1
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Imperatore JA, Then ML, McDougal KB, Mihailescu MR. Characterization of a G-Quadruplex Structure in Pre-miRNA-1229 and in Its Alzheimer's Disease-Associated Variant rs2291418: Implications for miRNA-1229 Maturation. Int J Mol Sci 2020; 21:ijms21030767. [PMID: 31991575 PMCID: PMC7037302 DOI: 10.3390/ijms21030767] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/15/2022] Open
Abstract
Alzheimer's disease (AD), the most common age-related neurodegenerative disease, is associated with various forms of cognitive and functional impairment that worsen with disease progression. AD is typically characterized as a protein misfolding disease, in which abnormal plaques form due to accumulation of tau and β-amyloid (Aβ) proteins. An assortment of proteins is responsible for the processing and trafficking of Aβ, including sortilin-related receptor 1 (SORL1). Recently, a genome-wide association study of microRNA-related variants found that a single nucleotide polymorphism (SNP) rs2291418 within premature microRNA-1229 (pre-miRNA-1229) is significantly associated with AD. Moreover, the levels of the mature miRNA-1229-3p, which has been shown to regulate the SORL1 translation, are increased in the rs2291418 pre-miRNA-1229 variant. In this study we used various biophysical techniques to show that pre-miRNA-1229 forms a G-quadruplex secondary structure that coexists in equilibrium with the canonical hairpin structure, potentially controlling the production of the mature miR-1229-3p, and furthermore, that the AD-associated SNP rs2291418 pre-miR-1229 changes the equilibrium between these structures. Thus, the G-quadruplex structure we identified within pre-miRNA-1229 could potentially act as a novel therapeutic target in AD.
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2
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Bergonzo C, Grishaev A. Maximizing accuracy of RNA structure in refinement against residual dipolar couplings. JOURNAL OF BIOMOLECULAR NMR 2019; 73:117-139. [PMID: 31049778 DOI: 10.1007/s10858-019-00236-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
Structural information about ribonucleic acid (RNA) is lagging behind that of proteins, in part due to its high charge and conformational variability. Molecular dynamics (MD) has played an important role in describing RNA structure, complementing information from both nuclear magnetic resonance (NMR), or X-ray crystallography. We examine the impact of the choice of the empirical force field for RNA structure refinement using cross-validation against residual dipolar couplings (RDCs) as structural accuracy reporter. Four force fields, representing both the state-of-the art in RNA simulation and the most popular selections in NMR structure determination, are compared for a prototypical A-RNA helix. RNA structural accuracy is also evaluated as a function of both density and nature of input NMR data including RDCs, anisotropic chemical shifts, and distance restraints. Our results show a complex interplay between the experimental restraints and the force fields indicating two best-performing choices: high-fidelity refinement in explicit solvent, and the conformational database-derived potentials. Accuracy of RNA models closely tracks the density of 1-bond C-H RDCs, with other data types having beneficial, but smaller effects. At lower RDC density, or when refining against NOEs only, the two selected force fields are capable of accurately describing RNA helices with little or no experimental RDC data, making them available for the higher order structure assembly or better quantification of the intramolecular dynamics. Unrestrained simulations of simple RNA motifs with state-of-the art MD force fields appear to capture the flexibility inherent in nucleic acids while also maintaining a good agreement with the experimental observables.
