recovers native-like structures more accurate than models submitted during the RNA-Puzzles trials. Remaining bottlenecks include conformational sampling for >80-nucleotide problems and scoring function limitations more generally. Supporting these conclusions, preregistered blind models for adenovirus VA-I RNA and five riboswitch complexes predicted native-like folds with 3- to 14 Å root-mean-square deviation accuracies. We present a FARFAR2 webserver and three large model archives (FARFAR2-Classics, FARFAR2-Motifs, and FARFAR2-Puzzles) to guide future applications and advances.
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Affiliation(s)
- Andrew Martin Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA.
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13
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Emami N, Pakchin PS, Ferdousi R. Computational predictive approaches for interaction and structure of aptamers. J Theor Biol 2020; 497:110268. [PMID: 32311376 DOI: 10.1016/j.jtbi.2020.110268] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/27/2020] [Accepted: 04/02/2020] [Indexed: 02/07/2023]
Abstract
Aptamers are short single-strand sequences that can bind to their specific targets with high affinity and specificity. Usually, aptamers are selected experimentally via systematic evolution of ligands by exponential enrichment (SELEX), an evolutionary process that consists of multiple cycles of selection and amplification. The SELEX process is expensive, time-consuming, and its success rates are relatively low. To overcome these difficulties, in recent years, several computational techniques have been developed in aptamer sciences that bring together different disciplines and branches of technologies. In this paper, a complementary review on computational predictive approaches of the aptamer has been organized. Generally, the computational prediction approaches of aptamer have been proposed to carry out in two main categories: interaction-based prediction and structure-based predictions. Furthermore, the available software packages and toolkits in this scope were reviewed. The aim of describing computational methods and tools in aptamer science is that aptamer scientists might take advantage of these computational techniques to develop more accurate and more sensitive aptamers.
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Affiliation(s)
- Neda Emami
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parvin Samadi Pakchin
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ferdousi
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Tabriz, Iran; Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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Su C, Weir JD, Zhang F, Yan H, Wu T. ENTRNA: a framework to predict RNA foldability. BMC Bioinformatics 2019; 20:373. [PMID: 31269893 PMCID: PMC6610807 DOI: 10.1186/s12859-019-2948-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 06/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions. Therefore, understanding RNA folding conformations, in particular, RNA secondary structures, is critical for elucidating biological functions. Existing literature has focused on RNA design as either an RNA structure prediction problem or an RNA inverse folding problem where free energy has played a key role. RESULTS In this research, we propose a Positive-Unlabeled data- driven framework termed ENTRNA. Other than free energy and commonly studied sequence and structural features, we propose a new feature, Sequence Segment Entropy (SSE), to measure the diversity of RNA sequences. ENTRNA is trained and cross-validated using 1024 pseudoknot-free RNAs and 1060 pseudoknotted RNAs from the RNASTRAND database respectively. To test the robustness of the ENTRNA, the models are further blind tested on 206 pseudoknot-free and 93 pseudoknotted RNAs from the PDB database. For pseudoknot-free RNAs, ENTRNA has 86.5% sensitivity on the training dataset and 80.6% sensitivity on the testing dataset. For pseudoknotted RNAs, ENTRNA shows 81.5% sensitivity on the training dataset and 71.0% on the testing dataset. To test the applicability of ENTRNA to long structural-complex RNA, we collect 5 laboratory synthetic RNAs ranging from 1618 to 1790 nucleotides. ENTRNA is able to predict the foldability of 4 RNAs. CONCLUSION In this article, we reformulate the RNA design problem as a foldability prediction problem which is to predict the likelihood of the co-existence of a sequence-structure pair. This new construct has the potential for both RNA structure prediction and the inverse folding problem. In addition, this new construct enables us to explore data-driven approaches in RNA research.
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Affiliation(s)
- Congzhe Su
- School of Computing, Informatics, Decision Systems Engineering, Arizona State University, Tempe, AZ 85281 USA
| | - Jeffery D. Weir
- Department of Operational Sciences, Graduate School of Engineering and Management, Air Force Institute of Technology, Wright-Patterson AFB, Dayton, OH 45433 USA
| | - Fei Zhang
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, AZ 85281 USA
| | - Hao Yan
- Biodesign Center for Molecular Design and Biomimetics, The Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, AZ 85281 USA
| | - Teresa Wu
- School of Computing, Informatics, Decision Systems Engineering, Arizona State University, Tempe, AZ 85281 USA
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15
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Pucci F, Schug A. Shedding light on the dark matter of the biomolecular structural universe: Progress in RNA 3D structure prediction. Methods 2019; 162-163:68-73. [DOI: 10.1016/j.ymeth.2019.04.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/12/2019] [Accepted: 04/22/2019] [Indexed: 11/25/2022] Open
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16
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Abstract
The structure of RNA has been a natural subject for mathematical modeling, inviting many innovative computational frameworks. This single-stranded polynucleotide chain can fold upon itself in numerous ways to form hydrogen-bonded segments, imperfect with single-stranded loops. Illustrating these paired and non-paired interaction networks, known as RNA's secondary (2D) structure, using mathematical graph objects has been illuminating for RNA structure analysis. Building upon such seminal work from the 1970s and 1980s, graph models are now used to study not only RNA structure but also describe RNA's recurring modular units, sample the conformational space accessible to RNAs, predict RNA's three-dimensional folds, and apply the combined aspects to novel RNA design. In this article, we outline the development of the RNA-As-Graphs (or RAG) approach and highlight current applications to RNA structure prediction and design.
