1
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Singh K, Reddy G. Excited States of apo-Guanidine-III Riboswitch Contribute to Guanidinium Binding through Both Conformational and Induced-Fit Mechanisms. J Chem Theory Comput 2024; 20:421-435. [PMID: 38134376 DOI: 10.1021/acs.jctc.3c00999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Riboswitches are mRNA segments that regulate gene expression through conformational changes driven by their cognate ligand binding. The ykkC motif forms a riboswitch class that selectively senses a guanidinium ion (Gdm+) and regulates the downstream expression of proteins which aid in the efflux of excess Gdm+ from the cells. The aptamer domain (AD) of the guanidine-III riboswitch forms an H-type pseudoknot with a triple helical domain that binds a Gdm+. We studied the binding of Gdm+ to the AD of the guanidine (ykkC)-III riboswitch using computer simulations to probe the specificity of the riboswitch to Gdm+ binding. We show that Gdm+ binding is a fast process occurring on the nanosecond time scale, with minimal conformational changes to the AD. Using machine learning and Markov-state models, we identified the excited conformational states of the AD, which have a high Gdm+ binding propensity, making the Gdm+ binding landscape complex exhibiting both conformational selection and induced-fit mechanisms. The proposed apo-AD excited states and their role in the ligand-sensing mechanism are amenable to experimental verification. Further, targeting these excited-state conformations in discovering new antibiotics can be explored.
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Affiliation(s)
- Kushal Singh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012 Karnataka, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru 560012 Karnataka, India
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2
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Hsueh SCC, Aina A, Plotkin SS. Ensemble Generation for Linear and Cyclic Peptides Using a Reservoir Replica Exchange Molecular Dynamics Implementation in GROMACS. J Phys Chem B 2022; 126:10384-10399. [PMID: 36410027 DOI: 10.1021/acs.jpcb.2c05470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The profile of shapes presented by a cyclic peptide modulates its therapeutic efficacy and is represented by the ensemble of its sampled conformations. Although some algorithms excel at creating a diverse ensemble of cyclic peptide conformations, they seldom address the entropic contribution of flexible conformations and often have significant practical difficulty producing an ensemble with converged and reliable thermodynamic properties. In this study, an accelerated molecular dynamics (MD) method, namely, reservoir replica exchange MD (R-REMD or Res-REMD), was implemented in GROMACS ver. 4.6.7 and benchmarked on two small cyclic peptide model systems: a cyclized furin cleavage site of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (cyclo-(CGPRRARSG)) and oxytocin (disulfide-bonded CYIQNCPLG). Additionally, we also benchmarked Res-REMD on alanine dipeptide and Trpzip2 to demonstrate its validity and efficiency over REMD. For Trpzip2, Res-REMD coupled with an umbrella-sampling-derived reservoir generated similar folded fractions as regular REMD but on a much faster time scale. For cyclic peptides, Res-REMD appeared to be marginally faster than REMD in ensemble generation. Finally, Res-REMD was more effective in sampling rare events such as trans to cis peptide bond isomerization. We provide a GitHub page with the modified GROMACS source code for running Res-REMD at https://github.com/PlotkinLab/Reservoir-REMD.
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Affiliation(s)
- Shawn C C Hsueh
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada
| | - Adekunle Aina
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada.,Genome Science and Technology Program, The University of British Columbia, Vancouver, BCV6T 1Z1, Canada
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3
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Binet T, Avalle B, Dávila Felipe M, Maffucci I. AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures. Bioinformatics 2022; 39:6849515. [PMID: 36440922 PMCID: PMC9805580 DOI: 10.1093/bioinformatics/btac752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/14/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION Comparing single-stranded nucleic acids (ssNAs) secondary structures is fundamental when investigating their function and evolution and predicting the effect of mutations on their structures. Many comparison metrics exist, although they are either too elaborate or not sensitive enough to distinguish close ssNAs structures. RESULTS In this context, we developed AptaMat, a simple and sensitive algorithm for ssNAs secondary structures comparison based on matrices representing the ssNAs secondary structures and a metric built upon the Manhattan distance in the plane. We applied AptaMat to several examples and compared the results to those obtained by the most frequently used metrics, namely the Hamming distance and the RNAdistance, and by a recently developed image-based approach. We showed that AptaMat is able to discriminate between similar sequences, outperforming all the other here considered metrics. In addition, we showed that AptaMat was able to correctly classify 14 RFAM families within a clustering procedure. AVAILABILITY AND IMPLEMENTATION The python code for AptaMat is available at https://github.com/GEC-git/AptaMat.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thomas Binet
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu, CS 60 319 - 60 203, Compiègne Cedex, France
| | - Bérangère Avalle
- Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu, CS 60 319 - 60 203, Compiègne Cedex, France
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4
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Dagenais P, Desjardins G, Legault P. An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme. Nucleic Acids Res 2021; 49:11959-11973. [PMID: 34718697 PMCID: PMC8599749 DOI: 10.1093/nar/gkab963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.
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Affiliation(s)
- Pierre Dagenais
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Geneviève Desjardins
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Pascale Legault
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
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5
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Gong Z, Yang S, Dong X, Yang QF, Zhu YL, Xiao Y, Tang C. Hierarchical Conformational Dynamics Confers Thermal Adaptability to preQ 1 RNA Riboswitches. J Mol Biol 2020; 432:4523-4543. [PMID: 32522558 DOI: 10.1016/j.jmb.2020.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/03/2020] [Accepted: 06/03/2020] [Indexed: 11/26/2022]
Abstract
Single-stranded noncoding regulatory RNAs, as exemplified by bacterial riboswitches, are highly dynamic. The conformational dynamics allow the riboswitch to reach maximum switching efficiency under appropriate conditions. Here we characterize the conformational dynamics of preQ1 riboswitches from mesophilic and thermophilic bacterial species at various temperatures. With the integrative use of small-angle X-ray scattering, NMR, and molecular dynamics simulations, we model the ensemble-structures of the preQ1 riboswitch aptamers without or with a ligand bound. We show that the preQ1 riboswitch is sufficiently dynamic and fluctuating among multiple folding intermediates only near the physiological temperature of the microorganism. The hierarchical folding dynamics of the RNA involves the docking of 3'-tail to form a second RNA helix and the helical stacking to form an H-type pseudoknot structure. Further, we show that RNA secondary and tertiary dynamics can be modulated by temperature and by the length of an internal loop. The coupled equilibria between RNA folding intermediates are essential for preQ1 binding, and a four-state exchange model can account for the change of ligand-triggered switching efficiency with temperature. Together, we have established a relationship between the hierarchical dynamics and riboswitch function, and illustrated how the RNA adapts to high temperature.
