1
|
Harish B, Wang J, Hayden EJ, Grabe B, Hiller W, Winter R, Royer CA. Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation. Biophys J 2022; 121:421-429. [PMID: 34971617 PMCID: PMC8822612 DOI: 10.1016/j.bpj.2021.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/12/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Fluorescent RNA aptamers have the potential to enable routine quantitation and localization of RNA molecules and serve as models for understanding biologically active aptamers. In recent years, several fluorescent aptamers have been selected and modified to improve their properties, revealing that small changes to the RNA or the ligands can modify significantly their fluorescent properties. Although structural biology approaches have revealed the bound, ground state of several fluorescent aptamers, characterization of low-abundance, excited states in these systems is crucial to understanding their folding pathways. Here we use pressure as an alternative variable to probe the suboptimal states of the Mango III aptamer with both fluorescence and NMR spectroscopy approaches. At moderate KCl concentrations, increasing pressure disrupted the G-quadruplex structure of the Mango III RNA and led to an intermediate with lower fluorescence. These observations indicate the existence of suboptimal RNA structural states that still bind the TO1-biotin fluorophore and moderately enhance fluorescence. At higher KCl concentration as well, the intermediate fluorescence state was populated at high pressure, but the G-quadruplex remained stable at high pressure, supporting the notion of parallel folding and/or binding pathways. These results demonstrate the usefulness of pressure for characterizing RNA folding intermediates.
Collapse
Affiliation(s)
| | - Jinqiu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy
| | | | - Bastian Grabe
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy,Corresponding author
| |
Collapse
|
2
|
Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution. Nature 2021; 596:603-607. [PMID: 34381213 PMCID: PMC8405103 DOI: 10.1038/s41586-021-03803-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution1-3. However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure-function relationships4, but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure-function relationships in ribozymes.
Collapse
|
3
|
Abstract
Classical enzyme kinetic theories are summarized and linked with modern discoveries here. The sequential catalytic events along time axis by enzyme are analyzed at the molecular level, and by using master equations, this writing tries to connect the microscopic molecular behavior of enzyme to kinetic data (like velocity and catalytic coefficient k) obtained in experiment: 1/k = t equals to the sum of the times taken by the constituent individual steps. The relationships between catalytic coefficient k, catalytic rate or velocity, the amount of time taken by each step and physical or biochemical conditions of the system are discussed, and the perspective and hypothetic equations proposed here regarding diffusion, conformational change, chemical conversion, product release steps and the whole catalytic cycle provide an interpretation of previous experimental observations and can be testified by future experiments.
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Tanaka T, Matsumura S, Furuta H, Ikawa Y. Tecto-GIRz: Engineered Group I Ribozyme the Catalytic Ability of Which Can Be Controlled by Self-Dimerization. Chembiochem 2016; 17:1448-55. [DOI: 10.1002/cbic.201600190] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Takahiro Tanaka
- Department of Chemistry and Biochemistry; Graduate School of Engineering; Kyushu University; Moto-oka 744 Nishi-ku Fukuoka 819-0395 Japan
| | - Shigeyoshi Matsumura
- Department of Chemistry; Graduate School of Science and Engineering; University of Toyama; Gofuku 3190 Toyama 930-8555 Japan
| | - Hiroyuki Furuta
- Department of Chemistry and Biochemistry; Graduate School of Engineering; Kyushu University; Moto-oka 744 Nishi-ku Fukuoka 819-0395 Japan
| | - Yoshiya Ikawa
- Department of Chemistry; Graduate School of Science and Engineering; University of Toyama; Gofuku 3190 Toyama 930-8555 Japan
| |
Collapse
|
7
|
Collins JC, Bedford JT, Greene LH. Elucidating the Key Determinants of Structure, Folding, and Stability for the ( 4β+ α ) Conformation of the B1 Domain of Protein G Using Bioinformatics Approaches. IEEE Trans Nanobioscience 2016; 15:140-7. [PMID: 27071185 DOI: 10.1109/tnb.2016.2546247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The B1 domain of protein G (GB1) is a small, 56 amino acid bacterial immunoglobulin-binding protein with a 4β+ α fold. Architecturally, it is composed of a two-layer sandwich consisting of a four-stranded β -sheet that packs against an α -helix. Using several bioinformatics approaches, we investigated which residues may be key determinants of this fold. We identified nine structurally conserved amino acids using a conservation analysis and propose they are critical to forming and stabilizing the fold. The nine conserved residues form a predominantly hydrophobic nucleus within the core of GB1. A network analysis of all the long-range interactions in the structure of GB1 in concert with a betweenness centrality analysis revealed the relative significance of each conserved amino acid residue based on the number and location of the interactions. This bioinformatics analysis provides an important foundation for the design and interpretation of both computational and experimental work which may be helpful in solving the protein folding problem.