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Affiliation(s)
- Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York University, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA; New York University ECNU - Center for Computational Chemistry at NYU Shanghai, 3663 North Zhongshan Road, Shanghai, 200062, China.
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17
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Hurst T, Xu X, Zhao P, Chen SJ. Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis. J Phys Chem B 2018; 122:4771-4783. [PMID: 29659274 DOI: 10.1021/acs.jpcb.8b00575] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.
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Affiliation(s)
- Travis Hurst
- Department of Physics, Department of Biochemistry , and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Xiaojun Xu
- Department of Physics, Department of Biochemistry , and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Peinan Zhao
- Department of Physics, Department of Biochemistry , and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry , and University of Missouri Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
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18
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Molecular chaperones maximize the native state yield on biological times by driving substrates out of equilibrium. Proc Natl Acad Sci U S A 2017; 114:E10919-E10927. [PMID: 29217641 DOI: 10.1073/pnas.1712962114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Molecular chaperones facilitate the folding of proteins and RNA in vivo. Under physiological conditions, the in vitro folding of Tetrahymena ribozyme by the RNA chaperone CYT-19 behaves paradoxically; increasing the chaperone concentration reduces the yield of native ribozymes. In contrast, the protein chaperone GroEL works as expected; the yield of the native substrate increases with chaperone concentration. The discrepant chaperone-assisted ribozyme folding thus contradicts the expectation that it operates as an efficient annealing machine. To resolve this paradox, we propose a minimal stochastic model based on the Iterative Annealing Mechanism (IAM) that offers a unified description of chaperone-mediated folding of both proteins and RNA. Our theory provides a general relation that quantitatively predicts how the yield of native states depends on chaperone concentration. Although the absolute yield of native states decreases in the Tetrahymena ribozyme, the product of the folding rate and the steady-state native yield increases in both cases. By using energy from ATP hydrolysis, both CYT-19 and GroEL drive their substrate concentrations far out of equilibrium, thus maximizing the native yield in a short time. This also holds when the substrate concentration exceeds that of GroEL. Our findings satisfy the expectation that proteins and RNA be folded by chaperones on biologically relevant time scales, even if the final yield is lower than what equilibrium thermodynamics would dictate. The theory predicts that the quantity of chaperones in vivo has evolved to optimize native state production of the folded states of RNA and proteins in a given time.
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19
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Jain S, Schlick T. F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly. J Mol Biol 2017; 429:3587-3605. [PMID: 28988954 PMCID: PMC5693719 DOI: 10.1016/j.jmb.2017.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/12/2017] [Accepted: 09/22/2017] [Indexed: 10/18/2022]
Abstract
Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce candidate graphs. However, for a more detailed study and analysis, construction of atomic from coarse-grained models is required. Here we present our graph-based fragment assembly algorithm (F-RAG) to convert candidate three-dimensional (3D) tree graph models, produced by RAGTOP into atomic structures. We use our related RAG-3D utilities to partition graphs into subgraphs and search for structurally similar atomic fragments in a data set of RNA 3D structures. The fragments are edited and superimposed using common residues, full atomic models are scored using RAGTOP's knowledge-based potential, and geometries of top scoring models is optimized. To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of residue interactions) with respect to experimentally solved structures and compare our results to other fragment assembly programs. For a set of 50 RNA structures, we obtain atomic models with reasonable geometries and interactions, particularly good for RNAs containing junctions. Additional improvements to our protocol and databases are outlined. These results provide a good foundation for further work on RNA structure prediction and design applications.
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Affiliation(s)
- Swati Jain
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 1001 Silver, 100 Washington Square East, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA; New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Room 340, Geography Building, North Zhongshan Road, 3663 Shanghai, China.
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20
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Abstract
In addition to continuous rapid progress in RNA structure determination, probing, and biophysical studies, the past decade has seen remarkable advances in the development of a new generation of RNA folding theories and models. In this article, we review RNA structure prediction models and models for ion-RNA and ligand-RNA interactions. These new models are becoming increasingly important for a mechanistic understanding of RNA function and quantitative design of RNA nanotechnology. We focus on new methods for physics-based, knowledge-based, and experimental data-directed modeling for RNA structures and explore the new theories for the predictions of metal ion and ligand binding sites and metal ion-dependent RNA stabilities. The integration of these new methods with theories about the cellular environment effects in RNA folding, such as molecular crowding and cotranscriptional kinetic effects, may ultimately lead to an all-encompassing RNA folding model.
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Affiliation(s)
- Li-Zhen Sun
- Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211;
| | - Dong Zhang
- Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211;
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and MU Informatics Institute, University of Missouri, Columbia, Missouri 65211;
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21
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Bell DR, Cheng SY, Salazar H, Ren P. Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations. Sci Rep 2017; 7:45812. [PMID: 28393861 PMCID: PMC5385882 DOI: 10.1038/srep45812] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 03/06/2017] [Indexed: 01/25/2023] Open
Abstract
We introduce a coarse-grained RNA model for molecular dynamics simulations, RACER (RnA CoarsE-gRained). RACER achieves accurate native structure prediction for a number of RNAs (average RMSD of 2.93 Å) and the sequence-specific variation of free energy is in excellent agreement with experimentally measured stabilities (R2 = 0.93). Using RACER, we identified hydrogen-bonding (or base pairing), base stacking, and electrostatic interactions as essential driving forces for RNA folding. Also, we found that separating pairing vs. stacking interactions allowed RACER to distinguish folded vs. unfolded states. In RACER, base pairing and stacking interactions each provide an approximate stability of 3-4 kcal/mol for an A-form helix. RACER was developed based on PDB structural statistics and experimental thermodynamic data. In contrast with previous work, RACER implements a novel effective vdW potential energy function, which led us to re-parameterize hydrogen bond and electrostatic potential energy functions. Further, RACER is validated and optimized using a simulated annealing protocol to generate potential energy vs. RMSD landscapes. Finally, RACER is tested using extensive equilibrium pulling simulations (0.86 ms total) on eleven RNA sequences (hairpins and duplexes).
