1
|
Escobar CA, Petersen RJ, Tonelli M, Fan L, Henzler-Wildman KA, Butcher SE. Solution Structure of Poly(UG) RNA. J Mol Biol 2023; 435:168340. [PMID: 37924862 PMCID: PMC10841838 DOI: 10.1016/j.jmb.2023.168340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Poly(UG) or "pUG" RNAs are UG or GU dinucleotide repeat sequences which are highly abundant in eukaryotes. Post-transcriptional addition of pUGs to RNA 3' ends marks mRNAs as vectors for gene silencing in C. elegans. We previously determined the crystal structure of pUG RNA bound to the ligand N-methyl mesoporphyrin IX (NMM), but the structure of free pUG RNA is unknown. Here we report the solution structure of the free pUG RNA (GU)12, as determined by nuclear magnetic resonance spectroscopy and small and wide-angle x-ray scattering (NMR-SAXS-WAXS). The low complexity sequence and 4-fold symmetry of the structure result in overlapped NMR signals that complicate chemical shift assignment. We therefore utilized single site-specific deoxyribose modifications which did not perturb the structure and introduced well-resolved methylene signals that are easily identified in NMR spectra. The solution structure ensemble has a root mean squared deviation (RMSD) of 0.62 Å and is a compact, left-handed quadruplex with a Z-form backbone, or "pUG fold." Overall, the structure agrees with the crystal structure of (GU)12 bound to NMM, indicating the pUG fold is unaltered by docking of the NMM ligand. The solution structure reveals conformational details that could not be resolved by x-ray crystallography, which explain how the pUG fold can form within longer RNAs.
Collapse
Affiliation(s)
- Cristian A Escobar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Riley J Petersen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Marco Tonelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of National Cancer Institute, Frederick, MD, USA
| | - Katherine A Henzler-Wildman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
2
|
Chandy SK, Raghavachari K. MIM-ML: A Novel Quantum Chemical Fragment-Based Random Forest Model for Accurate Prediction of NMR Chemical Shifts of Nucleic Acids. J Chem Theory Comput 2023; 19:6632-6642. [PMID: 37703522 DOI: 10.1021/acs.jctc.3c00563] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
We developed a random forest machine learning (ML) model for the prediction of 1H and 13C NMR chemical shifts of nucleic acids. Our ML model is trained entirely on reproducing computed chemical shifts obtained previously on 10 nucleic acids using a Molecules-in-Molecules (MIM) fragment-based density functional theory (DFT) protocol including microsolvation effects. Our ML model includes structural descriptors as well as electronic descriptors from an inexpensive low-level semiempirical calculation (GFN2-xTB) and trained on a relatively small number of DFT chemical shifts (2080 1H chemical shifts and 1780 13C chemical shifts on the 10 nucleic acids). The ML model is then used to make chemical shift predictions on 8 new nucleic acids ranging in size from 600 to 900 atoms and compared directly to experimental data. Though no experimental data was used in the training, the performance of our model is excellent (mean absolute deviation of 0.34 ppm for 1H chemical shifts and 2.52 ppm for 13C chemical shifts for the test set), despite having some nonstandard structures. A simple analysis suggests that both structural and electronic descriptors are critical for achieving reliable predictions. This is the first attempt to combine ML from fragment-based DFT calculations to predict experimental chemical shifts accurately, making the MIM-ML model a valuable tool for NMR predictions of nucleic acids.
Collapse
Affiliation(s)
- Sruthy K Chandy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
3
|
Pintea M, Mason N, Peiró-Franch A, Clark E, Samanta K, Glessi C, Schmidtke IL, Luxford T. Dissociative electron attachment to gold(I)-based compounds: 4,5-dichloro-1,3-diethyl-imidazolylidene trifluoromethyl gold(I). Front Chem 2023; 11:1028008. [PMID: 37405247 PMCID: PMC10315492 DOI: 10.3389/fchem.2023.1028008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
With the use of proton-NMR and powder XRD (XRPD) studies, the suitability of specific Au-focused electron beam induced deposition (FEBID) precursors has been investigated with low electron energy, structure, excited states and resonances, structural crystal modifications, flexibility, and vaporization level. 4,5-Dichloro-1,3-diethyl-imidazolylidene trifluoromethyl gold(I) is a compound that is a uniquely designed precursor to meet the needs of focused electron beam-induced deposition at the nanostructure level, which proves its capability in creating high purity structures, and its growing importance in other AuImx and AuClnB (where x and n are the number of radicals, B = CH, CH3, or Br) compounds in the radiation cancer therapy increases the efforts to design more suitable bonds in processes of SEM (scanning electron microscopy) deposition and in gas-phase studies. The investigation performed of its powder shape using the XRPD XPERT3 panalytical diffractometer based on CoKα lines shows changes to its structure with change in temperature, level of vacuum, and light; the sensitivity of this compound makes it highly interesting in particular to the radiation research. Used in FEBID, though its smaller number of C, H, and O atoms has lower levels of C contamination in the structures and on the surface, it replaces these bonds with C-Cl and C-N bonds that have lower bond-breaking energy. However, it still needs an extra purification step in the deposition process, either H2O, O2, or H jets.
Collapse
Affiliation(s)
- Maria Pintea
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | - Nigel Mason
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | - Anna Peiró-Franch
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | - Ewan Clark
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | - Kushal Samanta
- School of Physical Sciences, University of Kent, Canterbury, United Kingdom
| | | | | | - Thomas Luxford
- Department of Chemistry, J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czechia
| |
Collapse
|
4
|
Das NK, Hollmann NM, Vogt J, Sevdalis SE, Banna HA, Ojha M, Koirala D. Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element. Nat Commun 2023; 14:1955. [PMID: 37029118 PMCID: PMC10082201 DOI: 10.1038/s41467-023-37658-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.
Collapse
Affiliation(s)
- Naba K Das
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Nele M Hollmann
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
- Howard Hughes Medical Institute, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Jeff Vogt
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Spiridon E Sevdalis
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Hasan A Banna
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Manju Ojha
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, 21250, USA.
| |
Collapse
|
5
|
Wang J, Sha CM, Dokholyan NV. Combining Experimental Restraints and RNA 3D Structure Prediction in RNA Nanotechnology. Methods Mol Biol 2023; 2709:51-64. [PMID: 37572272 PMCID: PMC10680996 DOI: 10.1007/978-1-0716-3417-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Precise RNA tertiary structure prediction can aid in the design of RNA nanoparticles. However, most existing RNA tertiary structure prediction methods are limited to small RNAs with relatively simple secondary structures. Large RNA molecules usually have complex secondary structures, including multibranched loops and pseudoknots, allowing for highly flexible RNA geometries and multiple stable states. Various experiments and bioinformatics analyses can often provide information about the distance between atoms (or residues) in RNA, which can be used to guide the prediction of RNA tertiary structure. In this chapter, we will introduce a platform, iFoldNMR, that can incorporate non-exchangeable imino protons resonance data from NMR as restraints for RNA 3D structure prediction. We also introduce an algorithm, DVASS, which optimizes distance restraints for better RNA 3D structure prediction.