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Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China.
| | - Shuai Yang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Dong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Qing-Fen Yang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Yue-Ling Zhu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China
| | - Yi Xiao
- Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei Province 430074, China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, Hubei Province 430071, China; Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei Province 430074, China.
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6
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Abstract
RNA recognition frequently results in conformational changes that optimize intermolecular binding. As a consequence, the overall binding affinity of RNA to its binding partners depends not only on the intermolecular interactions formed in the bound state but also on the energy cost associated with changing the RNA conformational distribution. Measuring these "conformational penalties" is, however, challenging because bound RNA conformations tend to have equilibrium populations in the absence of the binding partner that fall outside detection by conventional biophysical methods. In this study we employ as a model system HIV-1 TAR RNA and its interaction with the ligand argininamide (ARG), a mimic of TAR's cognate protein binding partner, the transactivator Tat. We use NMR chemical shift perturbations and relaxation dispersion in combination with Bayesian inference to develop a detailed thermodynamic model of coupled conformational change and ligand binding. Starting from a comprehensive 12-state model of the equilibrium, we estimate the energies of six distinct detectable thermodynamic states that are not accessible by currently available methods. Our approach identifies a minimum of four RNA intermediates that differ in terms of the TAR conformation and ARG occupancy. The dominant bound TAR conformation features two bound ARG ligands and has an equilibrium population in the absence of ARG that is below detection limit. Consequently, even though ARG binds to TAR with an apparent overall weak affinity (Kdapp ≈ 0.2 mM), it binds the prefolded conformation with a Kd in the nM range. Our results show that conformational penalties can be major determinants of RNA-ligand binding affinity as well as a source of binding cooperativity, with important implications for a predictive understanding of how RNA is recognized and for RNA-targeted drug discovery.
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Affiliation(s)
- Nicole I. Orlovsky
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Terrence G. Oas
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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7
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Nishigaki K. III. Functions of short lifetime structures at large 9: case of nucleic acids. Brief Funct Genomics 2019; 18:205-210. [PMID: 30247522 DOI: 10.1093/bfgp/ely028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 11/12/2022] Open
Abstract
The short lifetime structures of nucleic acids are not well studied because of the poor recognition of their importance and the methodological difficulty. In case of proteins, which are a type of single-stranded biopolymers, the essential roles of their transient structures are well established. Therefore, the role of transient structures of nucleic acids is, naturally, of great interest. There have been multiple reports on the function-related unstable (transient) structures of single-stranded nucleotides, though not as many as at present. Recent methodological advances are now enabling us to observe structures with ultra-short lifetime (less than a nanosecond). On the other hand, the biological importance of transient structures of ribonucleicacid (RNA) is increasingly recognized because of the findings of novel functional RNAs such as microRNA. Therefore, the time has come to tackle the structure and function dynamic of RNA/deoxyribonucleic acid in relation to their transient, unstable structures. The specific properties of rapidity and diversity are hypothesized to be involved in unexplored phenomena in neuroscience.
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Affiliation(s)
- Koichi Nishigaki
- Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology,1-1 Asahidai, Nomi, Ishikaw, Japan.,Graduate School of Science and Technology, Saitama University, Shimo-okubo, Saitama City, Saitama, Japan
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8
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Girard N, Dagenais P, Lacroix-Labonté J, Legault P. A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation. Nucleic Acids Res 2019; 47:3739-3751. [PMID: 30993347 PMCID: PMC6468304 DOI: 10.1093/nar/gkz098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/17/2019] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
Investigating the dynamics of structural elements in functional RNAs is important to better understand their mechanism and for engineering RNAs with novel functions. Previously, we performed rational engineering studies with the Varkud satellite (VS) ribozyme and switched its specificity toward non-natural hairpin substrates through modification of a critical kissing-loop interaction (KLI). We identified functional VS ribozyme variants with surrogate KLIs (ribosomal RNA L88/L22 and human immunodeficiency virus-1 TAR/TAR*), but they displayed ∼100-fold lower cleavage activity. Here, we characterized the dynamics of KLIs to correlate dynamic properties with function and improve the activity of designer ribozymes. Using temperature replica exchange molecular dynamics, we determined that the natural KLI in the VS ribozyme supports conformational sampling of its closed and active state, whereas the surrogate KLIs display more restricted motions. Based on in vitro selection, the cleavage activity of a VS ribozyme variant with the TAR/TAR* KLI could be markedly improved by partly destabilizing the KLI but increasing conformation sampling. We formulated a mechanistic model for substrate binding in which the KLI dynamics contribute to formation of the active site. Our model supports the modular nature of RNA in which subdomain structure and dynamics contribute to define the thermodynamics and kinetics relevant to RNA function.