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Affiliation(s)
- David R. Bell
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sara Y. Cheng
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, United States
| | - Heber Salazar
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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22
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Modelling the three-dimensional structure of the right-terminal domain of pospiviroids. Sci Rep 2017; 7:711. [PMID: 28386073 PMCID: PMC5429643 DOI: 10.1038/s41598-017-00764-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/13/2017] [Indexed: 12/20/2022] Open
Abstract
Viroids, the smallest know plant pathogens, consist solely of a circular, single-stranded, non-coding RNA. Thus for all of their biological functions, like replication, processing, and transport, they have to present sequence or structural features to exploit host proteins. Viroid binding protein 1 (Virp1) is indispensable for replication of pospiviroids, the largest genus of viroids, in a host plant as well as in protoplasts. Virp1 is known to bind at two sites in the terminal right (TR) domain of pospiviroids; each site consists of a purine- (R-) and a pyrimidine- (Y-)rich motif that are partially base-paired to each other. Here we model the important structural features of the domain and show that it contains an internal loop of two Y · Y cis Watson-Crick/Watson-Crick (cWW) pairs, an asymmetric internal loop including a cWW and a trans Watson/Hoogsteen pair, and a thermodynamically quite stable hairpin loop with several stacking interactions. These features are discussed in connection to the known biological functions of the TR domain.
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23
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Taylor WR, Hamilton RS. Exploring RNA conformational space under sparse distance restraints. Sci Rep 2017; 7:44074. [PMID: 28281575 PMCID: PMC5345030 DOI: 10.1038/srep44074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/01/2017] [Indexed: 11/21/2022] Open
Abstract
We show that the application of a small number of restraints predicted by coevolution analysis can provide a powerful restriction on the conformational freedom of an RNA molecule. The greatest degree of restriction occurs when a contact is predicted between the distal ends of a pair of adjacent stemloops but even with this location additional flexibilities in the molecule can mask the contribution. Multiple cross-links, especially those including a pseudoknot provided the strongest restraint on conformational freedom with the effect being most apparent in topologically simple folds and less so if the fold is more topologically entwined. Little was expected for large structures (over 300 bases) and although a few strong localised restrictions were observed, they contributed little to the restraint of the overall fold. Although contacts predicted using a correlated mutation analysis can provide some powerful restrictions on the conformational freedom of RNA molecules, they are too erratic in their occurrence and distribution to provide a general approach to the problem of RNA 3D structure prediction from sequence.
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Affiliation(s)
- William R. Taylor
- Computational Cell and Molecular Biology, Francis Crick Institute, London, NW1 1AT, UK
| | - Russell S. Hamilton
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
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24
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Magnus M, Boniecki MJ, Dawson W, Bujnicki JM. SimRNAweb: a web server for RNA 3D structure modeling with optional restraints. Nucleic Acids Res 2016; 44:W315-9. [PMID: 27095203 PMCID: PMC4987879 DOI: 10.1093/nar/gkw279] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/06/2016] [Indexed: 12/02/2022] Open
Abstract
RNA function in many biological processes depends on the formation of three-dimensional (3D) structures. However, RNA structure is difficult to determine experimentally, which has prompted the development of predictive computational methods. Here, we introduce a user-friendly online interface for modeling RNA 3D structures using SimRNA, a method that uses a coarse-grained representation of RNA molecules, utilizes the Monte Carlo method to sample the conformational space, and relies on a statistical potential to describe the interactions in the folding process. SimRNAweb makes SimRNA accessible to users who do not normally use high performance computational facilities or are unfamiliar with using the command line tools. The simplest input consists of an RNA sequence to fold RNA de novo. Alternatively, a user can provide a 3D structure in the PDB format, for instance a preliminary model built with some other technique, to jump-start the modeling close to the expected final outcome. The user can optionally provide secondary structure and distance restraints, and can freeze a part of the starting 3D structure. SimRNAweb can be used to model single RNA sequences and RNA-RNA complexes (up to 52 chains). The webserver is available at http://genesilico.pl/SimRNAweb.
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Affiliation(s)
- Marcin Magnus
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Michał J Boniecki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Wayne Dawson
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland
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25
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Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS. 3D RNA and Functional Interactions from Evolutionary Couplings. Cell 2016; 165:963-75. [PMID: 27087444 DOI: 10.1016/j.cell.2016.03.030] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/15/2016] [Accepted: 03/18/2016] [Indexed: 11/18/2022]
Abstract
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces the research on the structure and functional interactions of these RNA gene sequences. We mine the evolutionary sequence record to derive precise information about the function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability models of sequence co-variation to infer evolutionarily constrained nucleotide-nucleotide interactions within RNA molecules and nucleotide-amino acid interactions in RNA-protein complexes. The predicted contacts allow all-atom blinded 3D structure prediction at good accuracy for several known RNA structures and RNA-protein complexes. For unknown structures, we predict contacts in 160 non-coding RNA families. Beyond 3D structure prediction, evolutionary couplings help identify important functional interactions-e.g., at switch points in riboswitches and at a complex nucleation site in HIV. Aided by increasing sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA.