Collapse
Affiliation(s)
- Jian Wang
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
| | - Congzhou M Sha
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
- Department of Engineering Science and Mechanics, Penn State University, State College, PA, USA
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA.
- Department of Engineering Science and Mechanics, Penn State University, State College, PA, USA.
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA.
- Department of Chemistry, Penn State University, State College, PA, USA.
- Department of Biomedical Engineering, Penn State University, State College, PA, USA.
| |
Collapse
|
6
|
Mollica L, Cupaioli FA, Rossetti G, Chiappori F. An overview of structural approaches to study therapeutic RNAs. Front Mol Biosci 2022; 9:1044126. [PMID: 36387283 PMCID: PMC9649582 DOI: 10.3389/fmolb.2022.1044126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2023] Open
Abstract
RNAs provide considerable opportunities as therapeutic agent to expand the plethora of classical therapeutic targets, from extracellular and surface proteins to intracellular nucleic acids and its regulators, in a wide range of diseases. RNA versatility can be exploited to recognize cell types, perform cell therapy, and develop new vaccine classes. Therapeutic RNAs (aptamers, antisense nucleotides, siRNA, miRNA, mRNA and CRISPR-Cas9) can modulate or induce protein expression, inhibit molecular interactions, achieve genome editing as well as exon-skipping. A common RNA thread, which makes it very promising for therapeutic applications, is its structure, flexibility, and binding specificity. Moreover, RNA displays peculiar structural plasticity compared to proteins as well as to DNA. Here we summarize the recent advances and applications of therapeutic RNAs, and the experimental and computational methods to analyze their structure, by biophysical techniques (liquid-state NMR, scattering, reactivity, and computational simulations), with a focus on dynamic and flexibility aspects and to binding analysis. This will provide insights on the currently available RNA therapeutic applications and on the best techniques to evaluate its dynamics and reactivity.
Collapse
Affiliation(s)
- Luca Mollica
- Department of Medical Biotechnologies and Translational Medicine, L.I.T.A/University of Milan, Milan, Italy
| | | | | | - Federica Chiappori
- National Research Council—Institute for Biomedical Technologies, Milan, Italy
| |
Collapse
|
7
|
Krivdin LB. Computational 1 H and 13 C NMR in structural and stereochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2022; 60:733-828. [PMID: 35182410 DOI: 10.1002/mrc.5260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Present review outlines the advances and perspectives of computational 1 H and 13 C NMR applied to the stereochemical studies of inorganic, organic, and bioorganic compounds, involving in particular natural products, carbohydrates, and carbonium ions. The first part of the review briefly outlines theoretical background of the modern computational methods applied to the calculation of chemical shifts and spin-spin coupling constants at the DFT and the non-empirical levels. The second part of the review deals with the achievements of the computational 1 H and 13 C NMR in the stereochemical investigation of a variety of inorganic, organic, and bioorganic compounds, providing in an abridged form the material partly discussed by the author in a series of parent reviews. Major attention is focused herewith on the publications of the recent years, which were not reviewed elsewhere.
Collapse
Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| |
Collapse
|
8
|
Liu Y, Kotar A, Hodges TL, Abdallah K, Taleb MH, Bitterman BA, Jaime S, Schaubroeck KJ, Mathew E, Morgenstern NW, Lohmeier A, Page JL, Ratanapanichkich M, Arhin G, Johnson BL, Cherepanov S, Moss SC, Zuniga G, Tilson NJ, Yeoh ZC, Johnson BA, Keane SC. NMR chemical shift assignments of RNA oligonucleotides to expand the RNA chemical shift database. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:479-490. [PMID: 34449019 DOI: 10.1007/s12104-021-10049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
Abstract
RNAs play myriad functional and regulatory roles in the cell. Despite their significance, three-dimensional structure elucidation of RNA molecules lags significantly behind that of proteins. NMR-based studies are often rate-limited by the assignment of chemical shifts. Automation of the chemical shift assignment process can greatly facilitate structural studies, however, accurate chemical shift predictions rely on a robust and complete chemical shift database for training. We searched the Biological Magnetic Resonance Data Bank (BMRB) to identify sequences that had no (or limited) chemical shift information. Here, we report the chemical shift assignments for 12 RNA hairpins designed specifically to help populate the BMRB.
Collapse
Affiliation(s)
- Yaping Liu
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Anita Kotar
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
- Current Address: Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Tracy L Hodges
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Kyrillos Abdallah
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Mallak H Taleb
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Brayden A Bitterman
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Sara Jaime
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Kyle J Schaubroeck
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Ethan Mathew
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Nicholas W Morgenstern
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Anthony Lohmeier
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Jordan L Page
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Matt Ratanapanichkich
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Grace Arhin
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Breanna L Johnson
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Stanislav Cherepanov
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Stephen C Moss
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Gisselle Zuniga
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Nicholas J Tilson
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA
| | - Zoe C Yeoh
- Department of Biological Chemistry, University of Michigan, 1150 W. Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Sarah C Keane
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA.
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
9
|
Zhang K, Frank AT. Probabilistic Modeling of RNA Ensembles Using NMR Chemical Shifts. J Phys Chem B 2021; 125:9970-9978. [PMID: 34449236 DOI: 10.1021/acs.jpcb.1c05651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
NMR-derived chemical shifts are structural fingerprints that are sensitive to the underlying conformational distributions of molecules. Thus, chemical shift data are now routinely used to infer the dynamical or conformational ensembles of peptides and proteins. However, for RNAs, techniques for inferring their conformational ensembles from chemical shift data have received less attention. Here, we used chemical shift data and the Bayesian/maximum entropy (BME) approach to model the secondary structure ensembles of several single-stranded RNAs. Inspection of the resulting ensembles indicates that the secondary structure of the highest weighted (most probable) conformer in the ensemble typically resembled the known NMR structure. Furthermore, using apo chemical shifts measured for the HIV-1 TAR RNA, we found that our framework reproduces the expected structure yet predicts the existence of a previously unobserved base pair, which we speculate may be sampled transiently. We expect that the chemical shift-based BME (CS-BME) framework we describe here should find utility as a general strategy for modeling RNA ensembles using chemical shift data.