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Affiliation(s)
- Christina Bergonzo
- National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Alexander Grishaev
- National Institute of Standards and Technology and Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
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3
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 327] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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4
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Havrila M, Zgarbová M, Jurečka P, Banáš P, Krepl M, Otyepka M, Šponer J. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields. J Phys Chem B 2015; 119:15176-90. [DOI: 10.1021/acs.jpcb.5b08876] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marek Havrila
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Marie Zgarbová
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
- CEITEC
- Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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5
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Abstract
![]()
Influenza A is an RNA virus with
a genome of eight negative sense
segments. Segment 7 mRNA contains a 3′ splice site for alternative
splicing to encode the essential M2 protein. On the basis of sequence
alignment and chemical mapping experiments, the secondary structure
surrounding the 3′ splice site has an internal loop, adenine
bulge, and hairpin loop when it is in the hairpin conformation that
exposes the 3′ splice site. We report structural features of
a three-dimensional model of the hairpin derived from nuclear magnetic
resonance spectra and simulated annealing with restrained molecular
dynamics. Additional insight was provided by modeling based on 1H chemical shifts. The internal loop containing the 3′
splice site has a dynamic guanosine and a stable imino (cis Watson–Crick/Watson–Crick) GA pair. The adenine bulge
also appears to be dynamic with the A either stacked in the stem or
forming a base triple with a Watson–Crick GC pair. The hairpin
loop is a GAAA tetraloop closed by an AC pair.
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Affiliation(s)
- Jonathan L Chen
- †Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Scott D Kennedy
- ‡Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Douglas H Turner
- †Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,§Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
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6
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Zhong Z, Soh LH, Lim MH, Chen G. A U⋅U Pair-to-U⋅C Pair Mutation-Induced RNA Native Structure Destabilisation and Stretching-Force-Induced RNA Misfolding. Chempluschem 2015; 80:1267-1278. [PMID: 31973291 DOI: 10.1002/cplu.201500144] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 04/21/2015] [Indexed: 12/21/2022]
Abstract
Little is known about how a non-Watson-Crick pair affects the RNA folding dynamics. We studied the effects of a U⋅U-to-U⋅C pair mutation on the folding of a hairpin in human telomerase RNA. The ensemble thermal melting of the hairpins shows an on-pathway intermediate with the disruption of the internal loop structure containing the U⋅U/U⋅C pairs. By using optical tweezers, we applied a stretching force on the terminal ends of the hairpins to probe directly the non-nearest-neighbour effects upon the mutations. The single U⋅U to U⋅C mutations are observed to 1) lower the mechanical unfolding force by approximately 1 picoNewton (pN) per mutation without affecting the unfolding reaction transition-state position (thus suggesting that removing a single hydrogen bond affects the structural dynamics at least two base pairs away), 2) result in more frequent misfolding into a small hairpin at approximately 10 pN and 3) shift the folding reaction transition-state position towards the native hairpin structure and slightly increase the mechanical folding kinetics (thus suggesting that untrapping from the misfolded state is not the rate-limiting step).
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Affiliation(s)
- Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore), Fax: (+65) 6791-1961
| | - Lai Huat Soh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore), Fax: (+65) 6791-1961
| | - Ming Hui Lim
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore), Fax: (+65) 6791-1961
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371 (Singapore), Fax: (+65) 6791-1961
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7
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Abstract
RNA dynamics play a fundamental role in many cellular functions. However, there is no general framework to describe these complex processes, which typically consist of many structural maneuvers that occur over timescales ranging from picoseconds to seconds. Here, we classify RNA dynamics into distinct modes representing transitions between basins on a hierarchical free-energy landscape. These transitions include large-scale secondary-structural transitions at >0.1-s timescales, base-pair/tertiary dynamics at microsecond-to-millisecond timescales, stacking dynamics at timescales ranging from nanoseconds to microseconds, and other "jittering" motions at timescales ranging from picoseconds to nanoseconds. We review various modes within these three different tiers, the different mechanisms by which they are used to regulate function, and how they can be coupled together to achieve greater functional complexity.