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Affiliation(s)
- Caleb Weinreb
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Adam J Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Program in Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - John B Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Torsten Gross
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Institute of Pathology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Chris Sander
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
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26
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Yan K, Arfat Y, Li D, Zhao F, Chen Z, Yin C, Sun Y, Hu L, Yang T, Qian A. Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Int J Mol Sci 2016; 17:ijms17010132. [PMID: 26805815 PMCID: PMC4730372 DOI: 10.3390/ijms17010132] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/18/2015] [Accepted: 01/12/2016] [Indexed: 12/31/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), which form a diverse class of RNAs, remain the least understood type of noncoding RNAs in terms of their nature and identification. Emerging evidence has revealed that a small number of newly discovered lncRNAs perform important and complex biological functions such as dosage compensation, chromatin regulation, genomic imprinting, and nuclear organization. However, understanding the wide range of functions of lncRNAs related to various processes of cellular networks remains a great experimental challenge. Structural versatility is critical for RNAs to perform various functions and provides new insights into probing the functions of lncRNAs. In recent years, the computational method of RNA structure prediction has been developed to analyze the structure of lncRNAs. This novel methodology has provided basic but indispensable information for the rapid, large-scale and in-depth research of lncRNAs. This review focuses on mainstream RNA structure prediction methods at the secondary and tertiary levels to offer an additional approach to investigating the functions of lncRNAs.
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Affiliation(s)
- Kun Yan
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yasir Arfat
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Dijie Li
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Fan Zhao
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Zhihao Chen
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Chong Yin
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yulong Sun
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Lifang Hu
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Tuanmin Yang
- Department of Bone Disease Oncology, Hong-Hui Hospital, Xi'an Jiaotong University College of Medicine, South Door slightly Friendship Road 555, Xi'an 710054, China.
| | - Airong Qian
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
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27
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Šulc P, Ouldridge TE, Romano F, Doye JPK, Louis AA. Modelling toehold-mediated RNA strand displacement. Biophys J 2016; 108:1238-47. [PMID: 25762335 DOI: 10.1016/j.bpj.2015.01.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/18/2015] [Accepted: 01/26/2015] [Indexed: 12/24/2022] Open
Abstract
We study the thermodynamics and kinetics of an RNA toehold-mediated strand displacement reaction with a recently developed coarse-grained model of RNA. Strand displacement, during which a single strand displaces a different strand previously bound to a complementary substrate strand, is an essential mechanism in active nucleic acid nanotechnology and has also been hypothesized to occur in vivo. We study the rate of displacement reactions as a function of the length of the toehold and temperature and make two experimentally testable predictions: that the displacement is faster if the toehold is placed at the 5' end of the substrate; and that the displacement slows down with increasing temperature for longer toeholds.
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Affiliation(s)
- Petr Šulc
- Center for Studies in Physics and Biology, Rockefeller University, New York, New York; Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom.
| | - Thomas E Ouldridge
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom; Department of Mathematics, Imperial College, London, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom
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28
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RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure. PLoS One 2015; 10:e0139900. [PMID: 26509713 PMCID: PMC4624896 DOI: 10.1371/journal.pone.0139900] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 08/17/2015] [Indexed: 01/09/2023] Open
Abstract
Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D module prediction tools and apply them on a 13-way vertebrate sequence-based alignment. We find that RNA 3D modules predicted by metaRNAmodules and JAR3D are significantly enriched in the screened windows compared to their shuffled counterparts. The initially estimated FDR of 47.0% is lowered to below 25% when certain 3D module predictions are present in the window of the 2D prediction. We discuss the implications and prospects for further development of computational strategies for detection of RNA 2D structure in genomic sequence.
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29
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De Leonardis E, Lutz B, Ratz S, Cocco S, Monasson R, Schug A, Weigt M. Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction. Nucleic Acids Res 2015; 43:10444-55. [PMID: 26420827 PMCID: PMC4666395 DOI: 10.1093/nar/gkv932] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/07/2015] [Indexed: 12/16/2022] Open
Abstract
Despite the biological importance of non-coding RNA, their structural characterization remains challenging. Making use of the rapidly growing sequence databases, we analyze nucleotide coevolution across homologous sequences via Direct-Coupling Analysis to detect nucleotide-nucleotide contacts. For a representative set of riboswitches, we show that the results of Direct-Coupling Analysis in combination with a generalized Nussinov algorithm systematically improve the results of RNA secondary structure prediction beyond traditional covariance approaches based on mutual information. Even more importantly, we show that the results of Direct-Coupling Analysis are enriched in tertiary structure contacts. By integrating these predictions into molecular modeling tools, systematically improved tertiary structure predictions can be obtained, as compared to using secondary structure information alone.