Collapse
Affiliation(s)
- Kexin Zhang
- Chemistry Department, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Aaron T Frank
- Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
10
|
Song Z, Gremminger T, Singh G, Cheng Y, Li J, Qiu L, Ji J, Lange MJ, Zuo X, Chen SJ, Zou X, Boris-Lawrie K, Heng X. The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity. Nucleic Acids Res 2021; 49:5925-5942. [PMID: 33978756 PMCID: PMC8191761 DOI: 10.1093/nar/gkab342] [Citation(s) in RCA: 7] [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: 03/18/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/24/2022] Open
Abstract
HIV-1 reverse transcription initiates at the primer binding site (PBS) in the viral genomic RNA (gRNA). Although the structure of the PBS-segment undergoes substantial rearrangement upon tRNALys3 annealing, the proper folding of the PBS-segment during gRNA packaging is important as it ensures loading of beneficial host factors. DHX9/RNA helicase A (RHA) is recruited to gRNA to enhance the processivity of reverse transcriptase. Because the molecular details of the interactions have yet to be defined, we solved the solution structure of the PBS-segment preferentially bound by RHA. Evidence is provided that PBS-segment adopts a previously undefined adenosine-rich three-way junction structure encompassing the primer activation stem (PAS), tRNA-like element (TLE) and tRNA annealing arm. Disruption of the PBS-segment three-way junction structure diminished reverse transcription products and led to reduced viral infectivity. Because of the existence of the tRNA annealing arm, the TLE and PAS form a bent helical structure that undergoes shape-dependent recognition by RHA double-stranded RNA binding domain 1 (dsRBD1). Mutagenesis and phylogenetic analyses provide evidence for conservation of the PBS-segment three-way junction structure that is preferentially bound by RHA in support of efficient reverse transcription, the hallmark step of HIV-1 replication.
Collapse
Affiliation(s)
- Zhenwei Song
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Thomas Gremminger
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Cheng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Jun Li
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Liming Qiu
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Juan Ji
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Margaret J Lange
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Shi-Jie Chen
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
- Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| |
Collapse
|
11
|
Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states. Nat Commun 2021; 12:1595. [PMID: 33707433 PMCID: PMC7952389 DOI: 10.1038/s41467-021-21840-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 02/10/2021] [Indexed: 11/26/2022] Open
Abstract
NH groups in proteins or nucleic acids are the most challenging target for chemical shift prediction. Here we show that the RNA base pair triplet motif dictates imino chemical shifts in its central base pair. A lookup table is established that links each type of base pair triplet to experimental chemical shifts of the central base pair, and can be used to predict imino chemical shifts of RNAs to remarkable accuracy. Strikingly, the semiempirical method can well interpret the variations of chemical shifts for different base pair triplets, and is even applicable to non-canonical motifs. This finding opens an avenue for predicting chemical shifts of more complicated RNA motifs. Furthermore, we combine the imino chemical shift prediction with NMR relaxation dispersion experiments targeting both 15N and 1HN of the imino group, and verify a previously characterized excited state of P5abc subdomain including an earlier speculated non-native G•G mismatch. Prediction of chemical shifts is critical for extracting structural and dynamic information from biomolecular NMR data. Here the authors report an RNA imino group chemical shift predictor, showing that the imino chemical shifts of a residue are dictated by the surrounding base pair triplet.
Collapse
|
12
|
Zhang H, Hall I, Nissley AJ, Abdallah K, Keane SC. A Tale of Two Transitions: The Unfolding Mechanism of the prfA RNA Thermosensor. Biochemistry 2020; 59:4533-4545. [PMID: 33231432 DOI: 10.1021/acs.biochem.0c00588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA thermosensors (RNATs), found in the 5' untranslated region (UTR) of some bacterial messenger RNAs (mRNAs), control the translation of the downstream gene in a temperature-dependent manner. In Listeria monocytogenes, the expression of a key transcription factor, PrfA, is mediated by an RNAT in its 5' UTR. PrfA functions as a master regulator of virulence in L. monocytogenes, controlling the expression of many virulence factors. The temperature-regulated expression of PrfA by its RNAT element serves as a signal of successful host invasion for the bacteria. Structurally, the prfA RNAT bears little resemblance to known families of RNATs, and prior studies demonstrated that the prfA RNAT is highly responsive over a narrow temperature range. Herein, we have undertaken a comprehensive mutational and thermodynamic analysis to ascertain the molecular determinants of temperature sensitivity. We provide evidence to support the idea that the prfA RNAT unfolding is different from that of cssA, a well-characterized RNAT, suggesting that these RNATs function via distinct mechanisms. Our data show that the unfolding of the prfA RNAT occurs in two distinct events and that the internal loops play an important role in mediating the cooperativity of RNAT unfolding. We further demonstrated that regions distal to the ribosome binding site (RBS) not only contribute to RNAT structural stability but also impact translation of the downstream message. Our collective results provide insight connecting the thermal stability of the prfA RNAT structure, unfolding energetics, and translational control.
Collapse
Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ian Hall
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amos J Nissley
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kyrillos Abdallah
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
13
|
Lawrence C, Grishaev A. Chemical shifts-based similarity restraints improve accuracy of RNA structures determined via NMR. RNA (NEW YORK, N.Y.) 2020; 26:2051-2061. [PMID: 32917774 PMCID: PMC7668244 DOI: 10.1261/rna.074617.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 08/19/2020] [Indexed: 06/01/2023]
Abstract
Determination of structure of RNA via NMR is complicated in large part by the lack of a precise parameterization linking the observed chemical shifts to the underlying geometric parameters. In contrast to proteins, where numerous high-resolution crystal structures serve as coordinate templates for this mapping, such models are rarely available for smaller oligonucleotides accessible via NMR, or they exhibit crystal packing and counter-ion binding artifacts that prevent their use for the chemical shifts analysis. On the other hand, NMR-determined structures of RNA often are not solved at the density of restraints required to precisely define the variable degrees of freedom. In this study we sidestep the problems of direct parameterization of the RNA chemical shifts/structure relationship and examine the effects of imposing local fragmental coordinate similarity restraints based on similarities of the experimental secondary ribose 13C/1H chemical shifts instead. The effect of such chemical shift similarity (CSS) restraints on the structural accuracy is assessed via residual dipolar coupling (RDC)-based cross-validation. Improvements in the coordinate accuracy are observed for all of the six RNA constructs considered here as test cases, which argues for routine inclusion of these terms during NMR-based oligonucleotide structure determination. Such accuracy improvements are expected to facilitate derivation of the chemical shift/structure relationships for RNA.