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8
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šponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 2012; 57:25-39. [PMID: 22525788 PMCID: PMC3775459 DOI: 10.1016/j.ymeth.2012.04.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/29/2022] Open
Abstract
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
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Affiliation(s)
- Jiří šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Xiaohui Cang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, 2000 East 30 South, University of Utah, Salt Lake City, UT 84112, United States
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9
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Bizarro CV, Alemany A, Ritort F. Non-specific binding of Na+ and Mg2+ to RNA determined by force spectroscopy methods. Nucleic Acids Res 2012; 40:6922-35. [PMID: 22492710 PMCID: PMC3413104 DOI: 10.1093/nar/gks289] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of monovalent and multivalent ions on RNA stability, and the thermodynamic parameters for secondary structure prediction have only been derived at 1M [Na(+)]. Here, by mechanically unfolding and folding a 20 bp RNA hairpin using optical tweezers, we study the RNA thermodynamics and kinetics at different monovalent and mixed monovalent/Mg(2+) salt conditions. We measure the unfolding and folding rupture forces and apply Kramers theory to extract accurate information about the hairpin free energy landscape under tension at a wide range of ionic conditions. We obtain non-specific corrections for the free energy of formation of the RNA hairpin and measure how the distance of the transition state to the folded state changes with force and ionic strength. We experimentally validate the Tightly Bound Ion model and obtain values for the persistence length of ssRNA. Finally, we test the approximate rule by which the non-specific binding affinity of divalent cations at a given concentration is equivalent to that of monovalent cations taken at 100-fold concentration for small molecular constructs.
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Affiliation(s)
- C V Bizarro
- Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain
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10
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Mustoe AM, Bailor MH, Teixeira RM, Brooks CL, Al-Hashimi HM. New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Res 2011; 40:892-904. [PMID: 21937512 PMCID: PMC3258142 DOI: 10.1093/nar/gkr751] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent studies have shown that topological constraints encoded at the RNA secondary structure level involving basic steric and stereochemical forces can significantly restrict the orientations sampled by helices across two-way RNA junctions. Here, we formulate these topological constraints in greater quantitative detail and use this topological framework to rationalize long-standing but poorly understood observations regarding the basic behavior of RNA two-way junctions. Notably, we show that the asymmetric nature of the A-form helix and the finite length of a bulge provide a physical basis for the experimentally observed directionality and bulge-length amplitude dependence of bulge induced inter-helical bends. We also find that the topologically allowed space can be modulated by variations in sequence, particularly with the addition of non-canonical GU base pairs at the junction, and, surprisingly, by the length of the 5′ and 3′ helices. A survey of two-way RNA junctions in the protein data bank confirms that junction residues have a strong preference to adopt looped-in, non-canonically base-paired conformations, providing a route for extending our bulge-directed framework to internal loop motifs and implying a simplified link between secondary and tertiary structure. Finally, our results uncover a new simple mechanism for coupling junction-induced topological constraints with tertiary interactions.
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Affiliation(s)
- Anthony M Mustoe
- Departments of Chemistry & Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109-1055, USA
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11
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Lerman YV, Kennedy SD, Shankar N, Parisien M, Major F, Turner DH. NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions. RNA (NEW YORK, N.Y.) 2011; 17:1664-77. [PMID: 21778280 PMCID: PMC3162332 DOI: 10.1261/rna.2641911] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 05/08/2011] [Indexed: 05/31/2023]
Abstract
The NMR solution structure is reported of a duplex, 5'GUGAAGCCCGU/3'UCACAGGAGGC, containing a 4 × 4 nucleotide internal loop from an R2 retrotransposon RNA. The loop contains three sheared purine-purine pairs and reveals a structural element found in other RNAs, which we refer to as the 3RRs motif. Optical melting measurements of the thermodynamics of the duplex indicate that the internal loop is 1.6 kcal/mol more stable at 37°C than predicted. The results identify the 3RRs motif as a common structural element that can facilitate prediction of 3D structure. Known examples include internal loops having the pairings: 5'GAA/3'AGG, 5'GAG/3'AGG, 5'GAA/3'AAG, and 5'AAG/3'AGG. The structural information is compared with predictions made with the MC-Sym program.