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Affiliation(s)
- Eleonora De Leonardis
- Computational and Quantitative Biology, Sorbonne Universités, Université Pierre et Marie Curie, UMR 7238, 75006 Paris, France Computational and Quantitative Biology, CNRS, UMR 7238, 75006 Paris, France Laboratoire de Physique Statistique de l'Ecole Normale Supérieure, associé au CNRS et à l'Université Pierre et Marie Curie, 75005 Paris, France
| | - Benjamin Lutz
- Steinbuch Centre for Computing, Karlsruher Institut für Technologie, 76133 Karlsruhe, Germany Fakultät für Physik, Karlsruher Institut für Technologie, 76133 Karlsruhe, Germany
| | - Sebastian Ratz
- Steinbuch Centre for Computing, Karlsruher Institut für Technologie, 76133 Karlsruhe, Germany Fakultät für Physik, Karlsruher Institut für Technologie, 76133 Karlsruhe, Germany
| | - Simona Cocco
- Laboratoire de Physique Statistique de l'Ecole Normale Supérieure, associé au CNRS et à l'Université Pierre et Marie Curie, 75005 Paris, France
| | - Rémi Monasson
- Laboratoire de Physique Théorique de l'Ecole Normale Supérieure, associé au CNRS et à l'Université Pierre et Marie Curie, 75005 Paris, France
| | - Alexander Schug
- Steinbuch Centre for Computing, Karlsruher Institut für Technologie, 76133 Karlsruhe, Germany
| | - Martin Weigt
- Computational and Quantitative Biology, Sorbonne Universités, Université Pierre et Marie Curie, UMR 7238, 75006 Paris, France Computational and Quantitative Biology, CNRS, UMR 7238, 75006 Paris, France
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30
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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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31
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Endoh T, Sugimoto N. Rational Design and Tuning of Functional RNA Switch to Control an Allosteric Intermolecular Interaction. Anal Chem 2015; 87:7628-35. [DOI: 10.1021/acs.analchem.5b00765] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier
Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojimaminamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier
Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojimaminamimachi, Kobe, 650-0047, Japan
- Graduate
School of Frontiers of Innovative
Research in Science and Technology (FIRST), Konan University, 7-1-20
Minatojimaminamimachi, Kobe, 650-0047, Japan
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32
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Cragnolini T, Derreumaux P, Pasquali S. Ab initio RNA folding. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:233102. [PMID: 25993396 DOI: 10.1088/0953-8984/27/23/233102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.
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Affiliation(s)
- Tristan Cragnolini
- Laboratoire de Biochimie Théorique UPR 9080 CNRS, Université Paris Diderot, Sorbonne, Paris Cité, IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France
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33
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Górska A, Jasiński M, Trylska J. MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids. Nucleic Acids Res 2015; 43:e114. [PMID: 26024667 PMCID: PMC4787793 DOI: 10.1093/nar/gkv559] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/15/2015] [Indexed: 12/18/2022] Open
Abstract
Structural biology experiments and structure prediction tools have provided many
high-resolution three-dimensional structures of nucleic acids. Also, molecular
dynamics force field parameters have been adapted to simulating charged and flexible
nucleic acid structures on microsecond time scales. Therefore, we can generate the
dynamics of DNA or RNA molecules, but we still lack adequate tools for the analysis
of the resulting huge amounts of data. We present MINT (Motif
Identifier for Nucleic acids Trajectory) — an automatic tool for analyzing
three-dimensional structures of RNA and DNA, and their full-atom molecular dynamics
trajectories or other conformation sets (e.g. X-ray or nuclear magnetic
resonance-derived structures). For each RNA or DNA conformation
MINT determines the hydrogen bonding network resolving the
base pairing patterns, identifies secondary structure motifs (helices, junctions,
loops, etc.) and pseudoknots. MINT also estimates the energy
of stacking and phosphate anion-base interactions. For many conformations, as in a
molecular dynamics trajectory, MINT provides averages of the
above structural and energetic features and their evolution. We show
MINT functionality based on all-atom explicit solvent
molecular dynamics trajectory of the 30S ribosomal subunit.
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Affiliation(s)
- Anna Górska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland Master studies at the Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, Warsaw, Poland
| | - Maciej Jasiński
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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34
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Tuszynska I, Magnus M, Jonak K, Dawson W, Bujnicki JM. NPDock: a web server for protein-nucleic acid docking. Nucleic Acids Res 2015; 43:W425-30. [PMID: 25977296 PMCID: PMC4489298 DOI: 10.1093/nar/gkv493] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/02/2015] [Indexed: 01/03/2023] Open
Abstract
Protein–RNA and protein–DNA interactions play fundamental roles in many biological processes. A detailed understanding of these interactions requires knowledge about protein–nucleic acid complex structures. Because the experimental determination of these complexes is time-consuming and perhaps futile in some instances, we have focused on computational docking methods starting from the separate structures. Docking methods are widely employed to study protein–protein interactions; however, only a few methods have been made available to model protein–nucleic acid complexes. Here, we describe NPDock (Nucleic acid–Protein Docking); a novel web server for predicting complexes of protein–nucleic acid structures which implements a computational workflow that includes docking, scoring of poses, clustering of the best-scored models and refinement of the most promising solutions. The NPDock server provides a user-friendly interface and 3D visualization of the results. The smallest set of input data consists of a protein structure and a DNA or RNA structure in PDB format. Advanced options are available to control specific details of the docking process and obtain intermediate results. The web server is available at http://genesilico.pl/NPDock.
