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Xu X, Chen SJ. Hierarchical Assembly of RNA Three-Dimensional Structures Based on Loop Templates. J Phys Chem B 2018; 122:5327-5335. [PMID: 29258305 DOI: 10.1021/acs.jpcb.7b10102] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The current RNA structure prediction methods cannot keep up the pace of the rapidly increasing number of sequences and the emerging new functions of RNAs. Template-based RNA three-dimensional structure prediction methods are restricted by the limited number of known RNA structures, and traditional motif-based search for the templates does not always lead to successful results. Here we report a new template search and assembly algorithm, the hierarchical loop template-assembly method (VfoldLA). The method searches for templates for single strand loop/junctions instead of the whole motifs, which often renders no available templates, or short fragments (several nucleotides), which requires a long computational time to assemble and refine. The VfoldLA method has the advantage of accounting for local and nonlocal interloop interactions. Benchmark tests indicate that this new method can provide low-resolution predictions for RNA conformations at different levels of structural complexities. Furthermore, the VfoldLA-predicted conformations may also serve as reliable putative models for further structure prediction and refinements. VfoldLA is accessible at http://rna.physics.missouri.edu/vfoldLA .
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Affiliation(s)
- Xiaojun Xu
- Institute of Bioinformatics and Medical Engineering , Jiangsu University of Technology , Changzhou , Jiangsu 213001 , China.,Department of Physics, Department of Biochemistry, and Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute , University of Missouri , Columbia , Missouri 65211 , United States
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2
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Abstract
Despite the success of RNA secondary structure prediction for simple, short RNAs, the problem of predicting RNAs with long-range tertiary folds remains. Furthermore, RNA 3D structure prediction is hampered by the lack of the knowledge about the tertiary contacts and their thermodynamic parameters. Low-resolution structural modeling enables us to estimate the conformational entropies for a number of tertiary folds through rigorous statistical mechanical calculations. The models lead to 3D tertiary folds at coarse-grained level. The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures. In this paper, we present an overview of RNA computational models for secondary and tertiary structures’ predictions and then focus on a recently developed RNA statistical mechanical model—the Vfold model. The main emphasis is placed on the physics behind the models, including the treatment of the non-canonical interactions in secondary and tertiary structure modelings, and the correlations to RNA functions.
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Affiliation(s)
- Xiaojun Xu
- />Department of Physics, University of Missouri, Columbia, MO 65211 USA
- />Department of Biochemistry, University of Missouri, Columbia, MO 65211 USA
- />Informatics Institute, University of Missouri, Columbia, MO 65211 USA
| | - Shi-Jie Chen
- />Department of Physics, University of Missouri, Columbia, MO 65211 USA
- />Department of Biochemistry, University of Missouri, Columbia, MO 65211 USA
- />Informatics Institute, University of Missouri, Columbia, MO 65211 USA
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3
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Xia Z, Bell DR, Shi Y, Ren P. RNA 3D structure prediction by using a coarse-grained model and experimental data. J Phys Chem B 2013; 117:3135-44. [PMID: 23438338 DOI: 10.1021/jp400751w] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
RNAs form complex secondary and three-dimensional structures, and their biological functions highly rely on their structures and dynamics. Here we developed a general coarse-grained framework for RNA 3D structure prediction. A new, hybrid coarse-grained model that explicitly describes the electrostatics and hydrogen-bond interactions has been constructed based on experimental structural statistics. With the simulated annealing simulation protocol, several RNAs of less than 30-nt were folded to within 4.0 Å of the native structures. In addition, with limited restraints on Watson-Crick basepairing based on the data from NMR spectroscopy and small-angle X-ray scattering (SAXS) information, the current model was able to characterize the complex tertiary structures of large size RNAs, such as 5S ribosome and U2/U6 snRNA. We also demonstrated that the pseudoknot structure was better captured when the coordinating Mg(2+) cations and limited basepairing restraints were included. The accuracy of our model has been compared favorably with other RNA structure prediction methods presented in the previous study of RNA-Puzzles. Therefore the coarse-grained model presented here offers a unique approach for accurate prediction and modeling of RNA structures.