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Affiliation(s)
- Nicolas Girard
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Pierre Dagenais
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Julie Lacroix-Labonté
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Pascale Legault
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
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9
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Denny SK, Greenleaf WJ. Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers. Cold Spring Harb Perspect Biol 2019; 11:a032300. [PMID: 30322887 PMCID: PMC6771372 DOI: 10.1101/cshperspect.a032300] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
High-throughput sequencing methods have revolutionized our ability to catalog the diversity of RNAs and RNA-protein interactions that can exist in our cells. However, the relationship between RNA sequence, structure, and function is enormously complex, demonstrating the need for methods that can provide quantitative thermodynamic and kinetic measurements of macromolecular interaction with RNA, at a scale commensurate with the sequence diversity of RNA. Here, we discuss a class of methods that extend the core functionality of DNA sequencers to enable high-throughput measurements of RNA folding and RNA-protein interactions. Topics discussed include a description of the method and multiple applications to RNA-binding proteins, riboswitch design and engineering, and RNA tertiary structure energetics.
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Affiliation(s)
- Sarah K Denny
- Stanford University Department of Genetics, Stanford, California 94305
| | - William J Greenleaf
- Stanford University Department of Genetics, Stanford, California 94305
- Stanford University Department of Applied Physics, Stanford, California 94025
- Chan Zuckerberg Biohub, San Francisco, California 94158
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10
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Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis. Biophys J 2019; 117:1674-1683. [PMID: 31590890 DOI: 10.1016/j.bpj.2019.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 11/22/2022] Open
Abstract
RNA functions are often kinetically controlled. The folding kinetics of RNAs involves global structural changes and local nucleotide movement, such as base flipping. The most elementary step in RNA folding is the closing and opening of a basepair. By integrating molecular dynamics simulation, master equation, and kinetic Monte Carlo simulation, we investigate the kinetics mechanism of RNA helix-terminal basepairing. The study reveals a six-state folding scheme with three dominant folding pathways of tens, hundreds, and thousands of nanoseconds of folding timescales, respectively. The overall kinetics is rate limited by the detrapping of a misfolded state with the overall folding time of 10-5 s. Moreover, the analysis examines the different roles of the various driving forces, such as the basepairing and stacking interactions and the ion binding/dissociation effects on structural changes. The results may provide useful insights for developing a basepair opening/closing rate model and further kinetics models of large RNAs.
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11
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Plumridge A, Katz AM, Calvey GD, Elber R, Kirmizialtin S, Pollack L. Revealing the distinct folding phases of an RNA three-helix junction. Nucleic Acids Res 2018; 46:7354-7365. [PMID: 29762712 PMCID: PMC6101490 DOI: 10.1093/nar/gky363] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/17/2018] [Accepted: 04/24/2018] [Indexed: 01/08/2023] Open
Abstract
Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Andrea M Katz
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - George D Calvey
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | - Ron Elber
- Department of Chemistry and Institute for Computational Engineering and Sciences (ICES) University of Texas at Austin, Austin, TX, USA
| | - Serdal Kirmizialtin
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
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12
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Denny SK, Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ. High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. Cell 2018; 174:377-390.e20. [PMID: 29961580 PMCID: PMC6053692 DOI: 10.1016/j.cell.2018.05.038] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/07/2018] [Accepted: 05/15/2018] [Indexed: 12/21/2022]
Abstract
RNAs fold into defined tertiary structures to function in critical biological processes. While quantitative models can predict RNA secondary structure stability, we are still unable to predict the thermodynamic stability of RNA tertiary structure. Here, we probe conformational preferences of diverse RNA two-way junctions to develop a predictive model for the formation of RNA tertiary structure. We quantitatively measured tertiary assembly energetics of >1,000 of RNA junctions inserted in multiple structural scaffolds to generate a "thermodynamic fingerprint" for each junction. Thermodynamic fingerprints enabled comparison of junction conformational preferences, revealing principles for how sequence influences 3-dimensional conformations. Utilizing fingerprints of junctions with known crystal structures, we generated ensembles for related junctions that predicted their thermodynamic effects on assembly formation. This work reveals sequence-structure-energetic relationships in RNA, demonstrates the capacity for diverse compensation strategies within tertiary structures, and provides a path to quantitative modeling of RNA folding energetics based on "ensemble modularity."
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Affiliation(s)
| | - Namita Bisaria
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph David Yesselman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.
| | - William James Greenleaf
- Program in Biophysics, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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13
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Bonilla S, Limouse C, Bisaria N, Gebala M, Mabuchi H, Herschlag D. Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway. J Am Chem Soc 2017; 139:18576-18589. [PMID: 29185740 PMCID: PMC5748328 DOI: 10.1021/jacs.7b08870] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Decades
of study of the RNA folding problem have revealed that
diverse and complex structured RNAs are built from a common set of
recurring structural motifs, leading to the perspective that a generalizable
model of RNA folding may be developed from understanding of the folding
properties of individual structural motifs. We used single-molecule
fluorescence to dissect the kinetic and thermodynamic properties of
a set of variants of a common tertiary structural motif, the tetraloop/tetraloop-receptor
(TL/TLR). Our results revealed a multistep TL/TLR folding pathway
in which preorganization of the ubiquitous AA-platform submotif precedes
the formation of the docking transition state and tertiary A-minor
hydrogen bond interactions form after the docking transition state.
Differences in ion dependences between TL/TLR variants indicated the
occurrence of sequence-dependent conformational rearrangements prior
to and after the formation of the docking transition state. Nevertheless,
varying the junction connecting the TL/TLR produced a common kinetic
and ionic effect for all variants, suggesting that the global conformational
search and compaction electrostatics are energetically independent
from the formation of the tertiary motif contacts. We also found that in vitro-selected variants, despite their similar stability
at high Mg2+ concentrations, are considerably less stable
than natural variants under near-physiological ionic conditions, and
the occurrence of the TL/TLR sequence variants in Nature correlates
with their thermodynamic stability in isolation. Overall, our findings
are consistent with modular but complex energetic properties of RNA
structural motifs and will aid in the eventual quantitative description
of RNA folding from its secondary and tertiary structural elements.