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Affiliation(s)
- Irina Tuszynska
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland Institute of Informatics, University of Warsaw, Banacha 2, PL-02-097 Warsaw, Poland
| | - Marcin Magnus
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Katarzyna Jonak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Wayne Dawson
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland
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35
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Šulc P, Romano F, Ouldridge TE, Doye JPK, Louis AA. A nucleotide-level coarse-grained model of RNA. J Chem Phys 2015; 140:235102. [PMID: 24952569 DOI: 10.1063/1.4881424] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant physics for RNA hybridization and the structure of single- and double-stranded RNA. In order to explore its strengths and weaknesses, we test the model in a range of nanotechnological and biological settings. Applications explored include the folding thermodynamics of a pseudoknot, the formation of a kissing loop complex, the structure of a hexagonal RNA nanoring, and the unzipping of a hairpin motif. We argue that the model can be used for efficient simulations of the structure of systems with thousands of base pairs, and for the assembly of systems of up to hundreds of base pairs. The source code implementing the model is released for public use.
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Affiliation(s)
- Petr Šulc
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Thomas E Ouldridge
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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36
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Ding L, Xue X, LaMarca S, Mohebbi M, Samad A, Malmberg RL, Cai L. Accurate prediction of RNA nucleotide interactions with backbone k-tree model. Bioinformatics 2015; 31:2660-7. [PMID: 25886978 DOI: 10.1093/bioinformatics/btv210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/12/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Given the importance of non-coding RNAs to cellular regulatory functions, it would be highly desirable to have accurate computational prediction of RNA 3D structure, a task which remains challenging. Even for a short RNA sequence, the space of tertiary conformations is immense; existing methods to identify native-like conformations mostly resort to random sampling of conformations to achieve computational feasibility. However, native conformations may not be examined and prediction accuracy may be compromised due to sampling. State-of-the-art methods have yet to deliver satisfactory predictions for RNAs of length beyond 50 nucleotides. RESULTS This paper presents a method to tackle a key step in the RNA 3D structure prediction problem, the prediction of the nucleotide interactions that constitute the desired 3D structure. The research is based on a novel graph model, called a backbone k-tree, to tightly constrain the nucleotide interaction relationships considered for RNA 3D structures. It is shown that the new model makes it possible to efficiently predict the optimal set of nucleotide interactions (including the non-canonical interactions in all recently revealed families) from the query sequence along with known or predicted canonical basepairs. The preliminary results indicate that in most cases the new method can predict with a high accuracy the nucleotide interactions that constitute the 3D structure of the query sequence. It thus provides a useful tool for the accurate prediction of RNA 3D structure. AVAILABILITY AND IMPLEMENTATION The source package for BkTree is available at http://rna-informatics.uga.edu/index.php?f=software&p=BkTree. CONTACT lding@uga.edu or cai@cs.uga.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | | | - Abdul Samad
- Department of Computer Science, BUITEMS, Pakistan
| | - Russell L Malmberg
- Institute of Bioinformatics and Department of Plant Biology, University of Georgia, GA 30602, USA and
| | - Liming Cai
- Department of Computer Science, Institute of Bioinformatics and
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37
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RNA folding: structure prediction, folding kinetics and ion electrostatics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 827:143-83. [PMID: 25387965 DOI: 10.1007/978-94-017-9245-5_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.
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38
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Samish I, Bourne PE, Najmanovich RJ. Achievements and challenges in structural bioinformatics and computational biophysics. Bioinformatics 2014; 31:146-50. [PMID: 25488929 PMCID: PMC4271151 DOI: 10.1093/bioinformatics/btu769] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Motivation: The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. Results: An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. Conclusion: The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. Contact:Rafael.Najmanovich@USherbrooke.ca
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Affiliation(s)
- Ilan Samish
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada
| | - Philip E Bourne
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada
| | - Rafael J Najmanovich
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel, Ort Braude College, Karmiel, 2161002, Israel, Office of the Director, National Institutes of Health, Bethesda, MD 20814, USA and Department of Biochemistry, University of Sherbrooke, Sherbrooke, J1H 5N4, Canada
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39
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Guilhot-Gaudeffroy A, Froidevaux C, Azé J, Bernauer J. Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities. PLoS One 2014; 9:e108928. [PMID: 25268579 PMCID: PMC4182525 DOI: 10.1371/journal.pone.0108928] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 09/05/2014] [Indexed: 12/03/2022] Open
Abstract
Protein-RNA complexes provide a wide range of essential functions in the cell. Their atomic experimental structure solving, despite essential to the understanding of these functions, is often difficult and expensive. Docking approaches that have been developed for proteins are often challenging to adapt for RNA because of its inherent flexibility and the structural data available being relatively scarce. In this study we adapted the RosettaDock protocol for protein-RNA complexes both at the nucleotide and atomic levels. Using a genetic algorithm-based strategy, and a non-redundant protein-RNA dataset, we derived a RosettaDock scoring scheme able not only to discriminate but also score efficiently docking decoys. The approach proved to be both efficient and robust for generating and identifying suitable structures when applied to two protein-RNA docking benchmarks in both bound and unbound settings. It also compares well to existing strategies. This is the first approach that currently offers a multi-level optimized scoring approach integrated in a full docking suite, leading the way to adaptive fully flexible strategies.