Collapse
Affiliation(s)
- Chad Lawrence
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
| | - Alexander Grishaev
- Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, USA
- Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| |
Collapse
|
14
|
Advanced approaches for elucidating structures of large RNAs using NMR spectroscopy and complementary methods. Methods 2020; 183:93-107. [DOI: 10.1016/j.ymeth.2020.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 11/23/2022] Open
|
15
|
Becette OB, Zong G, Chen B, Taiwo KM, Case DA, Dayie TK. Solution NMR readily reveals distinct structural folds and interactions in doubly 13C- and 19F-labeled RNAs. SCIENCE ADVANCES 2020; 6:6/41/eabc6572. [PMID: 33028531 PMCID: PMC7541061 DOI: 10.1126/sciadv.abc6572] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/18/2020] [Indexed: 06/10/2023]
Abstract
RNAs form critical components of biological processes implicated in human diseases, making them attractive for small-molecule therapeutics. Expanding the sites accessible to nuclear magnetic resonance (NMR) spectroscopy will provide atomic-level insights into RNA interactions. Here, we present an efficient strategy to introduce 19F-13C spin pairs into RNA by using a 5-fluorouridine-5'-triphosphate and T7 RNA polymerase-based in vitro transcription. Incorporating the 19F-13C label in two model RNAs produces linewidths that are twice as sharp as the commonly used 1H-13C spin pair. Furthermore, the high sensitivity of the 19F nucleus allows for clear delineation of helical and nonhelical regions as well as GU wobble and Watson-Crick base pairs. Last, the 19F-13C label enables rapid identification of a small-molecule binding pocket within human hepatitis B virus encapsidation signal epsilon (hHBV ε) RNA. We anticipate that the methods described herein will expand the size limitations of RNA NMR and aid with RNA-drug discovery efforts.
Collapse
Affiliation(s)
- Owen B Becette
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - Bin Chen
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - Kehinde M Taiwo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - T Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20782, USA.
| |
Collapse
|
16
|
Boyd PS, Brown JB, Brown JD, Catazaro J, Chaudry I, Ding P, Dong X, Marchant J, O’Hern CT, Singh K, Swanson C, Summers MF, Yasin S. NMR Studies of Retroviral Genome Packaging. Viruses 2020; 12:v12101115. [PMID: 33008123 PMCID: PMC7599994 DOI: 10.3390/v12101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/03/2022] Open
Abstract
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
Collapse
|
17
|
Brown JD, Kharytonchyk S, Chaudry I, Iyer AS, Carter H, Becker G, Desai Y, Glang L, Choi SH, Singh K, Lopresti MW, Orellana M, Rodriguez T, Oboh U, Hijji J, Ghinger FG, Stewart K, Francis D, Edwards B, Chen P, Case DA, Telesnitsky A, Summers MF. Structural basis for transcriptional start site control of HIV-1 RNA fate. Science 2020; 368:413-417. [PMID: 32327595 PMCID: PMC7351118 DOI: 10.1126/science.aaz7959] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/24/2020] [Indexed: 12/20/2022]
Abstract
Heterogeneous transcriptional start site usage by HIV-1 produces 5'-capped RNAs beginning with one, two, or three 5'-guanosines (Cap1G, Cap2G, or Cap3G, respectively) that are either selected for packaging as genomes (Cap1G) or retained in cells as translatable messenger RNAs (mRNAs) (Cap2G and Cap3G). To understand how 5'-guanosine number influences fate, we probed the structures of capped HIV-1 leader RNAs by deuterium-edited nuclear magnetic resonance. The Cap1G transcript adopts a dimeric multihairpin structure that sequesters the cap, inhibits interactions with eukaryotic translation initiation factor 4E, and resists decapping. The Cap2G and Cap3G transcripts adopt an alternate structure with an elongated central helix, exposed splice donor residues, and an accessible cap. Extensive remodeling, achieved at the energetic cost of a G-C base pair, explains how a single 5'-guanosine modifies the function of a ~9-kilobase HIV-1 transcript.
Collapse
Affiliation(s)
- Joshua D Brown
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Issac Chaudry
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Aishwarya S Iyer
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Hannah Carter
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Ghazal Becker
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Yash Desai
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Lindsay Glang
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Seung H Choi
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Karndeep Singh
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Michael W Lopresti
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Matthew Orellana
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Tatiana Rodriguez
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Ubiomo Oboh
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Jana Hijji
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Frances Grace Ghinger
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Kailan Stewart
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Dillion Francis
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Bryce Edwards
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Patrick Chen
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - David A Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA.
| | - Michael F Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
| |
Collapse
|
18
|
Krivdin LB. Computational 1 H NMR: Part 3. Biochemical studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:15-30. [PMID: 31286566 DOI: 10.1002/mrc.4895] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 06/09/2023]
Abstract
This is the third and the last part of three closely interrelated reviews dealing with computation of 1 H nuclear magnetic resonance chemical shifts and 1 H-1 H spin-spin coupling constants. Present review deals with the computation of these parameters in biologically active natural products, carbohydrates, and other molecules of biological origin focusing on stereochemical applications of computational 1 H nuclear magnetic resonance to these objects.
Collapse
Affiliation(s)
- Leonid B Krivdin
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
- Department of Chemistry, Angarsk State Technical University, Angarsk, Russia
| |
Collapse
|
19
|
Marchant J, Summers MF, Johnson BA. Assigning NMR spectra of RNA, peptides and small organic molecules using molecular network visualization software. JOURNAL OF BIOMOLECULAR NMR 2019; 73:525-529. [PMID: 31325088 PMCID: PMC6859155 DOI: 10.1007/s10858-019-00271-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
NMR assignment typically involves analysis of peaks across multiple NMR spectra. Chemical shifts of peaks are measured before being assigned to atoms using a variety of methods. These approaches quickly become complicated by overlap, ambiguity, and the complexity of correlating assignments among multiple spectra. Here we propose an alternative approach in which a network of linked peak-boxes is generated at the predicted positions of peaks across all spectra. These peak-boxes correlate known relationships and can be matched to the observed spectra. The method is illustrated with RNA, but a variety of molecular types should be readily tractable with this approach.