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Affiliation(s)
- Yelena V. Lerman
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
| | - Scott D. Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Neelaabh Shankar
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Marc Parisien
- Department of Computer Science and Operations Research, University of Montreal, Montreal, Quebec H3C CJ7, Canada
| | - Francois Major
- Department of Computer Science and Operations Research, University of Montreal, Montreal, Quebec H3C CJ7, Canada
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
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12
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Gardner DP, Ren P, Ozer S, Gutell RR. Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure. J Mol Biol 2011; 413:473-83. [PMID: 21889515 DOI: 10.1016/j.jmb.2011.08.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 08/12/2011] [Accepted: 08/16/2011] [Indexed: 01/19/2023]
Abstract
RNA is directly associated with a growing number of functions within the cell. The accurate prediction of different RNA higher-order structures from their nucleic acid sequences will provide insight into their functions and molecular mechanics. We have been determining statistical potentials for a collection of structural elements that is larger than the number of structural elements determined with experimentally determined energy values. The experimentally derived free energies and the statistical potentials for canonical base-pair stacks are analogous, demonstrating that statistical potentials derived from comparative data can be used as an alternative energetic parameter. A new computational infrastructure-RNA Comparative Analysis Database (rCAD)-that utilizes a relational database was developed to manipulate and analyze very large sequence alignments and secondary-structure data sets. Using rCAD, we determined a richer set of energetic parameters for RNA fundamental structural elements including hairpin and internal loops. A new version of RNAfold was developed to utilize these statistical potentials. Overall, these new statistical potentials for hairpin and internal loops integrated into the new version of RNAfold demonstrated significant improvements in the prediction accuracy of RNA secondary structure.
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Affiliation(s)
- David P Gardner
- Center for Computational Biology and Bioinformatics, Section of Integrative Biology in the School of Biological Sciences, University of Texas at Austin, Austin, TX 78712, USA
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13
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Sklenovský P, Florová P, Banáš P, Réblová K, Lankaš F, Otyepka M, Šponer J. Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs. J Chem Theory Comput 2011; 7:2963-80. [PMID: 26605485 DOI: 10.1021/ct200204t] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Reverse kink-turn is a recurrent elbow-like RNA building block occurring in the ribosome and in the group I intron. Its sequence signature almost matches that of the conventional kink-turn. However, the reverse and conventional kink-turns have opposite directions of bending. The reverse kink-turn lacks basically any tertiary interaction between its stems. We report unrestrained, explicit solvent molecular dynamics simulations of ribosomal and intron reverse kink-turns (54 simulations with 7.4 μs of data in total) with different variants (ff94, ff99, ff99bsc0, ff99χOL, and ff99bsc0χOL) of the Cornell et al. force field. We test several ion conditions and two water models. The simulations characterize the directional intrinsic flexibility of reverse kink-turns pertinent to their folded functional geometries. The reverse kink-turns are the most flexible RNA motifs studied so far by explicit solvent simulations which are capable at the present simulation time scale to spontaneously and reversibly sample a wide range of geometries from tightly kinked ones through flexible intermediates up to extended, unkinked structures. A possible biochemical role of the flexibility is discussed. Among the tested force fields, the latest χOL variant is essential to obtaining stable trajectories while all force field versions lacking the χ correction are prone to a swift degradation toward senseless ladder-like structures of stems, characterized by high-anti glycosidic torsions. The type of explicit water model affects the simulations considerably more than concentration and the type of ions.