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Affiliation(s)
- Adrien Guilhot-Gaudeffroy
- AMIB Project, Inria Saclay-Île de France, Palaiseau, France
- Laboratoire de Recherche en Informatique (LRI), CNRS UMR 8623, Université Paris-Sud, Orsay, France
- Laboratoire d'Informatique de l'École Polytechnique (LIX), CNRS UMR 7161, École Polytechnique, Palaiseau, France
| | - Christine Froidevaux
- AMIB Project, Inria Saclay-Île de France, Palaiseau, France
- Laboratoire de Recherche en Informatique (LRI), CNRS UMR 8623, Université Paris-Sud, Orsay, France
| | - Jérôme Azé
- AMIB Project, Inria Saclay-Île de France, Palaiseau, France
- Laboratoire de Recherche en Informatique (LRI), CNRS UMR 8623, Université Paris-Sud, Orsay, France
- Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), CNRS UMR 5506, Université Montpellier 2, Montpellier, France
| | - Julie Bernauer
- AMIB Project, Inria Saclay-Île de France, Palaiseau, France
- Laboratoire d'Informatique de l'École Polytechnique (LIX), CNRS UMR 7161, École Polytechnique, Palaiseau, France
- * E-mail:
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40
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Shi YZ, Wang FH, Wu YY, Tan ZJ. A coarse-grained model with implicit salt for RNAs: Predicting 3D structure, stability and salt effect. J Chem Phys 2014; 141:105102. [DOI: 10.1063/1.4894752] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Ya-Zhou Shi
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Feng-Hua Wang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yuan-Yan Wu
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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41
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Faoro C, Ataide SF. Ribonomic approaches to study the RNA-binding proteome. FEBS Lett 2014; 588:3649-64. [PMID: 25150170 DOI: 10.1016/j.febslet.2014.07.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/04/2014] [Accepted: 07/04/2014] [Indexed: 01/23/2023]
Abstract
Gene expression is controlled through a complex interplay among mRNAs, non-coding RNAs and RNA-binding proteins (RBPs), which all assemble along with other RNA-associated factors in dynamic and functional ribonucleoprotein complexes (RNPs). To date, our understanding of RBPs is largely limited to proteins with known or predicted RNA-binding domains. However, various methods have been recently developed to capture an RNA of interest and comprehensively identify its associated RBPs. In this review, we discuss the RNA-affinity purification methods followed by mass spectrometry analysis (AP-MS); RBP screening within protein libraries and computational methods that can be used to study the RNA-binding proteome (RBPome).
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Affiliation(s)
- Camilla Faoro
- School of Molecular Biosciences, University of Sydney, NSW, Australia
| | - Sandro F Ataide
- School of Molecular Biosciences, University of Sydney, NSW, Australia.
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42
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Altaf-Ul-Amin M, Afendi FM, Kiboi SK, Kanaya S. Systems biology in the context of big data and networks. BIOMED RESEARCH INTERNATIONAL 2014; 2014:428570. [PMID: 24982882 PMCID: PMC4058291 DOI: 10.1155/2014/428570] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/08/2014] [Accepted: 05/01/2014] [Indexed: 12/02/2022]
Abstract
Science is going through two rapidly changing phenomena: one is the increasing capabilities of the computers and software tools from terabytes to petabytes and beyond, and the other is the advancement in high-throughput molecular biology producing piles of data related to genomes, transcriptomes, proteomes, metabolomes, interactomes, and so on. Biology has become a data intensive science and as a consequence biology and computer science have become complementary to each other bridged by other branches of science such as statistics, mathematics, physics, and chemistry. The combination of versatile knowledge has caused the advent of big-data biology, network biology, and other new branches of biology. Network biology for instance facilitates the system-level understanding of the cell or cellular components and subprocesses. It is often also referred to as systems biology. The purpose of this field is to understand organisms or cells as a whole at various levels of functions and mechanisms. Systems biology is now facing the challenges of analyzing big molecular biological data and huge biological networks. This review gives an overview of the progress in big-data biology, and data handling and also introduces some applications of networks and multivariate analysis in systems biology.
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43
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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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44
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Magnus M, Matelska D, Łach G, Chojnowski G, Boniecki MJ, Purta E, Dawson W, Dunin-Horkawicz S, Bujnicki JM. Computational modeling of RNA 3D structures, with the aid of experimental restraints. RNA Biol 2014; 11:522-36. [PMID: 24785264 PMCID: PMC4152360 DOI: 10.4161/rna.28826] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/01/2014] [Accepted: 04/08/2014] [Indexed: 11/19/2022] Open
Abstract
In addition to mRNAs whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of RNAs depends on their structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that simulate either the physical process of RNA structure formation ("Greek science" approach) or utilize information derived from known structures of other RNA molecules ("Babylonian science" approach). All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases, the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other. In this work, we review computational approaches for RNA structure prediction, with emphasis on implementations (particular programs) that can utilize restraints derived from experimental analyses. We also list experimental approaches, whose results can be relatively easily used by computational methods. Finally, we describe case studies where computational and experimental analyses were successfully combined to determine RNA structures that would remain out of reach for each of these approaches applied separately.