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Affiliation(s)
- Zhen Xia
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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4
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Zhang J, Bian Y, Lin H, Wang W. RNA fragment modeling with a nucleobase discrete-state model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:021909. [PMID: 22463246 DOI: 10.1103/physreve.85.021909] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 12/30/2011] [Indexed: 05/24/2023]
Abstract
In this work we develop an approach for predicting the tertiary structures of RNA fragments by combining an RNA nucleobase discrete state (RNAnbds) model, a sequential Monte Carlo method, and a statistical potential. The RNAnbds model is designed for optimizing the configuration of nucleobases with respect to their preceding ones along the sequence and their spatial neighbors, in contrast to previous works that focus on RNA backbones. The tests of our approach with the fragments taken from a small RNA pseudoknot and a 23S ribosome RNA show that for short fragments (<10 nucleotides), the root mean square deviations (RMSDs) between the predicted and the experimental ones are generally smaller than 3 Å; for slightly longer fragments (10-15 nucleotides), most RMSDs are smaller than 4 Å. The comparison of our method with another physics-based predictor with a testing set containing nine loops shows that ours is superior in both accuracy and efficiency. Our approach is useful in facilitating RNA three-dimensional structure prediction as well as loop modeling. It also holds the promise of providing insight into the structural ensembles of RNA loops.
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Affiliation(s)
- Jian Zhang
- National Laboratory of Solid State Microstructure and School of Business, Nanjing University, China
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5
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Xia Z, Gardner DP, Gutell RR, Ren P. Coarse-grained model for simulation of RNA three-dimensional structures. J Phys Chem B 2010; 114:13497-506. [PMID: 20883011 PMCID: PMC2989335 DOI: 10.1021/jp104926t] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The accurate prediction of an RNA's three-dimensional structure from its "primary structure" will have a tremendous influence on the experimental design and its interpretation and ultimately our understanding of the many functions of RNA. This paper presents a general coarse-grained (CG) potential for modeling RNA 3-D structures. Each nucleotide is represented by five pseudo atoms, two for the backbone (one for the phosphate and another for the sugar) and three for the base to represent base-stacking interactions. The CG potential has been parametrized from statistical analysis of 688 RNA experimental structures. Molecular dynamic simulations of 15 RNA molecules with the length of 12-27 nucleotides have been performed using the CG potential, with performance comparable to that from all-atom simulations. For ~75% of systems tested, simulated annealing led to native-like structures at least once out of multiple repeated runs. Furthermore, with weak distance restraints based on the knowledge of three to five canonical Watson-Crick pairs, all 15 RNAs tested are successfully folded to within 6.5 Å of native structures using the CG potential and simulated annealing. The results reveal that with a limited secondary structure model the current CG potential can reliably predict the 3-D structures for small RNA molecules. We also explored an all-atom force field to construct atomic structures from the CG simulations.
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Affiliation(s)
- Zhen Xia
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
| | - David Paul Gardner
- Section of Integrative Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, TX 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX 78712
| | - Robin R. Gutell
- Section of Integrative Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, TX 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX 78712
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, TX 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX 78712
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6
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Joung IS, Persil Çetinkol Ö, Hud NV, Cheatham TE. Molecular dynamics simulations and coupled nucleotide substitution experiments indicate the nature of A{middle dot}A base pairing and a putative structure of the coralyne-induced homo-adenine duplex. Nucleic Acids Res 2009; 37:7715-27. [PMID: 19850721 PMCID: PMC2794157 DOI: 10.1093/nar/gkp730] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 08/17/2009] [Accepted: 08/19/2009] [Indexed: 01/18/2023] Open
Abstract
Coralyne is an alkaloid drug that binds homo-adenine DNA (and RNA) oligonucleotides more tightly than it does Watson-Crick DNA. Hud's laboratory has shown that poly(dA) in the presence of coralyne forms an anti-parallel duplex, however attempts to determine the structure by NMR spectroscopy and X-ray crystallography have been unsuccessful. Assuming adenine-adenine hydrogen bonding between the two poly(dA) strands, we constructed 40 hypothetical homo-(dA) anti-parallel duplexes and docked coralyne into the six most favorable duplex structures. The two most stable structures had trans glycosidic bonds, but distinct pairing geometries, i.e. either Watson-Crick Hoogsteen (transWH) or Watson-Crick Watson-Crick (transWW) with stability of transWH > transWW. To narrow down the possibilities, 7-deaza adenine base substitutions (dA-->7) were engineered into homo-(dA) sequences. These substitutions significantly reduced the thermal stability of the coralyne-induced homo-(dA) structure. These experiments strongly suggest the involvement of N7 in the coralyne-induced A.A base pairs. Moreover, due to the differential effect on melting as a function of the location of the dA-->7 mutations, these results are consistent with the N1-N7 base pairing of the transWH pairs. Together, the simulation and base substitution experiments predict that the coralyne-induced homo-(dA) duplex structure adopts the transWH geometry.