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Affiliation(s)
- Petr Sklenovský
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Florová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Filip Lankaš
- Centre for Complex Molecular Systems and Biomolecules, Institute of Organic Chemistry and Biochemistry , Flemingovo nam. 2, 166 10 Praha 6, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
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14
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Šponer J, Šponer JE, Petrov AI, Leontis NB. Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? J Phys Chem B 2010; 114:15723-41. [PMID: 21049899 PMCID: PMC4868365 DOI: 10.1021/jp104361m] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In this feature article, we provide a side-by-side introduction for two research fields: quantum chemical calculations of molecular interaction in nucleic acids and RNA structural bioinformatics. Our main aim is to demonstrate that these research areas, while largely separated in contemporary literature, have substantial potential to complement each other that could significantly contribute to our understanding of the exciting world of nucleic acids. We identify research questions amenable to the combined application of modern ab initio methods and bioinformatics analysis of experimental structures while also assessing the limitations of these approaches. The ultimate aim is to attain valuable physicochemical insights regarding the nature of the fundamental molecular interactions and how they shape RNA structures, dynamics, function, and evolution.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Anton I. Petrov
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Neocles B. Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
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15
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Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. Computational approaches for RNA energy parameter estimation. RNA (NEW YORK, N.Y.) 2010; 16:2304-18. [PMID: 20940338 PMCID: PMC2995392 DOI: 10.1261/rna.1950510] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Methods for efficient and accurate prediction of RNA structure are increasingly valuable, given the current rapid advances in understanding the diverse functions of RNA molecules in the cell. To enhance the accuracy of secondary structure predictions, we developed and refined optimization techniques for the estimation of energy parameters. We build on two previous approaches to RNA free-energy parameter estimation: (1) the Constraint Generation (CG) method, which iteratively generates constraints that enforce known structures to have energies lower than other structures for the same molecule; and (2) the Boltzmann Likelihood (BL) method, which infers a set of RNA free-energy parameters that maximize the conditional likelihood of a set of reference RNA structures. Here, we extend these approaches in two main ways: We propose (1) a max-margin extension of CG, and (2) a novel linear Gaussian Bayesian network that models feature relationships, which effectively makes use of sparse data by sharing statistical strength between parameters. We obtain significant improvements in the accuracy of RNA minimum free-energy pseudoknot-free secondary structure prediction when measured on a comprehensive set of 2518 RNA molecules with reference structures. Our parameters can be used in conjunction with software that predicts RNA secondary structures, RNA hybridization, or ensembles of structures. Our data, software, results, and parameter sets in various formats are freely available at http://www.cs.ubc.ca/labs/beta/Projects/RNA-Params.
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Affiliation(s)
- Mirela Andronescu
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
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16
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Davis AR, Kirkpatrick CC, Znosko BM. Structural characterization of naturally occurring RNA single mismatches. Nucleic Acids Res 2010; 39:1081-94. [PMID: 20876693 PMCID: PMC3035445 DOI: 10.1093/nar/gkq793] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the most prevalent types of RNA secondary structure motifs are single mismatches, which occur when two canonical pairs are separated by a single non-canonical pair. To determine sequence–structure relationships and to identify structural patterns, we have systematically located, annotated and compared all available occurrences of the 30 most frequently occurring single mismatch-nearest neighbor sequence combinations found in experimentally determined 3D structures of RNA-containing molecules deposited into the Protein Data Bank. Hydrogen bonding, stacking and interaction of nucleotide edges for the mismatched and nearest neighbor base pairs are described and compared, allowing for the identification of several structural patterns. Such a database and comparison will allow researchers to gain insight into the structural features of unstudied sequences and to quickly look-up studied sequences.
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Affiliation(s)
- Amber R Davis
- Department of Chemistry, Saint Louis University, St Louis, MO 63103, USA
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17
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Besseová I, Réblová K, Leontis NB, Sponer J. Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res 2010; 38:6247-64. [PMID: 20507916 PMCID: PMC2952862 DOI: 10.1093/nar/gkq414] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We present extensive explicit solvent molecular dynamics analysis of three RNA three-way junctions (3WJs) from the large ribosomal subunit: the 3WJ formed by Helices 90–92 (H90–H92) of 23S rRNA; the 3WJ formed by H42–H44 organizing the GTPase associated center (GAC) of 23S rRNA; and the 3WJ of 5S rRNA. H92 near the peptidyl transferase center binds the 3′-CCA end of amino-acylated tRNA. The GAC binds protein factors and stimulates GTP hydrolysis driving protein synthesis. The 5S rRNA binds the central protuberance and A-site finger (ASF) involved in bridges with the 30S subunit. The simulations reveal that all three 3WJs possess significant anisotropic hinge-like flexibility between their stacked stems and dynamics within the compact regions of their adjacent stems. The A-site 3WJ dynamics may facilitate accommodation of tRNA, while the 5S 3WJ flexibility appears to be essential for coordinated movements of ASF and 5S rRNA. The GAC 3WJ may support large-scale dynamics of the L7/L12-stalk region. The simulations reveal that H42–H44 rRNA segments are not fully relaxed and in the X-ray structures they are bent towards the large subunit. The bending may be related to L10 binding and is distributed between the 3WJ and the H42–H97 contact.