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Affiliation(s)
- Steve Bonilla
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Charles Limouse
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Namita Bisaria
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Magdalena Gebala
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Hideo Mabuchi
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Chemical Engineering, ‡Department of Applied Physics, §Department of Biochemistry, ∥Department of Chemistry, ⊥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
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14
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Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies. J Mol Model 2017; 23:311. [DOI: 10.1007/s00894-017-3480-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 09/19/2017] [Indexed: 11/26/2022]
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15
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Jegousse C, Yang Y, Zhan J, Wang J, Zhou Y. Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA. PLoS One 2017; 12:e0184722. [PMID: 28910383 PMCID: PMC5598986 DOI: 10.1371/journal.pone.0184722] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/29/2017] [Indexed: 12/02/2022] Open
Abstract
Temperature adaptation of bacterial RNAs is a subject of both fundamental and practical interest because it will allow a better understanding of molecular mechanism of RNA folding with potential industrial application of functional thermophilic or psychrophilic RNAs. Here, we performed a comprehensive study of rRNA, tRNA, and mRNA of more than 200 bacterial species with optimal growth temperatures (OGT) ranging from 4°C to 95°C. We investigated temperature adaptation at primary, secondary and tertiary structure levels. We showed that unlike mRNA, tRNA and rRNA were optimized for their structures at compositional levels with significant tertiary structural features even for their corresponding randomly permutated sequences. tRNA and rRNA are more exposed to solvent but remain structured for hyperthermophiles with nearly OGT-independent fluctuation of solvent accessible surface area within a single RNA chain. mRNA in hyperthermophiles is essentially the same as random sequences without tertiary structures although many mRNA in mesophiles and psychrophiles have well-defined tertiary structures based on their low overall solvent exposure with clear separation of deeply buried from partly exposed bases as in tRNA and rRNA. These results provide new insight into temperature adaptation of different RNAs.
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MESH Headings
- Bacteria/genetics
- Databases, Genetic
- Models, Molecular
- Nucleic Acid Conformation
- RNA Folding/drug effects
- RNA, Bacterial/chemistry
- RNA, Bacterial/drug effects
- RNA, Messenger/chemistry
- RNA, Messenger/drug effects
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/drug effects
- RNA, Transfer/chemistry
- RNA, Transfer/drug effects
- Solvents/pharmacology
- Temperature
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Affiliation(s)
- Clara Jegousse
- UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière, Nantes, France
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- * E-mail:
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16
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Q Nguyen KK, Gomez YK, Bakhom M, Radcliffe A, La P, Rochelle D, Lee JW, Sorin EJ. Ensemble simulations: folding, unfolding and misfolding of a high-efficiency frameshifting RNA pseudoknot. Nucleic Acids Res 2017; 45:4893-4904. [PMID: 28115636 PMCID: PMC5416846 DOI: 10.1093/nar/gkx012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/11/2017] [Indexed: 12/11/2022] Open
Abstract
Massive all-atom molecular dynamics simulations were conducted across a distributed computing network to study the folding, unfolding, misfolding and conformational plasticity of the high-efficiency frameshifting double mutant of the 26 nt potato leaf roll virus RNA pseudoknot. Our robust sampling, which included over 40 starting structures spanning the spectrum from the extended unfolded state to the native fold, yielded nearly 120 μs of cumulative sampling time. Conformational microstate transitions on the 1.0 ns to 10.0 μs timescales were observed, with post-equilibration sampling providing detailed representations of the conformational free energy landscape and the complex folding mechanism inherent to the pseudoknot motif. Herein, we identify and characterize two alternative native structures, three intermediate states, and numerous misfolded states, the latter of which have not previously been characterized via atomistic simulation techniques. While in line with previous thermodynamics-based models of a general RNA folding mechanism, our observations indicate that stem-strand-sequence-separation may serve as an alternative predictor of the order of stem formation during pseudoknot folding. Our results contradict a model of frameshifting based on structural rigidity and resistance to mechanical unfolding, and instead strongly support more recent studies in which conformational plasticity is identified as a determining factor in frameshifting efficiency.
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Affiliation(s)
- Khai K Q Nguyen
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.,Department of Computer Engineering & Computer Science, California State University Long Beach, Long Beach, CA 90840, USA
| | - Yessica K Gomez
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA.,Department of Physics & Astronomy, California State University Long Beach, Long Beach, CA 90840, USA
| | - Mona Bakhom
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Amethyst Radcliffe
- Department of Physics & Astronomy, California State University Long Beach, Long Beach, CA 90840, USA
| | - Phuc La
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Dakota Rochelle
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Ji Won Lee
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
| | - Eric J Sorin
- Department of Chemistry & Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
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17
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Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics. Proc Natl Acad Sci U S A 2017; 114:E7688-E7696. [PMID: 28839094 DOI: 10.1073/pnas.1703507114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Decades of study of the architecture and function of structured RNAs have led to the perspective that RNA tertiary structure is modular, made of locally stable domains that retain their structure across RNAs. We formalize a hypothesis inspired by this modularity-that RNA folding thermodynamics and kinetics can be quantitatively predicted from separable energetic contributions of the individual components of a complex RNA. This reconstitution hypothesis considers RNA tertiary folding in terms of ΔGalign, the probability of aligning tertiary contact partners, and ΔGtert, the favorable energetic contribution from the formation of tertiary contacts in an aligned state. This hypothesis predicts that changes in the alignment of tertiary contacts from different connecting helices and junctions (ΔGHJH) or from changes in the electrostatic environment (ΔG+/-) will not affect the energetic perturbation from a mutation in a tertiary contact (ΔΔGtert). Consistent with these predictions, single-molecule FRET measurements of folding of model RNAs revealed constant ΔΔGtert values for mutations in a tertiary contact embedded in different structural contexts and under different electrostatic conditions. The kinetic effects of these mutations provide further support for modular behavior of RNA elements and suggest that tertiary mutations may be used to identify rate-limiting steps and dissect folding and assembly pathways for complex RNAs. Overall, our model and results are foundational for a predictive understanding of RNA folding that will allow manipulation of RNA folding thermodynamics and kinetics. Conversely, the approaches herein can identify cases where an independent, additive model cannot be applied and so require additional investigation.