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Affiliation(s)
- In Suk Joung
- Department of Bioengineering, College of Engineering, University of Utah, Salt Lake City, UT 84112, School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, Department of Medicinal Chemistry and Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Özgül Persil Çetinkol
- Department of Bioengineering, College of Engineering, University of Utah, Salt Lake City, UT 84112, School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, Department of Medicinal Chemistry and Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Nicholas V. Hud
- Department of Bioengineering, College of Engineering, University of Utah, Salt Lake City, UT 84112, School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, Department of Medicinal Chemistry and Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Thomas E. Cheatham
- Department of Bioengineering, College of Engineering, University of Utah, Salt Lake City, UT 84112, School of Chemistry and Biochemistry, Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332-0400, Department of Medicinal Chemistry and Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
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7
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Das R, Baker D. Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci U S A 2007; 104:14664-9. [PMID: 17726102 PMCID: PMC1955458 DOI: 10.1073/pnas.0703836104] [Citation(s) in RCA: 328] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Indexed: 11/18/2022] Open
Abstract
RNA tertiary structure prediction has been based almost entirely on base-pairing constraints derived from phylogenetic covariation analysis. We describe here a complementary approach, inspired by the Rosetta low-resolution protein structure prediction method, that seeks the lowest energy tertiary structure for a given RNA sequence without using evolutionary information. In a benchmark test of 20 RNA sequences with known structure and lengths of approximately 30 nt, the new method reproduces better than 90% of Watson-Crick base pairs, comparable with the accuracy of secondary structure prediction methods. In more than half the cases, at least one of the top five models agrees with the native structure to better than 4 A rmsd over the backbone. Most importantly, the method recapitulates more than one-third of non-Watson-Crick base pairs seen in the native structures. Tandem stacks of "sheared" base pairs, base triplets, and pseudoknots are among the noncanonical features reproduced in the models. In the cases in which none of the top five models were native-like, higher energy conformations similar to the native structures are still sampled frequently but not assigned low energies. These results suggest that modest improvements in the energy function, together with the incorporation of information from phylogenetic covariance, may allow confident and accurate structure prediction for larger and more complex RNA chains.
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Affiliation(s)
- Rhiju Das
- Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Box 357350, Seattle, WA 98195
| | - David Baker
- Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Box 357350, Seattle, WA 98195
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8
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Shapiro BA, Yingling YG, Kasprzak W, Bindewald E. Bridging the gap in RNA structure prediction. Curr Opin Struct Biol 2007; 17:157-65. [PMID: 17383172 DOI: 10.1016/j.sbi.2007.03.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 01/11/2007] [Accepted: 03/12/2007] [Indexed: 11/24/2022]
Abstract
The field of RNA structure prediction has experienced significant advances in the past several years, thanks to the availability of new experimental data and improved computational methodologies. These methods determine RNA secondary structures and pseudoknots from sequence alignments, thermodynamics-based dynamic programming algorithms, genetic algorithms and combined approaches. Computational RNA three-dimensional modeling uses this information in conjunction with manual manipulation, constraint satisfaction methods, molecular mechanics and molecular dynamics. The ultimate goal of automatically producing RNA three-dimensional models from given secondary and tertiary structure data, however, is still not fully realized. Recent developments in the computational prediction of RNA structure have helped bridge the gap between RNA secondary structure prediction, including pseudoknots, and three-dimensional modeling of RNA.
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Affiliation(s)
- Bruce A Shapiro
- Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA.