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Affiliation(s)
- Ivana Besseová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
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18
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Réblová K, Střelcová Z, Kulhánek P, Beššeová I, Mathews DH, Van Nostrand K, Yildirim I, Turner DH, Šponer J. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5′-UAA/5′-GAN Internal Loops Studied by Molecular Dynamics Methods. J Chem Theory Comput 2010; 6:910-29. [DOI: 10.1021/ct900440t] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Zora Střelcová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Petr Kulhánek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Ivana Beššeová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - David H. Mathews
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Keith Van Nostrand
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Ilyas Yildirim
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Douglas H. Turner
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic, Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642, Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, and Department of Chemistry, University of
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19
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Réblová K, Střelcová Z, Kulhánek P, Beššeová I, Mathews DH, Nostrand KV, Yildirim I, Turner DH, Šponer J. An RNA molecular switch: Intrinsic flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN internal loops studied by molecular dynamics methods. J Chem Theory Comput 2010; 2010:910-929. [PMID: 21132104 PMCID: PMC2994019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Functional RNA molecules such as ribosomal RNAs frequently contain highly conserved internal loops with a 5'-UAA/5'-GAN (UAA/GAN) consensus sequence. The UAA/GAN internal loops adopt distinctive structure inconsistent with secondary structure predictions. The structure has a narrow major groove and forms a trans Hoogsteen/Sugar edge (tHS) A/G base pair followed by an unpaired stacked adenine, a trans Watson-Crick/Hoogsteen (tWH) U/A base pair and finally by a bulged nucleotide (N). The structure is further stabilized by a three-adenine stack and base-phosphate interaction. In the ribosome, the UAA/GAN internal loops are involved in extensive tertiary contacts, mainly as donors of A-minor interactions. Further, this sequence can adopt an alternative 2D/3D pattern stabilized by a four-adenine stack involved in a smaller number of tertiary interactions. The solution structure of an isolated UAA/GAA internal loop shows substantially rearranged base pairing with three consecutive non-Watson-Crick base pairs. Its A/U base pair adopts an incomplete cis Watson-Crick/Sugar edge (cWS) A/U conformation instead of the expected Watson-Crick arrangement. We performed 3.1 µs of explicit solvent molecular dynamics (MD) simulations of the X-ray and NMR UAA/GAN structures, supplemented by MM-PBSA free energy calculations, locally enhanced sampling (LES) runs, targeted MD (TMD) and nudged elastic band (NEB) analysis. We compared parm99 and parmbsc0 force fields and net-neutralizing Na(+) vs. excess salt KCl ion environments. Both force fields provide a similar description of the simulated structures, with the parmbsc0 leading to modest narrowing of the major groove. The excess salt simulations also cause a similar effect. While the NMR structure is entirely stable in simulations, the simulated X-ray structure shows considerable widening of the major groove, loss of base-phosphate interaction and other instabilities. The alternative X-ray geometry even undergoes conformational transition towards the solution 2D structure. Free energy calculations confirm that the X-ray arrangement is less stable than the solution structure. LES, TMD and NEB provide a rather consistent pathway for interconversion between the X-ray and NMR structures. In simulations, the incomplete cWS A/U base pair of the NMR structure is water mediated and alternates with the canonical A-U base pair, which is not indicated by the NMR data. Completion of full cWS A/U base pair is prevented by the overall internal loop arrangement. In summary, the simulations confirm that the UAA/GAN internal loop is a molecular switch RNA module that adopts its functional geometry upon specific tertiary contexts.