Collapse
Affiliation(s)
- Jan Marchant
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
- Howard Hughes Medical Institute, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Bruce A Johnson
- Structural Biology Initiative, CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
| |
Collapse
|
20
|
Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation. Proc Natl Acad Sci U S A 2019; 116:16847-16855. [PMID: 31375637 DOI: 10.1073/pnas.1901530116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Structured RNAs and RNA complexes underlie biological processes ranging from control of gene expression to protein translation. Approximately 50% of nucleotides within known structured RNAs are folded into Watson-Crick (WC) base pairs, and sequence changes that preserve these pairs are typically assumed to preserve higher-order RNA structure and binding of macromolecule partners. Here, we report that indirect effects of the helix sequence on RNA tertiary stability are, in fact, significant but are nevertheless predictable from a simple computational model called RNAMake-∆∆G. When tested through the RNA on a massively parallel array (RNA-MaP) experimental platform, blind predictions for >1500 variants of the tectoRNA heterodimer model system achieve high accuracy (rmsd 0.34 and 0.77 kcal/mol for sequence and length changes, respectively). Detailed comparison of predictions to experiments support a microscopic picture of how helix sequence changes subtly modulate conformational fluctuations at each base-pair step, which accumulate to impact RNA tertiary structure stability. Our study reveals a previously overlooked phenomenon in RNA structure formation and provides a framework of computation and experiment for understanding helix conformational preferences and their impact across biological RNA and RNA-protein assemblies.
Collapse
|
21
|
Rangadurai A, Szymaski ES, Kimsey IJ, Shi H, Al-Hashimi HM. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R 1ρ relaxation dispersion. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 112-113:55-102. [PMID: 31481159 PMCID: PMC6727989 DOI: 10.1016/j.pnmrs.2019.05.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 05/10/2023]
Abstract
This review describes off-resonance R1ρ relaxation dispersion NMR methods for characterizing microsecond-to-millisecond chemical exchange in uniformly 13C/15N labeled nucleic acids in solution. The review opens with a historical account of key developments that formed the basis for modern R1ρ techniques used to study chemical exchange in biomolecules. A vector model is then used to describe the R1ρ relaxation dispersion experiment, and how the exchange contribution to relaxation varies with the amplitude and frequency offset of an applied spin-locking field, as well as the population, exchange rate, and differences in chemical shifts of two exchanging species. Mathematical treatment of chemical exchange based on the Bloch-McConnell equations is then presented and used to examine relaxation dispersion profiles for more complex exchange scenarios including three-state exchange. Pulse sequences that employ selective Hartmann-Hahn cross-polarization transfers to excite individual 13C or 15N spins are then described for measuring off-resonance R1ρ(13C) and R1ρ(15N) in uniformly 13C/15N labeled DNA and RNA samples prepared using commercially available 13C/15N labeled nucleotide triphosphates. Approaches for analyzing R1ρ data measured at a single static magnetic field to extract a full set of exchange parameters are then presented that rely on numerical integration of the Bloch-McConnell equations or the use of algebraic expressions. Methods for determining structures of nucleic acid excited states are then reviewed that rely on mutations and chemical modifications to bias conformational equilibria, as well as structure-based approaches to calculate chemical shifts. Applications of the methodology to the study of DNA and RNA conformational dynamics are reviewed and the biological significance of the exchange processes is briefly discussed.
Collapse
Affiliation(s)
- Atul Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Eric S Szymaski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Isaac J Kimsey
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Nymirum, 4324 S. Alston Avenue, Durham, NC 27713, USA(1)
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA; Department of Chemistry, Duke University, Durham, NC 27710, USA.
| |
Collapse
|
22
|
Zhang H, Keane SC. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1541. [PMID: 31025514 PMCID: PMC7169810 DOI: 10.1002/wrna.1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high-resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
Collapse
Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
23
|
Marchant J, Bax A, Summers MF. Accurate Measurement of Residual Dipolar Couplings in Large RNAs by Variable Flip Angle NMR. J Am Chem Soc 2018; 140:6978-6983. [PMID: 29757635 PMCID: PMC6021016 DOI: 10.1021/jacs.8b03298] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
NMR approaches using nucleotide-specific deuterium labeling schemes have enabled structural studies of biologically relevant RNAs of increasing size and complexity. Although local structure is well-determined using these methods, definition of global structural features, including relative orientations of independent helices, remains a challenge. Residual dipolar couplings, a potential source of orientation information, have not been obtainable for large RNAs due to poor sensitivity resulting from rapid heteronuclear signal decay. Here we report a novel multiple quantum NMR method for RDC determination that employs flip angle variation rather than a coupling evolution period. The accuracy of the method and its utility for establishing interhelical orientations are demonstrated for a 36-nucleotide RNA, for which comparative data could be obtained. Applied to a 78 kDa Rev response element from the HIV-1 virus, which has an effective rotational correlation time of ca. 160 ns, the method yields sensitivity gains of an order of magnitude or greater over existing approaches. Solution-state access to structural organization in RNAs of at least 230 nucleotides is now possible.
Collapse
Affiliation(s)
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes, Digestive and Kidney Diseases , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | | |
Collapse
|
24
|
Nerli S, McShan AC, Sgourakis NG. Chemical shift-based methods in NMR structure determination. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 106-107:1-25. [PMID: 31047599 PMCID: PMC6788782 DOI: 10.1016/j.pnmrs.2018.03.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 05/08/2023]
Abstract
Chemical shifts are highly sensitive probes harnessed by NMR spectroscopists and structural biologists as conformational parameters to characterize a range of biological molecules. Traditionally, assignment of chemical shifts has been a labor-intensive process requiring numerous samples and a suite of multidimensional experiments. Over the past two decades, the development of complementary computational approaches has bolstered the analysis, interpretation and utilization of chemical shifts for elucidation of high resolution protein and nucleic acid structures. Here, we review the development and application of chemical shift-based methods for structure determination with a focus on ab initio fragment assembly, comparative modeling, oligomeric systems, and automated assignment methods. Throughout our discussion, we point out practical uses, as well as advantages and caveats, of using chemical shifts in structure modeling. We additionally highlight (i) hybrid methods that employ chemical shifts with other types of NMR restraints (residual dipolar couplings, paramagnetic relaxation enhancements and pseudocontact shifts) that allow for improved accuracy and resolution of generated 3D structures, (ii) the utilization of chemical shifts to model the structures of sparsely populated excited states, and (iii) modeling of sidechain conformations. Finally, we briefly discuss the advantages of contemporary methods that employ sparse NMR data recorded using site-specific isotope labeling schemes for chemical shift-driven structure determination of larger molecules. With this review, we aim to emphasize the accessibility and versatility of chemical shifts for structure determination of challenging biological systems, and to point out emerging areas of development that lead us towards the next generation of tools.