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18
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Clay MC, Ganser LR, Merriman DK, Al-Hashimi HM. Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics. Nucleic Acids Res 2017; 45:e134. [PMID: 28609788 PMCID: PMC5737546 DOI: 10.1093/nar/gkx525] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/01/2017] [Accepted: 06/05/2017] [Indexed: 11/15/2022] Open
Abstract
Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples. Application to HIV-1 TAR exposed slow modes of sugar repuckering dynamics at the μs and ms timescale accompanying transitions between non-helical (C2΄-endo) to helical (C3΄-endo) conformations during formation of two distinct excited states. In contrast, we did not obtain any evidence for slow sugar repuckering dynamics for nucleotides in a variety of structural contexts that do not undergo non-helical to helical transitions. Our results outline a route for significantly improving the conformational characterization of RNA excited states and suggest that slow modes of repuckering dynamics gated by transient changes in secondary structure are quite common in RNA.
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Affiliation(s)
- Mary C. Clay
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura R. Ganser
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
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19
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Woods CT, Lackey L, Williams B, Dokholyan NV, Gotz D, Laederach A. Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. Biophys J 2017. [PMID: 28625696 PMCID: PMC5529173 DOI: 10.1016/j.bpj.2017.05.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
When a ribonucleic acid (RNA) molecule folds, it often does not adopt a single, well-defined conformation. The folding energy landscape of an RNA is highly dependent on its nucleotide sequence and molecular environment. Cellular molecules sometimes alter the energy landscape, thereby changing the ensemble of likely low-energy conformations. The effects of these energy landscape changes on the conformational ensemble are particularly challenging to visualize for large RNAs. We have created a robust approach for visualizing the conformational ensemble of RNAs that is well suited for in vitro versus in vivo comparisons. Our method creates a stable map of conformational space for a given RNA sequence. We first identify single point mutations in the RNA that maximally sample suboptimal conformational space based on the ensemble’s partition function. Then, we cluster these diverse ensembles to identify the most diverse partition functions for Boltzmann stochastic sampling. By using, to our knowledge, a novel nestedness distance metric, we iteratively add mutant suboptimal ensembles to converge on a stable 2D map of conformational space. We then compute the selective 2′ hydroxyl acylation by primer extension (SHAPE)-directed ensemble for the RNA folding under different conditions, and we project these ensembles on the map to visualize. To validate our approach, we established a conformational map of the Vibrio vulnificus add adenine riboswitch that reveals five classes of structures. In the presence of adenine, projection of the SHAPE-directed sampling correctly identified the on-conformation; without the ligand, only off-conformations were visualized. We also collected the whole-transcript in vitro and in vivo SHAPE-MaP for human β-actin messenger RNA that revealed similar global folds in both conditions. Nonetheless, a comparison of in vitro and in vivo data revealed that specific regions exhibited significantly different SHAPE-MaP profiles indicative of structural rearrangements, including rearrangement consistent with binding of the zipcode protein in a region distal to the stop codon.
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Affiliation(s)
- Chanin T Woods
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Benfeard Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David Gotz
- Carolina Health Informatics Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alain Laederach
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
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20
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Plumridge A, Meisburger SP, Pollack L. Visualizing single-stranded nucleic acids in solution. Nucleic Acids Res 2017; 45:e66. [PMID: 28034955 PMCID: PMC5435967 DOI: 10.1093/nar/gkw1297] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 02/06/2023] Open
Abstract
Single-stranded nucleic acids (ssNAs) are ubiquitous in many key cellular functions. Their flexibility limits both the number of high-resolution structures available, leaving only a small number of protein-ssNA crystal structures, while forcing solution investigations to report ensemble averages. A description of the conformational distributions of ssNAs is essential to more fully characterize biologically relevant interactions. We combine small angle X-ray scattering (SAXS) with ensemble-optimization methods (EOM) to dynamically build and refine sets of ssNA structures. By constructing candidate chains in representative dinucleotide steps and refining the models against SAXS data, a broad array of structures can be obtained to match varying solution conditions and strand sequences. In addition to the distribution of large scale structural parameters, this approach reveals, for the first time, intricate details of the phosphate backbone and underlying strand conformations. Such information on unperturbed strands will critically inform a detailed understanding of an array of problems including protein-ssNA binding, RNA folding and the polymer nature of NAs. In addition, this scheme, which couples EOM selection with an iteratively refining pool to give confidence in the underlying structures, is likely extendable to the study of other flexible systems.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | | | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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21
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Borkar AN, Vallurupalli P, Camilloni C, Kay LE, Vendruscolo M. Simultaneous NMR characterisation of multiple minima in the free energy landscape of an RNA UUCG tetraloop. Phys Chem Chem Phys 2017; 19:2797-2804. [PMID: 28067358 PMCID: PMC6529357 DOI: 10.1039/c6cp08313g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules in solution tend to undergo structural fluctuations of relatively large amplitude and to populate a range of different conformations some of which with low populations. It is still very challenging, however, to characterise the structures of these low populated states and to understand their functional roles. In the present study, we address this problem by using NMR residual dipolar couplings (RDCs) as structural restraints in replica-averaged metadynamics (RAM) simulations. By applying this approach to a 14-mer RNA hairpin containing the prototypical UUCG tetraloop motif, we show that it is possible to construct the free energy landscape of this RNA molecule. This free energy landscapes reveals the surprisingly rich dynamics of the UUCG tetraloop and identifies the multiple substates that exist in equilibrium owing to thermal fluctuations. The approach that we present is general and can be applied to the study of the free energy landscapes of other RNA or RNA-protein systems.