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Affiliation(s)
- Kamila Réblová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - Zora Střelcová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Petr Kulhánek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Ivana Beššeová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
| | - David H. Mathews
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642
| | - Keith Van Nostrand
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, New York 14642
| | - Ilyas Yildirim
- Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627-0216
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic
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20
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Timsit Y, Acosta Z, Allemand F, Chiaruttini C, Springer M. The role of disordered ribosomal protein extensions in the early steps of eubacterial 50 S ribosomal subunit assembly. Int J Mol Sci 2009; 10:817-834. [PMID: 19399222 PMCID: PMC2672003 DOI: 10.3390/ijms10030817] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 02/23/2009] [Accepted: 02/24/2009] [Indexed: 12/23/2022] Open
Abstract
Although during the past decade research has shown the functional importance of disorder in proteins, many of the structural and dynamics properties of intrinsically unstructured proteins (IUPs) remain to be elucidated. This review is focused on the role of the extensions of the ribosomal proteins in the early steps of the assembly of the eubacterial 50 S subunit. The recent crystallographic structures of the ribosomal particles have revealed the picture of a complex assembly pathway that condenses the rRNA and the ribosomal proteins into active ribosomes. However, little is know about the molecular mechanisms of this process. It is thought that the long basic r-protein extensions that penetrate deeply into the subunit cores play a key role through disorder-order transitions and/or co-folding mechanisms. A current view is that such structural transitions may facilitate the proper rRNA folding. In this paper, the structures of the proteins L3, L4, L13, L20, L22 and L24 that have been experimentally found to be essential for the first steps of ribosome assembly have been compared. On the basis of their structural and dynamics properties, three categories of extensions have been identified. Each of them seems to play a distinct function. Among them, only the coil-helix transition that occurs in a phylogenetically conserved cluster of basic residues of the L20 extension appears to be strictly required for the large subunit assembly in eubacteria. The role of alpha helix-coil transitions in 23 S RNA folding is discussed in the light of the calcium binding protein calmodulin that shares many structural and dynamics properties with L20.
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Affiliation(s)
- Youri Timsit
- Laboratoire de Cristallographie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
- Author to whom correspondence should be addressed; E-mail:
; Tel. +01-58-41-51-66
| | - Zahir Acosta
- Laboratoire de Cristallographie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
| | - Frédéric Allemand
- Laboratoire de Biochimie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
(F.A.);
(C.C.);
(M.S.)
| | - Claude Chiaruttini
- Laboratoire de Biochimie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
(F.A.);
(C.C.);
(M.S.)
| | - Mathias Springer
- Laboratoire de Biochimie, Institut de Biologie Physico-Chimique CNRS, 13, rue Pierre et Marie Curie, 75005 Paris, France; E-Mail:
(F.A.);
(C.C.);
(M.S.)
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21
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James L, Sargueil B. RNA secondary structure of the feline immunodeficiency virus 5'UTR and Gag coding region. Nucleic Acids Res 2008; 36:4653-66. [PMID: 18625613 PMCID: PMC2504303 DOI: 10.1093/nar/gkn447] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The 5′ untranslated region (5′UTR) of lentiviral genomic RNA is highly structured, and is the site of multiple RNA–RNA and RNA–protein interactions throughout the viral life cycle. The 5′UTR plays a critical role during transcription, translational regulation, genome dimerization, reverse transcription priming and encapsidation. The 5′UTR structures of human lentiviruses have been extensively studied, yet the respective role and conformation of each domain is still controversial. To gain insight into the structure-function relationship of lentiviral 5′UTRs, we modelled the RNA structure of the feline immunodeficiency virus (FIV), a virus that is evolutionarily distant from the primate viruses. Through combined chemical and enzymatic structure probing and a thorough phylogenetic study, we establish a model for the secondary structure of the 5′UTR and Gag coding region. This work highlights properties common to all lentiviruses, like the primer binding site structure and the presence of a stable stem-loop at the 5′ extremity. We find that FIV has also evolved specific features, including a long stem loop overlapping the end of the 5′UTR and the beginning of the coding region. In addition, we observed footprints of Gag protein on each side of the initiation codon, this sheds light on the role of the sequences required for encapsidation.