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9
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Gavory G, Symmons MF, Ghosh YK, Klenerman D, Balasubramanian S. Structural analysis of the catalytic core of human telomerase RNA by FRET and molecular modeling. Biochemistry 2006; 45:13304-11. [PMID: 17073451 PMCID: PMC2196208 DOI: 10.1021/bi061150a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Telomerase is the ribonucleoprotein reverse transcriptase involved in the maintenance of the telomeres, the termini of eukaryotic chromosomes. The RNA component of human telomerase (hTR) consists of 451 nucleotides with the 5' half folding into a highly conserved catalytic core comprising the template region and an adjacent pseudoknot domain (nucleotides 1-208). While the secondary structure of hTR is established, there is little understanding of its three-dimensional (3D) architecture. Here, we have used fluorescence resonance energy transfer (FRET) between fluorescently labelled peptide nucleic acids, hybridized to defined single stranded regions of full length hTR, to evaluate long-range distances. Using molecular modeling, the distance constraints derived by FRET were subsequently used, together with the known secondary structure, to generate a 3D model of the catalytic core of hTR. An overlay of a large set of models generated has provided a low-resolution structure (6.5-8.0 A) that can readily be refined as new structural information becomes available. A notable feature of the modeled structure is the positioning of the template adjacent to the pseudoknot, which brings a number of conserved nucleotides close in space.
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Affiliation(s)
- Gérald Gavory
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Martyn F. Symmons
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, U.K
| | | | - David Klenerman
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Shankar Balasubramanian
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, U.K
- To whom correspondence should be addressed. Tel: +44-1223-336347. Fax: +44-1223-336362. E-mail:
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11
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12
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Seo HS, Cooperman BS. Large-scale motions within ribosomal 50S subunits as demonstrated using photolabile oligonucleotides. Bioorg Chem 2002; 30:163-87. [PMID: 12406702 DOI: 10.1006/bioo.2002.1255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Photolabile oligonucleotides (PHONTs) bind to rRNA sequences to which they are complementary and, on photolysis, incorporate into neighboring ribosomal components. Here we report on photocrosslinking results obtained with PHONTs targeting 23S rRNA nucleotides 1882-1892, in the long lateral arm of the 50S subunit (PHONT 1892), and 1085-1093, in the L11 binding domain (PHONT 1093). Photolysis of the PHONT 1892.50S and PHONT 1093.50S complexes leads to formation of 'long-range' crosslinks from C1892 to U1094/A1095 and G1950, and from G1093 to U1712/1716 and U1926, that are clearly incompatible with published crystal structures of 50S subunits. These results provide strong evidence that within the 50S subunit (a) the L11 binding domain can extend in an arm-like fashion, accessing large areas of the ribosome, and (b) the lateral arm can bend about the noncanonical helix at its center. Such motions may have functional relevance in identifying regions that undergo major conformational change as the ribosome moves through its catalytic cycle.
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Affiliation(s)
- Hyuk-Soo Seo
- Department of Chemistry, University of Pennsylvania, Philadelphia, 19104, USA
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Dolan MA, Babin P, Wollenzien P. Construction and analysis of base-paired regions of the 16S rRNA in the 30S ribosomal subunit determined by constraint satisfaction molecular modelling. J Mol Graph Model 2002; 19:495-513. [PMID: 11552678 DOI: 10.1016/s1093-3263(00)00097-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Structure models for each of the secondary structure regions from the Escherichia coli 16S rRNA (58 separate elements) were constructed using a constraint satisfaction modelling program to determine which helices deviated from classic A-form geometry. Constraints for each rRNA element included the comparative secondary structure, H-bonding conformations predicted from patterns of base-pair covariation, tertiary interactions predicted from covariation analysis, chemical probing data, rRNA-rRNA crosslinking information, and coordinates from solved structures. Models for each element were built using the MC-SYM modelling algorithm and subsequently were subjected to energy minimization to correct unfavorable geometry. Approximately two-thirds of the structures that result from the input data are very similar to A-form geometry. In the remaining instances, the presence of internal loops and bulges, some sequences (and sequence covariants) and accessory information require deviation from A-form geometry. The structures of regions containing more complex base-pairing arrangements including the central pseudoknot, the 530 region, and the pseudoknot involving base-pairing between G570-U571/A865-C866 and G861-C862/G867-C868 were predicted by this approach. These molecular models provide insight into the connection between patterns of H-bonding, the presence of unpaired nucleotides, and the overall geometry of each element.