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Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Pramodh Vallurupalli
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Canada M5S 1A8
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Canada M5S 1A8
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22
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Yang Y, Li X, Zhao H, Zhan J, Wang J, Zhou Y. Genome-scale characterization of RNA tertiary structures and their functional impact by RNA solvent accessibility prediction. RNA (NEW YORK, N.Y.) 2017; 23:14-22. [PMID: 27807179 PMCID: PMC5159645 DOI: 10.1261/rna.057364.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
As most RNA structures are elusive to structure determination, obtaining solvent accessible surface areas (ASAs) of nucleotides in an RNA structure is an important first step to characterize potential functional sites and core structural regions. Here, we developed RNAsnap, the first machine-learning method trained on protein-bound RNA structures for solvent accessibility prediction. Built on sequence profiles from multiple sequence alignment (RNAsnap-prof), the method provided robust prediction in fivefold cross-validation and an independent test (Pearson correlation coefficients, r, between predicted and actual ASA values are 0.66 and 0.63, respectively). Application of the method to 6178 mRNAs revealed its positive correlation to mRNA accessibility by dimethyl sulphate (DMS) experimentally measured in vivo (r = 0.37) but not in vitro (r = 0.07), despite the lack of training on mRNAs and the fact that DMS accessibility is only an approximation to solvent accessibility. We further found strong association across coding and noncoding regions between predicted solvent accessibility of the mutation site of a single nucleotide variant (SNV) and the frequency of that variant in the population for 2.2 million SNVs obtained in the 1000 Genomes Project. Moreover, mapping solvent accessibility of RNAs to the human genome indicated that introns, 5' cap of 5' and 3' cap of 3' untranslated regions, are more solvent accessible, consistent with their respective functional roles. These results support conformational selections as the mechanism for the formation of RNA-protein complexes and highlight the utility of genome-scale characterization of RNA tertiary structures by RNAsnap. The server and its stand-alone downloadable version are available at http://sparks-lab.org.
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Affiliation(s)
- Yuedong Yang
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD 4222, Australia
| | - Xiaomei Li
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD 4222, Australia
- School of Computer Science and Information Engineering, Hefei University of Technology, Hefei 230009, China
| | - Huiying Zhao
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland 4222, Australia
| | - Jian Zhan
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD 4222, Australia
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD 4222, Australia
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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23
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Zaccai G, Natali F, Peters J, Řihová M, Zimmerman E, Ollivier J, Combet J, Maurel MC, Bashan A, Yonath A. The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering. Sci Rep 2016; 6:37138. [PMID: 27849042 PMCID: PMC5111069 DOI: 10.1038/srep37138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/25/2016] [Indexed: 01/08/2023] Open
Abstract
Conformational changes associated with ribosome function have been identified by X-ray crystallography and cryo-electron microscopy. These methods, however, inform poorly on timescales. Neutron scattering is well adapted for direct measurements of thermal molecular dynamics, the ‘lubricant’ for the conformational fluctuations required for biological activity. The method was applied to compare water dynamics and conformational fluctuations in the 30 S and 50 S ribosomal subunits from Haloarcula marismortui, under high salt, stable conditions. Similar free and hydration water diffusion parameters are found for both subunits. With respect to the 50 S subunit, the 30 S is characterized by a softer force constant and larger mean square displacements (MSD), which would facilitate conformational adjustments required for messenger and transfer RNA binding. It has been shown previously that systems from mesophiles and extremophiles are adapted to have similar MSD under their respective physiological conditions. This suggests that the results presented are not specific to halophiles in high salt but a general property of ribosome dynamics under corresponding, active conditions. The current study opens new perspectives for neutron scattering characterization of component functional molecular dynamics within the ribosome.
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Affiliation(s)
- Giuseppe Zaccai
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Francesca Natali
- Institut Laue Langevin, F-38042 Grenoble, France.,CNR-IOM, OGG, F-38042 Grenoble, France
| | - Judith Peters
- Institut Laue Langevin, F-38042 Grenoble, France.,Univ. Grenoble Alpes, LiPhy, F-38044 Grenoble, France
| | - Martina Řihová
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France.,Institute of Physics, Charles University, Faculty of Mathematics and Physics, CZ-121 16 Prague, Czech Republic
| | - Ella Zimmerman
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - J Ollivier
- Institut Laue Langevin, F-38042 Grenoble, France
| | - J Combet
- Institut Laue Langevin, F-38042 Grenoble, France.,Institut Charles Sadron, CNRS-UdS, 67034 Strasbourg Cedex 2, France
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité, ISYEB - UMR 7205- CNRS, MNHN, UPMC, EPHE UPMC, Sorbonne Universités, 57 rue Cuvier, CP 50, 75005 Paris, France
| | - Anat Bashan
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
| | - Ada Yonath
- Weizmann Institute, Department of Structural Biology, 76100 Rehovot, Israel
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24
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Gracia B, Xue Y, Bisaria N, Herschlag D, Al-Hashimi HM, Russell R. RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. J Mol Biol 2016; 428:3972-3985. [PMID: 27452365 PMCID: PMC5048535 DOI: 10.1016/j.jmb.2016.07.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 11/27/2022]
Abstract
Structured RNAs fold through multiple pathways, but we have little understanding of the molecular features that dictate folding pathways and determine rates along a given pathway. Here, we asked whether folding of a complex RNA can be understood from its structural modules. In a two-piece version of the Tetrahymena group I ribozyme, the separated P5abc subdomain folds to local native secondary and tertiary structure in a linked transition and assembles with the ribozyme core via three tertiary contacts: a kissing loop (P14), a metal core-receptor interaction, and a tetraloop-receptor interaction, the first two of which are expected to depend on native P5abc structure from the local transition. Native gel, NMR, and chemical footprinting experiments showed that mutations that destabilize the native P5abc structure slowed assembly up to 100-fold, indicating that P5abc folds first and then assembles with the core by conformational selection. However, rate decreases beyond 100-fold were not observed because an alternative pathway becomes dominant, with nonnative P5abc binding the core and then undergoing an induced-fit rearrangement. P14 is formed in the rate-limiting step along the conformational selection pathway but after the rate-limiting step along the induced-fit pathway. Strikingly, the assembly rate along the conformational selection pathway resembles that of an isolated kissing loop similar to P14, and the rate along the induced-fit pathway resembles that of an isolated tetraloop-receptor interaction. Our results indicate substantial modularity in RNA folding and assembly and suggest that these processes can be understood in terms of underlying structural modules.