Collapse
Affiliation(s)
- Santrupti Nerli
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States; Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Andrew C McShan
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States
| | - Nikolaos G Sgourakis
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, United States.
| |
Collapse
|
25
|
Zhang K, Keane SC, Su Z, Irobalieva RN, Chen M, Van V, Sciandra CA, Marchant J, Heng X, Schmid MF, Case DA, Ludtke SJ, Summers MF, Chiu W. Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach. Structure 2018; 26:490-498.e3. [PMID: 29398526 PMCID: PMC5842133 DOI: 10.1016/j.str.2018.01.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/12/2017] [Accepted: 01/03/2018] [Indexed: 02/01/2023]
Abstract
Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS]2; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs.
Collapse
Affiliation(s)
- Kaiming Zhang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah C Keane
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Zhaoming Su
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rossitza N Irobalieva
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muyuan Chen
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Verna Van
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Carly A Sciandra
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Jan Marchant
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri-Columbia, Columbia, MO 65211, USA
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - David A Case
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Michael F Summers
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), Baltimore, MD 21250, USA.
| | - Wah Chiu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
26
|
Williams B, Zhao B, Tandon A, Ding F, Weeks KM, Zhang Q, Dokholyan NV. Structure modeling of RNA using sparse NMR constraints. Nucleic Acids Res 2018; 45:12638-12647. [PMID: 29165648 PMCID: PMC5728392 DOI: 10.1093/nar/gkx1058] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/18/2017] [Indexed: 01/04/2023] Open
Abstract
RNAs fold into distinct molecular conformations that are often essential for their functions. Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge. Here, we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid and accurate structure modeling of complex RNAs. We show that sparse distance constraints from imino resonances, which can be readily obtained from routine NMR experiments and easier to compile than laborious assignments of non-solvent-exchangeable protons, are sufficient to direct a DMD search for low-energy RNA conformers. Benchmarking on a set of RNAs with complex folds spanning up to 56 nucleotides in length yields structural models that recapitulate experimentally determined structures with all-heavy-atom RMSDs ranging from 2.4 to 6.5 Å. This platform represents an efficient approach for high-throughput RNA structure modeling and will facilitate analysis of diverse, newly discovered functional RNAs.
Collapse
Affiliation(s)
- Benfeard Williams
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bo Zhao
- Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Arpit Tandon
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Molecular and Cellular Biophysics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
27
|
Kranawetter C, Brady S, Sun L, Schroeder M, Chen SJ, Heng X. Nuclear Magnetic Resonance Study of RNA Structures at the 3'-End of the Hepatitis C Virus Genome. Biochemistry 2017; 56:4972-4984. [PMID: 28829576 DOI: 10.1021/acs.biochem.7b00573] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The 3'-end of the genomic RNA of the hepatitis C virus (HCV) embeds conserved elements that regulate viral RNA synthesis and protein translation by mechanisms that have yet to be elucidated. Previous studies with oligo-RNA fragments have led to multiple, mutually exclusive secondary structure predictions, indicating that HCV RNA structure may be context-dependent. Here we employed a nuclear magnetic resonance (NMR) approach that involves long-range adenosine interaction detection, coupled with site-specific 2H labeling, to probe the structure of the intact 3'-end of the HCV genome (385 nucleotides). Our data reveal that the 3'-end exists as an equilibrium mixture of two conformations: an open conformation in which the 98 nucleotides of the 3'-tail (3'X) form a two-stem-loop structure with the kissing-loop residues sequestered and a closed conformation in which the 3'X rearranges its structure and forms a long-range kissing-loop interaction with an upstream cis-acting element 5BSL3.2. The long-range kissing species is favored under high-Mg2+ conditions, and the intervening sequences do not affect the equilibrium as their secondary structures remain unchanged. The open and closed conformations are consistent with the reported function regulation of viral RNA synthesis and protein translation, respectively. Our NMR detection of these RNA conformations and the structural equilibrium in the 3'-end of the HCV genome support its roles in coordinating various steps of HCV replication.
Collapse
Affiliation(s)
- Clayton Kranawetter
- Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Samantha Brady
- Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Lizhen Sun
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States
| | - Mark Schroeder
- Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Informatics Institute, University of Missouri , Columbia, Missouri 65211, United States
| | - Xiao Heng
- Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States
| |
Collapse
|
28
|
Chen JL, VanEtten DM, Fountain MA, Yildirim I, Disney MD. Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1. Biochemistry 2017; 56:3463-3474. [PMID: 28617590 PMCID: PMC5810133 DOI: 10.1021/acs.biochem.7b00252] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 × 1 internal loops of r(3×CAG) are stabilized by one-hydrogen bond (cis Watson-Crick/Watson-Crick) AA pairs, while those of r(3×CUG) prefer one- or two-hydrogen bond (cis Watson-Crick/Watson-Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.
Collapse
Affiliation(s)
- Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Damian M. VanEtten
- Department of Chemistry and Biochemistry, State University of New York at Fredonia, Fredonia, New York 14063, United States
| | - Matthew A. Fountain
- Department of Chemistry and Biochemistry, State University of New York at Fredonia, Fredonia, New York 14063, United States
| | - Ilyas Yildirim
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
- Department of Chemistry and Biochemistry, Florida Atlantic University, Jupiter, Florida 33458, United States
| |
Collapse
|
29
|
Steiner E, Schlagnitweit J, Lundström P, Petzold K. Capturing Excited States in the Fast-Intermediate Exchange Limit in Biological Systems Using 1H NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Emilie Steiner
- Department of Medical Biochemistry and Biophysics; Karolinska Institute; 10435 Stockholm Sweden
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics; Karolinska Institute; 10435 Stockholm Sweden
| | - Patrik Lundström
- Department of Physics, Chemistry and Biology; Linköping University; 58183 Linköping Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics; Karolinska Institute; 10435 Stockholm Sweden
| |
Collapse
|
30
|
Steiner E, Schlagnitweit J, Lundström P, Petzold K. Capturing Excited States in the Fast-Intermediate Exchange Limit in Biological Systems Using 1 H NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:15869-15872. [PMID: 27860024 DOI: 10.1002/anie.201609102] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Indexed: 12/14/2022]
Abstract
Changes in molecular structure are essential for the function of biomolecules. Characterization of these structural fluctuations can illuminate alternative states and help in correlating structure to function. NMR relaxation dispersion (RD) is currently the only method for detecting these alternative, high-energy states. In this study, we present a versatile 1 H R1ρ RD experiment that not only extends the exchange timescales at least three times beyond the rate limits of 13 C/15 N R1ρ and ten times for CPMG experiments, but also makes use of easily accessible probes, thus allowing a general description of biologically important excited states. This technique can be used to extract chemical shifts for the structural characterization of excited states and to elucidate complex excited states.