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Affiliation(s)
- M A Dolan
- Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-762, USA
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Metzler DE, Metzler CM, Sauke DJ. Ribosomes and the Synthesis of Proteins. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Auerbach T, Pioletti M, Avila H, Anagnostopoulos K, Weinstein S, Franceschi F, Yonath A. Genetic and biochemical manipulations of the small ribosomal subunit from Thermus thermophilus HB8. J Biomol Struct Dyn 2000; 17:617-28. [PMID: 10698100 DOI: 10.1080/07391102.2000.10506553] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Crystals of the small ribosomal subunit from Thermus thermophilus diffract to 3A and exhibit reasonable isomorphism and moderate resistance to irradiation. A 5A MIR map of this particle shows a similar shape to the part assigned to this particle within the cryo-EM reconstructions of the whole ribosome and contains regions interpretable either as RNA chains or as protein motifs. To assist phasing at higher resolution we introduced recombinant methods aimed at extensive selenation for MAD phasing. We are focusing on several ribosomal proteins that can be quantitatively detached by chemical means. These proteins can be modified and subsequently reconstituted into depleted ribosomal cores. They also can be used for binding heavy atoms, by incorporating chemically reactive binding sites, such as -SH groups, into them. In parallel we are co-crystallizing the ribosomal particles with tailor made ligands, such as antibiotics or cDNA to which heavy-atoms have been attached or diffuse the latter compounds into already formed crystals.
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Affiliation(s)
- T Auerbach
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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Tocilj A, Schlünzen F, Janell D, Glühmann M, Hansen HA, Harms J, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A. The small ribosomal subunit from Thermus thermophilus at 4.5 A resolution: pattern fittings and the identification of a functional site. Proc Natl Acad Sci U S A 1999; 96:14252-7. [PMID: 10588692 PMCID: PMC24423 DOI: 10.1073/pnas.96.25.14252] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The electron density map of the small ribosomal subunit from Thermus thermophilus, constructed at 4.5 A resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal RNA and proteins. Unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein S13 at a position compatible with previous assignments, whereas the surface of S11 was localized at a distance of about twice its diameter from the site suggested for its center by neutron scattering. Proteins S5 and S7, whose structures have been determined crystallographically, were visually placed in the map with no alterations in their conformations. Regions suitable to host the fold of protein S15 were detected in several positions, all at a significant distance from the location of this protein in the neutron scattering map. Targeting the 16S RNA region, where mRNA docks to allow the formation of the initiation complex by a mercurated mRNA analog, led to the characterization of its vicinity.
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Affiliation(s)
- A Tocilj
- Max Planck Research Unit for Ribosomal Structure, 22603 Hamburg, Germany
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Bukhtiyarov Y, Druzina Z, Cooperman BS. Identification of 23S rRNA nucleotides neighboring the P-loop in the Escherichia coli 50S subunit. Nucleic Acids Res 1999; 27:4376-84. [PMID: 10536145 PMCID: PMC148719 DOI: 10.1093/nar/27.22.4376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the synthesis of a radioactive, photolabile 2'-O-methyloligoRNA probe, 2258-53/52(SAz)-48, PHONT1, and its exploitation in identifying 23S rRNA nucleotides neighboring the so-called 'P-loop'. The probe is complementary to nt 2248-2258 in Escherichia coli 50S subunits. PHONT1 contains a p-azidophenacyl group attached to a phosphorothioate bridge between the nucleotides complementary to the positions 2252-2253, such that the photogenerated nitrene is maximally 17-19 A from 23S RNA nucleotides G2252 and G2253. PHONT1 binds to the 50S subunit, and photoincorporates within or immediately adjacent to its target site, as well as into several nucleotides falling between G2357 and A2430. The significance of these results for the structure of the peptidyl transferase center is considered. The PHONT approach is generally applicable to studies of complex RNA-containing molecules.
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Affiliation(s)
- Y Bukhtiyarov
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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