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Affiliation(s)
- Laurie James
- CNRS UPR2167 - Centre de Génétique Moléculaire, Avenue de la Terrasse, 91190 Gif sur yvette, France
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22
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Mokdad A, Frankel AD. ISFOLD: structure prediction of base pairs in non-helical RNA motifs from isostericity signatures in their sequence alignments. J Biomol Struct Dyn 2008; 25:467-72. [PMID: 18282001 DOI: 10.1080/07391102.2008.10531239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The existence and identity of non-Watson-Crick base pairs (bps) within RNA bulges, internal loops, and hairpin loops cannot reliably be predicted by existing algorithms. We have developed the Isfold (Isosteric Folding) program as a tool to examine patterns of nucleotide substitutions from sequence alignments or mutation experiments and identify plausible bp interactions. We infer these interactions based on the observation that each non-Watson-Crick bp has a signature pattern of isosteric substitutions where mutations can be made that preserve the 3D structure. Isfold produces a dynamic representation of predicted bps within defined motifs in order of their probabilities. The software was developed under Windows XP, and is capable of running on PC and MAC with Matlab 7.1 (SP3) or higher. A PC stand-alone version that does not require Matlab also is available. This software and a user manual are freely available at www.ucsf.edu/frankel/isfold.
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Affiliation(s)
- Ali Mokdad
- Department of Biochemistry and Biophysics, University of California at San Francisco, 600 16th Street, San Francisco, CA 94143-2280, USA.
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23
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Parisien M, Major F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 2008; 452:51-5. [PMID: 18322526 DOI: 10.1038/nature06684] [Citation(s) in RCA: 590] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2007] [Accepted: 01/11/2008] [Indexed: 12/17/2022]
Abstract
The classical RNA secondary structure model considers A.U and G.C Watson-Crick as well as G.U wobble base pairs. Here we substitute it for a new one, in which sets of nucleotide cyclic motifs define RNA structures. This model allows us to unify all base pairing energetic contributions in an effective scoring function to tackle the problem of RNA folding. We show how pipelining two computer algorithms based on nucleotide cyclic motifs, MC-Fold and MC-Sym, reproduces a series of experimentally determined RNA three-dimensional structures from the sequence. This demonstrates how crucial the consideration of all base-pairing interactions is in filling the gap between sequence and structure. We use the pipeline to define rules of precursor microRNA folding in double helices, despite the presence of a number of presumed mismatches and bulges, and to propose a new model of the human immunodeficiency virus-1 -1 frame-shifting element.
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Affiliation(s)
- Marc Parisien
- Institute for Research in Immunology and Cancer, Department of Computer Science and Operations Research, Université de Montréal, PO Box 6128, Downtown Station, Montréal, Québec H3C 3J7, Canada
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24
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Lisi V, Major F. A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence structure relationships. RNA (NEW YORK, N.Y.) 2007; 13:1537-45. [PMID: 17652406 PMCID: PMC1950765 DOI: 10.1261/rna.597507] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Despite an increasing number of experimentally determined RNA structures, the gap between the number of structures and that of RNA families is still growing. To overcome this limitation, efficient and reliable RNA modeling methodologies must be developed. In order to reach this goal, here, we show how triloop sequence-structure relationships have been inferred through a systematic analysis of all triloops found in available high-resolution structures. The structural annotation of all triloops allowed us to define discrete states of the triloop's conformational space, and therefore an explicit sequence-to-structure relation. The sequence-structure relationships inferred from this explicit relation are presented in a convenient modeling table that provides a limited set of possible three-dimensional structures given any triloop sequence. The table is indexed by the two nucleotides that form the triloop's flanking base pair, since they are shown to provide the most information about the triloop three-dimensional structures. We also report the observations in the X-ray crystallographic structures of important conformational variations, which we believe might be the result of RNA dynamic.
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Affiliation(s)
- Véronique Lisi
- Institute for Research in Immunology and Cancer, Department of Computer Science and Operations Research, Université de Montréal, Québec, Canada
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