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Affiliation(s)
- Marcin Magnus
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw, Poland
| | - Dorota Matelska
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw, Poland
| | - Grzegorz Łach
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw, Poland
| | - Grzegorz Chojnowski
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw, Poland
| | - Michal J Boniecki
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw, Poland
| | - Elzbieta Purta
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw, Poland
| | - Wayne Dawson
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw, Poland
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering; International Institute of Molecular and Cell Biology; Warsaw, Poland
- Laboratory of Structural Bioinformatics; Institute of Molecular Biology and Biotechnology; Faculty of Biology; Adam Mickiewicz University; Poznan, Poland
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45
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Graph-based sampling for approximating global helical topologies of RNA. Proc Natl Acad Sci U S A 2014; 111:4079-84. [PMID: 24591615 DOI: 10.1073/pnas.1318893111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A current challenge in RNA structure prediction is the description of global helical arrangements compatible with a given secondary structure. Here we address this problem by developing a hierarchical graph sampling/data mining approach to reduce conformational space and accelerate global sampling of candidate topologies. Starting from a 2D structure, we construct an initial graph from size measures deduced from solved RNAs and junction topologies predicted by our data-mining algorithm RNAJAG trained on known RNAs. We sample these graphs in 3D space guided by knowledge-based statistical potentials derived from bending and torsion measures of internal loops as well as radii of gyration for known RNAs. Graph sampling results for 30 representative RNAs are analyzed and compared with reference graphs from both solved structures and predicted structures by available programs. This comparison indicates promise for our graph-based sampling approach for characterizing global helical arrangements in large RNAs: graph rmsds range from 2.52 to 28.24 Å for RNAs of size 25-158 nucleotides, and more than half of our graph predictions improve upon other programs. The efficiency in graph sampling, however, implies an additional step of translating candidate graphs into atomic models. Such models can be built with the same idea of graph partitioning and build-up procedures we used for RNA design.
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Kielpinski LJ, Vinther J. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility. Nucleic Acids Res 2014; 42:e70. [PMID: 24569351 PMCID: PMC4005689 DOI: 10.1093/nar/gku167] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hydroxyl Radical Footprinting (HRF) is a tried-and-tested method for analysis of the tertiary structure of RNA and for identification of protein footprints on RNA. The hydroxyl radical reaction breaks accessible parts of the RNA backbone, thereby allowing ribose accessibility to be determined by detection of reverse transcriptase termination sites. Current methods for HRF rely on reverse transcription of a single primer and detection by fluorescent fragments by capillary electrophoresis. Here, we describe an accurate and efficient massive parallel-sequencing-based method for probing RNA accessibility with hydroxyl radicals, called HRF-Seq. Using random priming and a novel barcoding scheme, we show that HRF-Seq dramatically increases the throughput of HRF experiments and facilitates the parallel analysis of multiple RNAs or experimental conditions. Moreover, we demonstrate that HRF-Seq data for the Escherichia coli 16S rRNA correlates well with the ribose accessible surface area as determined by X-ray crystallography and have a resolution that readily allows the difference in accessibility caused by exposure of one side of RNA helices to be observed.
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Affiliation(s)
- Lukasz Jan Kielpinski
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
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Harrison JG, Zheng YB, Beal PA, Tantillo DJ. Computational approaches to predicting the impact of novel bases on RNA structure and stability. ACS Chem Biol 2013; 8:2354-9. [PMID: 24063428 DOI: 10.1021/cb4006062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The use of computational modeling techniques to gain insight into nucleobase interactions has been a challenging endeavor to date. Accurate treatment requires the tackling of many challenges but also holds the promise of great rewards. The development of effective computational approaches to predict the binding affinities of nucleobases and analogues can, for example, streamline the process of developing novel nucleobase modifications, which should facilitate the development of new RNAi-based therapeutics. This brief review focuses on available computational approaches to predicting base pairing affinity in RNA-based contexts such as nucleobase-nucleobase interactions in duplexes and nucleobase-protein interactions. The challenges associated with such modeling along with potential future directions for the field are highlighted.
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Affiliation(s)
- Jason G. Harrison
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Yvonne B. Zheng
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Peter A. Beal
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
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Somarowthu S, Legiewicz M, Keating KS, Pyle AM. Visualizing the ai5γ group IIB intron. Nucleic Acids Res 2013; 42:1947-58. [PMID: 24203709 PMCID: PMC3919574 DOI: 10.1093/nar/gkt1051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has become apparent that much of cellular metabolism is controlled by large well-folded noncoding RNA molecules. In addition to crystallographic approaches, computational methods are needed for visualizing the 3D structure of large RNAs. Here, we modeled the molecular structure of the ai5γ group IIB intron from yeast using the crystal structure of a bacterial group IIC homolog. This was accomplished by adapting strategies for homology and de novo modeling, and creating a new computational tool for RNA refinement. The resulting model was validated experimentally using a combination of structure-guided mutagenesis and RNA structure probing. The model provides major insights into the mechanism and regulation of splicing, such as the position of the branch-site before and after the second step of splicing, and the location of subdomains that control target specificity, underscoring the feasibility of modeling large functional RNA molecules.
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Affiliation(s)
- Srinivas Somarowthu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA, Department of Chemistry, Yale University, New Haven, CT 06511, USA and Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Treat cancers by targeting survivin: Just a dream or future reality? Cancer Treat Rev 2013; 39:802-11. [DOI: 10.1016/j.ctrv.2013.02.002] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/29/2013] [Accepted: 02/02/2013] [Indexed: 12/14/2022]
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50
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Large-scale study of long non-coding RNA functions based on structure and expression features. SCIENCE CHINA-LIFE SCIENCES 2013; 56:953-9. [PMID: 24091687 DOI: 10.1007/s11427-013-4556-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/02/2013] [Indexed: 02/01/2023]
Abstract
Mammals and other complex organisms can transcribe an abundance of long non-coding RNAs (lncRNAs) that fulfill a wide variety of regulatory roles in many biological processes. These roles, including as scaffolds and as guides for protein-coding genes, mainly depend on the structure and expression level of lncRNAs. In this review, we focus on the current methods for analyzing lncRNA structure and expression, which is basic but necessary information for in-depth, large-scale analysis of lncRNA functions.
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