Collapse
Affiliation(s)
- Emilie Steiner
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 10435, Stockholm, Sweden
| | - Judith Schlagnitweit
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 10435, Stockholm, Sweden
| | - Patrik Lundström
- Department of Physics, Chemistry and Biology, Linköping University, 58183, Linköping, Sweden
| | - Katja Petzold
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 10435, Stockholm, Sweden
| |
Collapse
|
31
|
NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome. Proc Natl Acad Sci U S A 2016; 113:13033-13038. [PMID: 27791166 DOI: 10.1073/pnas.1614785113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5'-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a 2H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5'-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5' (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a 2H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.
Collapse
|
32
|
Abstract
Knowledge of RNA secondary structure is often sufficient to identify relationships between the structure of RNA and processing pathways, and the design of therapeutics. Nuclear magnetic resonance (NMR) can identify types of nucleotide base pairs and the sequence, thus limiting possible secondary structures. Because NMR experiments, like chemical mapping, are performed in solution, not in single crystals, experiments can be initiated as soon as the biomolecule is expressed and purified. This chapter summarizes NMR methods that permit rapid identification of RNA secondary structure, information that can be used as supplements to chemical mapping, and/or as preliminary steps required for 3D structure determination. The primary aim is to provide guidelines to enable a researcher with minimal knowledge of NMR to quickly extract secondary structure information from basic datasets. Instrumental and sample considerations that can maximize data quality are discussed along with some details for optimal data acquisition and processing parameters. Approaches for identifying base pair types in both unlabeled and isotopically labeled RNA are covered. Common problems, such as missing signals and overlaps, and approaches to address them are considered. Programs under development for merging NMR data with structure prediction algorithms are briefly discussed.
Collapse
Affiliation(s)
- Scott D Kennedy
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA.
| |
Collapse
|
33
|
Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection. Proc Natl Acad Sci U S A 2015; 112:E6446-55. [PMID: 26554019 DOI: 10.1073/pnas.1512088112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirus Israeli acute paralysis virus (IAPV) IRES PKI domain can uncouple 0 and +1 frame translation, suggesting that the structure adopts distinct conformations that contribute to 0 or +1 frame translation. Using a reconstituted translation system, we show that ribosomes assembled on mutant IRESs that direct exclusive 0 or +1 frame translation lack reading frame fidelity. Finally, a nuclear magnetic resonance/small-angle X-ray scattering hybrid approach reveals that the PKI domain of the IAPV IRES adopts an RNA structure that resembles a complete tRNA. The tRNA shape-mimicry enables the viral IRES to gain access to the ribosome tRNA-binding sites and form intermolecular contacts with the ribosome that are necessary for initiating IRES translation in a specific reading frame.
Collapse
|
34
|
Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints. Biochemistry 2015; 54:6769-82. [PMID: 26451676 PMCID: PMC4666457 DOI: 10.1021/acs.biochem.5b00833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Knowledge
of RNA
structure is necessary to determine structure–function relationships
and to facilitate design of potential therapeutics.
RNA secondary structure prediction can be improved by applying constraints
from nuclear magnetic resonance (NMR) experiments to a dynamic programming
algorithm. Imino proton walks from NOESY spectra reveal double-stranded
regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs,
UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to
identify constraints for the 5′ to 3′ directionality
of base pairs in helices. The 5′ to 3′ directionality
constraints were incorporated into an NMR-assisted prediction of secondary
structure (NAPSS-CS) program. When it was tested on 18 structures,
including nine pseudoknots, the sensitivity and positive predictive
value were improved relative to those of three unrestrained programs.
The prediction accuracy for the pseudoknots improved the most. The
program also facilitates assignment of chemical shifts to individual
nucleotides, a necessary step for determining three-dimensional structure.
Collapse
Affiliation(s)
- Jonathan L Chen
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Stanislav Bellaousov
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Jason D Tubbs
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Michael J Lopez
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - David H Mathews
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States.,Center for RNA Biology, University of Rochester , Rochester, New York 14642, United States
| | - Douglas H Turner
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester , Rochester, New York 14642, United States
| |
Collapse
|
35
|
Zhao B, Zhang Q. Measuring Residual Dipolar Couplings in Excited Conformational States of Nucleic Acids by CEST NMR Spectroscopy. J Am Chem Soc 2015; 137:13480-3. [PMID: 26462068 DOI: 10.1021/jacs.5b09014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Nucleic acids undergo structural transitions to access sparsely populated and transiently lived conformational states--or excited conformational states--that play important roles in diverse biological processes. Despite ever-increasing detection of these functionally essential states, 3D structure determination of excited states (ESs) of RNA remains elusive. This is largely due to challenges in obtaining high-resolution structural constraints in these ESs by conventional structural biology approaches. Here, we present nucleic-acid-optimized chemical exchange saturation transfer (CEST) NMR spectroscopy for measuring residual dipolar couplings (RDCs), which provide unique long-range angular constraints in ESs of nucleic acids. We demonstrate these approaches on a fluoride riboswitch, where one-bond (13)C-(1)H RDCs from both base and sugar moieties provide direct structural probes into an ES of the ligand-free riboswitch.
Collapse
Affiliation(s)
- Bo Zhao
- Department of Biochemistry and Biophysics and ‡Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Qi Zhang
- Department of Biochemistry and Biophysics and ‡Department of Chemistry, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| |
Collapse
|
36
|
Brown JD, Summers MF, Johnson BA. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression. JOURNAL OF BIOMOLECULAR NMR 2015; 63:39-52. [PMID: 26141454 PMCID: PMC4669054 DOI: 10.1007/s10858-015-9961-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 06/29/2015] [Indexed: 05/29/2023]
Abstract
The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR and (13)C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and (1)H and (13)C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA (1)H and (13)C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.
Collapse
Affiliation(s)
- Joshua D Brown
- Howard Hughes Medical Institute, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Michael F Summers
- Howard Hughes Medical Institute, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Bruce A Johnson
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
- One Moon Scientific, Inc., 839 Grant Ave., Westfield, NJ, 07090, USA.