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Affiliation(s)
- Brant Gracia
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Yi Xue
- Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Namita Bisaria
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Chemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Rick Russell
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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25
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Sutton JL, Pollack L. Tuning RNA Flexibility with Helix Length and Junction Sequence. Biophys J 2016; 109:2644-2653. [PMID: 26682821 DOI: 10.1016/j.bpj.2015.10.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/25/2015] [Accepted: 10/27/2015] [Indexed: 12/11/2022] Open
Abstract
The increasing awareness of RNA's central role in biology calls for a new understanding of how RNAs, like proteins, recognize biological partners. Because RNA is inherently flexible, it assumes a variety of conformations. This conformational flexibility can be a critical aspect of how RNA attracts and binds molecular partners. Structurally, RNA consists of rigid basepaired duplexes, separated by flexible non-basepaired regions. Here, using an RNA system consisting of two short helices, connected by a single-stranded (non-basepaired) junction, we explore the role of helix length and junction sequence in determining the range of conformations available to a model RNA. Single-molecule Förster resonance energy transfer reports on the RNA conformation as a function of either mono- or divalent ion concentration. Electrostatic repulsion between helices dominates at low salt concentration, whereas junction sequence effects determine the conformations at high salt concentration. Near physiological salt concentrations, RNA conformation is sensitive to both helix length and junction sequence, suggesting a means for sensitively tuning RNA conformations.
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Affiliation(s)
- Julie L Sutton
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York.
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26
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Shi YZ, Jin L, Wang FH, Zhu XL, Tan ZJ. Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions. Biophys J 2016; 109:2654-2665. [PMID: 26682822 DOI: 10.1016/j.bpj.2015.11.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/09/2015] [Accepted: 11/06/2015] [Indexed: 10/24/2022] Open
Abstract
A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility, and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a three-bead coarse-grained predictive model with implicit salt/solvent potentials. In this study, we further develop the model by improving the implicit-salt electrostatic potential and including a sequence-dependent coaxial stacking potential to enable the model to simulate RNA 3D structure folding in divalent/monovalent ion solutions. The model presented here can predict 3D structures of RNA hairpins with bulges/internal loops (<77 nucleotides) from their sequences at the corresponding experimental ion conditions with an overall improved accuracy compared to the experimental data; the model also makes reliable predictions for the flexibility of RNA hairpins with bulge loops of different lengths at several divalent/monovalent ion conditions. In addition, the model successfully predicts the stability of RNA hairpins with various loops/stems in divalent/monovalent ion solutions.
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Affiliation(s)
- Ya-Zhou Shi
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of the Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Lei Jin
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of the Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Feng-Hua Wang
- Engineering Training Center, Jianghan University, Wuhan, China
| | - Xiao-Long Zhu
- Department of Physics, School of Physics and Information Engineering, Jianghan University, Wuhan, China
| | - Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of the Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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27
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Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway. Proc Natl Acad Sci U S A 2016; 113:E4956-65. [PMID: 27493222 DOI: 10.1073/pnas.1525082113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The past decade has seen a wealth of 3D structural information about complex structured RNAs and identification of functional intermediates. Nevertheless, developing a complete and predictive understanding of the folding and function of these RNAs in biology will require connection of individual rate and equilibrium constants to structural changes that occur in individual folding steps and further relating these steps to the properties and behavior of isolated, simplified systems. To accomplish these goals we used the considerable structural knowledge of the folded, unfolded, and intermediate states of P4-P6 RNA. We enumerated structural states and possible folding transitions and determined rate and equilibrium constants for the transitions between these states using single-molecule FRET with a series of mutant P4-P6 variants. Comparisons with simplified constructs containing an isolated tertiary contact suggest that a given tertiary interaction has a stereotyped rate for breaking that may help identify structural transitions within complex RNAs and simplify the prediction of folding kinetics and thermodynamics for structured RNAs from their parts. The preferred folding pathway involves initial formation of the proximal tertiary contact. However, this preference was only ∼10 fold and could be reversed by a single point mutation, indicating that a model akin to a protein-folding contact order model will not suffice to describe RNA folding. Instead, our results suggest a strong analogy with a modified RNA diffusion-collision model in which tertiary elements within preformed secondary structures collide, with the success of these collisions dependent on whether the tertiary elements are in their rare binding-competent conformations.
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink–Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling. Biochemistry 2016; 55:4295-305. [DOI: 10.1021/acs.biochem.6b00287] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jackie M. Esquiaqui
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eileen M. Sherman
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Jing-Dong Ye
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Gail E. Fanucci
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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29
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Thyme SB, Akhmetova L, Montague TG, Valen E, Schier AF. Internal guide RNA interactions interfere with Cas9-mediated cleavage. Nat Commun 2016; 7:11750. [PMID: 27282953 PMCID: PMC4906408 DOI: 10.1038/ncomms11750] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 04/27/2016] [Indexed: 01/11/2023] Open
Abstract
The CRISPR/Cas system uses guide RNAs (gRNAs) to direct sequence-specific DNA cleavage. Not every gRNA elicits cleavage and the mechanisms that govern gRNA activity have not been resolved. Low activity could result from either failure to form a functional Cas9-gRNA complex or inability to recognize targets in vivo. Here we show that both phenomena influence Cas9 activity by comparing mutagenesis rates in zebrafish embryos with in vitro cleavage assays. In vivo, our results suggest that genomic factors such as CTCF inhibit mutagenesis. Comparing near-identical gRNA sequences with different in vitro activities reveals that internal gRNA interactions reduce cleavage. Even though gRNAs containing these structures do not yield cleavage-competent complexes, they can compete with active gRNAs for binding to Cas9. These results reveal that both genomic context and internal gRNA interactions can interfere with Cas9-mediated cleavage and illuminate previously uncharacterized features of Cas9-gRNA complex formation.