Collapse
|
8
|
Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4-P6 RNA by smFRET. Biochem Soc Trans 2016; 43:172-8. [PMID: 25849913 DOI: 10.1042/bst20140268] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Structured RNA molecules play roles in central biological processes and understanding the basic forces and features that govern RNA folding kinetics and thermodynamics can help elucidate principles that underlie biological function. Here we investigate one such feature, the specific interaction of monovalent cations with a structured RNA, the P4-P6 domain of the Tetrahymena ribozyme. We employ single molecule FRET (smFRET) approaches as these allow determination of folding equilibrium and rate constants over a wide range of stabilities and thus allow direct comparisons without the need for extrapolation. These experiments provide additional evidence for specific binding of monovalent cations, Na+ and K+, to the RNA tetraloop-tetraloop receptor (TL-TLR) tertiary motif. These ions facilitate both folding and unfolding, consistent with an ability to help order the TLR for binding and further stabilize the tertiary contact subsequent to attainment of the folding transition state.
Collapse
|
9
|
Lee HT, Kilburn D, Behrouzi R, Briber RM, Woodson SA. Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme. Nucleic Acids Res 2015; 43:1170-6. [PMID: 25541198 PMCID: PMC4333387 DOI: 10.1093/nar/gku1335] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 11/13/2022] Open
Abstract
The native structure of the Azoarcus group I ribozyme is stabilized by the cooperative formation of tertiary interactions between double helical domains. Thus, even single mutations that break this network of tertiary interactions reduce ribozyme activity in physiological Mg(2+) concentrations. Here, we report that molecular crowding comparable to that in the cell compensates for destabilizing mutations in the Azoarcus ribozyme. Small angle X-ray scattering, native polyacrylamide gel electrophoresis and activity assays were used to compare folding free energies in dilute and crowded solutions containing 18% PEG1000. Crowder molecules allowed the wild-type and mutant ribozymes to fold at similarly low Mg(2+) concentrations and stabilized the active structure of the mutant ribozymes under physiological conditions. This compensation helps explains why ribozyme mutations are often less deleterious in the cell than in the test tube. Nevertheless, crowding did not rescue the high fraction of folded but less active structures formed by double and triple mutants. We conclude that crowding broadens the fitness landscape by stabilizing compact RNA structures without improving the specificity of self-assembly.
Collapse
Affiliation(s)
- Hui-Ting Lee
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Duncan Kilburn
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA Center for Neutron Scattering Research, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD 20899, USA
| | - Reza Behrouzi
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Robert M Briber
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Sarah A Woodson
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| |
Collapse
|
10
|
DEAD-box helicase proteins disrupt RNA tertiary structure through helix capture. PLoS Biol 2014; 12:e1001981. [PMID: 25350280 PMCID: PMC4211656 DOI: 10.1371/journal.pbio.1001981] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/18/2014] [Indexed: 01/11/2023] Open
Abstract
Single-molecule fluorescence experiments reveal how DEAD-box proteins unfold structured RNAs to promote conformational transitions and refolding to the native functional state. DEAD-box helicase proteins accelerate folding and rearrangements of highly structured RNAs and RNA–protein complexes (RNPs) in many essential cellular processes. Although DEAD-box proteins have been shown to use ATP to unwind short RNA helices, it is not known how they disrupt RNA tertiary structure. Here, we use single molecule fluorescence to show that the DEAD-box protein CYT-19 disrupts tertiary structure in a group I intron using a helix capture mechanism. CYT-19 binds to a helix within the structured RNA only after the helix spontaneously loses its tertiary contacts, and then CYT-19 uses ATP to unwind the helix, liberating the product strands. Ded1, a multifunctional yeast DEAD-box protein, gives analogous results with small but reproducible differences that may reflect its in vivo roles. The requirement for spontaneous dynamics likely targets DEAD-box proteins toward less stable RNA structures, which are likely to experience greater dynamic fluctuations, and provides a satisfying explanation for previous correlations between RNA stability and CYT-19 unfolding efficiency. Biologically, the ability to sense RNA stability probably biases DEAD-box proteins to act preferentially on less stable misfolded structures and thereby to promote native folding while minimizing spurious interactions with stable, natively folded RNAs. In addition, this straightforward mechanism for RNA remodeling does not require any specific structural environment of the helicase core and is likely to be relevant for DEAD-box proteins that promote RNA rearrangements of RNP complexes including the spliceosome and ribosome. In addition to carrying genetic information from DNA to protein, RNAs function in many essential cellular processes. This often requires the RNA to form a specific three-dimensional structure, and some functions require cycling between multiple structures. However, RNAs have a strong propensity to become trapped in nonfunctional, misfolded structures. Due to the intrinsic stability of local structure for RNA, these misfolded species can be long-lived and therefore accumulate. ATP-dependent RNA chaperone proteins called DEAD-box proteins are known to promote native RNA folding by disrupting misfolded structures. Although these proteins can unwind short RNA helices, the mechanism by which they act upon higher order tertiary contacts is unknown. Our current work shows that DEAD-box proteins capture transiently exposed RNA helices, preventing any tertiary contacts from reforming and potentially destabilizing the global RNA architecture. Helix unwinding by the DEAD-box protein then allows the product RNA strands to form new contacts. This helix capture mechanism for manipulation of RNA tertiary structure does not require a specific binding motif or structural environment and may be general for DEAD-box helicase proteins that act on structured RNAs.
Collapse
|