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Affiliation(s)
- Summer B. Thyme
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, BIOL 1020, Cambridge, Massachusetts 02138, USA
| | - Laila Akhmetova
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, BIOL 1020, Cambridge, Massachusetts 02138, USA
| | - Tessa G. Montague
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, BIOL 1020, Cambridge, Massachusetts 02138, USA
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgaten 55, 5008 Bergen, Norway
| | - Alexander F. Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
- FAS Center for Systems Biology, Harvard University, Harvard, Massachusetts 02138, USA
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30
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Nucleic acid polymeric properties and electrostatics: Directly comparing theory and simulation with experiment. Adv Colloid Interface Sci 2016; 232:49-56. [PMID: 26482088 DOI: 10.1016/j.cis.2015.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/18/2015] [Accepted: 09/29/2015] [Indexed: 11/24/2022]
Abstract
Nucleic acids are biopolymers that carry genetic information and are also involved in various gene regulation functions such as gene silencing and protein translation. Because of their negatively charged backbones, nucleic acids are polyelectrolytes. To adequately understand nucleic acid folding and function, we need to properly describe its i) polymer/polyelectrolyte properties and ii) associating ion atmosphere. While various theories and simulation models have been developed to describe nucleic acids and the ions around them, many of these theories/simulations have not been well evaluated due to complexities in comparison with experiment. In this review, I discuss some recent experiments that have been strategically designed for straightforward comparison with theories and simulation models. Such data serve as excellent benchmarks to identify limitations in prevailing theories and simulation parameters.
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31
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Shi X, Huang L, Lilley DMJ, Harbury PB, Herschlag D. The solution structural ensembles of RNA kink-turn motifs and their protein complexes. Nat Chem Biol 2016; 12:146-52. [PMID: 26727239 PMCID: PMC4755865 DOI: 10.1038/nchembio.1997] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/04/2015] [Indexed: 12/22/2022]
Abstract
With the growing number of crystal structures of RNA and RNA-protein complexes, a critical next step is understanding the dynamic solution behavior of these entities in terms of conformational ensembles and energy landscapes. To this end, we have used X-ray scattering interferometry (XSI) to probe the ubiquitous RNA kink-turn motif and its complexes with the canonical kink-turn binding protein L7Ae. XSI revealed that the folded kink-turn is best described as a restricted conformational ensemble. The ions present in solution alter the nature of this ensemble, and protein binding can perturb the kink-turn ensemble without collapsing it to a unique state. This study demonstrates how XSI can reveal structural and ensemble properties of RNAs and RNA-protein complexes and uncovers the behavior of an important RNA-protein motif. This type of information will be necessary to understand, predict and engineer the behavior and function of RNAs and their protein complexes.
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Affiliation(s)
- Xuesong Shi
- Department of Biochemistry, Stanford University, Stanford, California, USA
| | - Lin Huang
- Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - David M J Lilley
- Nucleic Acid Structure Research Group, School of Life Sciences, University of Dundee, Dundee, UK
| | - Pehr B Harbury
- Department of Biochemistry, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California, USA
- ChEM-H, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
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32
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Xu X, Yu T, Chen SJ. Understanding the kinetic mechanism of RNA single base pair formation. Proc Natl Acad Sci U S A 2016; 113:116-21. [PMID: 26699466 PMCID: PMC4711849 DOI: 10.1073/pnas.1517511113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RNA functions are intrinsically tied to folding kinetics. The most elementary step in RNA folding is the closing and opening of a base pair. Understanding this elementary rate process is the basis for RNA folding kinetics studies. Previous studies mostly focused on the unfolding of base pairs. Here, based on a hybrid approach, we investigate the folding process at level of single base pairing/stacking. The study, which integrates molecular dynamics simulation, kinetic Monte Carlo simulation, and master equation methods, uncovers two alternative dominant pathways: Starting from the unfolded state, the nucleotide backbone first folds to the native conformation, followed by subsequent adjustment of the base conformation. During the base conformational rearrangement, the backbone either retains the native conformation or switches to nonnative conformations in order to lower the kinetic barrier for base rearrangement. The method enables quantification of kinetic partitioning among the different pathways. Moreover, the simulation reveals several intriguing ion binding/dissociation signatures for the conformational changes. Our approach may be useful for developing a base pair opening/closing rate model.
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Affiliation(s)
- Xiaojun Xu
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211
| | - Tao Yu
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211; Department of Physics, Jianghan University, Wuhan, Hubei 430056, China
| | - Shi-Jie Chen
- Department of Physics, University of Missouri, Columbia, MO 65211; Department of Biochemistry, University of Missouri, Columbia, MO 65211; Informatics Institute, University of Missouri, Columbia, MO 65211;
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33
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Abstract
The 60-nt GTPase center (GAC) of 23S rRNA has a phylogenetically conserved secondary structure with two hairpin loops and a 3-way junction. It folds into an intricate tertiary structure upon addition of Mg(2+) ions, which is stabilized by the L11 protein in cocrystal structures. Here, we monitor the kinetics of its tertiary folding and Mg(2+)-dependent intermediate states by observing selected nucleobases that contribute specific interactions to the GAC tertiary structure in the cocrystals. The fluorescent nucleobase 2-aminopurine replaced three individual adenines, two of which make long-range stacking interactions and one that also forms hydrogen bonds. Each site reveals a unique response to Mg(2+) addition and temperature, reflecting its environmental change from secondary to tertiary structure. Stopped-flow fluorescence experiments revealed that kinetics of tertiary structure formation upon addition of MgCl2 are also site specific, with local conformational changes occurring from 5 ms to 4s and with global folding from 1 to 5s. Site-specific substitution with (15)N-nucleobases allowed observation of stable hydrogen bond formation by NMR experiments. Equilibrium titration experiments indicate that a stable folding intermediate is present at stoichiometric concentrations of Mg(2+) and suggest that there are two initial sites of Mg(2+) ion association.
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