- CUNY Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
| |
Collapse
|
37
|
Keane SC, Heng X, Lu K, Kharytonchyk S, Ramakrishnan V, Carter G, Barton S, Hosic A, Florwick A, Santos J, Bolden NC, McCowin S, Case DA, Johnson BA, Salemi M, Telesnitsky A, Summers MF. RNA structure. Structure of the HIV-1 RNA packaging signal. Science 2015; 348:917-21. [PMID: 25999508 PMCID: PMC4492308 DOI: 10.1126/science.aaa9266] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The 5' leader of the HIV-1 genome contains conserved elements that direct selective packaging of the unspliced, dimeric viral RNA into assembling particles. By using a (2)H-edited nuclear magnetic resonance (NMR) approach, we determined the structure of a 155-nucleotide region of the leader that is independently capable of directing packaging (core encapsidation signal; Ψ(CES)). The RNA adopts an unexpected tandem three-way junction structure, in which residues of the major splice donor and translation initiation sites are sequestered by long-range base pairing and guanosines essential for both packaging and high-affinity binding to the cognate Gag protein are exposed in helical junctions. The structure reveals how translation is attenuated, Gag binding promoted, and unspliced dimeric genomes selected, by the RNA conformer that directs packaging.
Collapse
Affiliation(s)
- Sarah C Keane
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Xiao Heng
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Kun Lu
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Siarhei Kharytonchyk
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA
| | - Venkateswaran Ramakrishnan
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Gregory Carter
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Shawn Barton
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Azra Hosic
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Alyssa Florwick
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Justin Santos
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Nicholas C Bolden
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Sayo McCowin
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Bruce A Johnson
- One Moon Scientific, Incorporated, 839 Grant Avenue, Westfield, NJ 07090, USA, and City University of New York (CUNY) Advanced Science Research Center, 85 St. Nicholas Terrace, New York, NY 10031, USA
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Alice Telesnitsky
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-5620, USA.
| | - Michael F Summers
- Howard Hughes Medical Institute (HHMI) and Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA.
| |
Collapse
|
38
|
Abstract
![]()
Influenza A is an RNA virus with
a genome of eight negative sense
segments. Segment 7 mRNA contains a 3′ splice site for alternative
splicing to encode the essential M2 protein. On the basis of sequence
alignment and chemical mapping experiments, the secondary structure
surrounding the 3′ splice site has an internal loop, adenine
bulge, and hairpin loop when it is in the hairpin conformation that
exposes the 3′ splice site. We report structural features of
a three-dimensional model of the hairpin derived from nuclear magnetic
resonance spectra and simulated annealing with restrained molecular
dynamics. Additional insight was provided by modeling based on 1H chemical shifts. The internal loop containing the 3′
splice site has a dynamic guanosine and a stable imino (cis Watson–Crick/Watson–Crick) GA pair. The adenine bulge
also appears to be dynamic with the A either stacked in the stem or
forming a base triple with a Watson–Crick GC pair. The hairpin
loop is a GAAA tetraloop closed by an AC pair.
Collapse
Affiliation(s)
- Jonathan L Chen
- †Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Scott D Kennedy
- ‡Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, United States
| | - Douglas H Turner
- †Department of Chemistry, University of Rochester, Rochester, New York 14627, United States.,§Center for RNA Biology, University of Rochester, Rochester, New York 14627, United States
| |
Collapse
|
39
|
Ng KS, Lam SL. NMR proton chemical shift prediction of C·C mismatches in B-DNA. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 252:87-93. [PMID: 25681800 DOI: 10.1016/j.jmr.2015.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 05/15/2023]
Abstract
Accurate prediction of DNA chemical shifts facilitates resonance assignment and allows recognition of different conformational features. Based on the nearest neighbor model and base pair replacement approach, we have determined a set of triplet chemical shift values and correction factors for predicting the proton chemical shifts of B-DNA containing an internal C·C mismatch. Our results provide a reliable chemical shift prediction with an accuracy of 0.07 ppm for non-labile protons and 0.09 ppm for labile protons. In addition, we have also shown that the correction factors for C·C mismatches can be used interchangeably with those for T·T mismatches. As a result, we have generalized a set of correction factors for predicting the flanking residue chemical shifts of pyrimidine·pyrimidine mismatches.
Collapse
Affiliation(s)
- Kui Sang Ng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
| |
Collapse
|
40
|
Sathyamoorthy B, Lee J, Kimsey I, Ganser L, Al-Hashimi H. Development and application of aromatic [(13)C, (1)H] SOFAST-HMQC NMR experiment for nucleic acids. JOURNAL OF BIOMOLECULAR NMR 2014; 60:77-83. [PMID: 25186910 PMCID: PMC4324173 DOI: 10.1007/s10858-014-9856-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/19/2014] [Indexed: 05/20/2023]
Abstract
Higher sensitivity of NMR spectrometers and novel isotopic labeling schemes have ushered the development of rapid data acquisition methodologies, improving the time resolution with which NMR data can be acquired. For nucleic acids, longitudinal relaxation optimization in conjunction with Ernst angle excitation (SOFAST-HMQC) for imino protons, in addition to rendering rapid pulsing, has been demonstrated to yield significant improvements in sensitivity per unit time. Extending such methodology to other spins offers a viable prospect to measure additional chemical shifts, thereby broadening their utilization for various applications. Here, we introduce the 2D [(13)C, (1)H] aromatic SOFAST-HMQC that results in overall sensitivity gain of 1.4- to 1.7-fold relative to the conventional HMQC and can also be extended to yield long-range heteronuclear chemical shifts such as the adenine imino nitrogens N1, N3, N7 and N9. The applications of these experiments range from monitoring real-time biochemical processes, drug/ligand screening, and to collecting data at very low sample concentration and/or in cases where isotopic enrichment cannot be achieved.
Collapse
Affiliation(s)
| | - Janghyun Lee
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Isaac Kimsey
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Laura Ganser
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | | |
Collapse
|
41
|
Frank AT, Law SM, Brooks CL. A simple and fast approach for predicting (1)H and (13)C chemical shifts: toward chemical shift-guided simulations of RNA. J Phys Chem B 2014; 118:12168-75. [PMID: 25255209 PMCID: PMC4207130 DOI: 10.1021/jp508342x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We introduce a simple and fast approach
for predicting RNA chemical
shifts from interatomic distances that performs with an accuracy similar
to existing predictors and enables the first chemical shift-restrained
simulations of RNA to be carried out. Our analysis demonstrates that
the applied restraints can effectively guide conformational sampling
toward regions of space that are more consistent with chemical shifts
than the initial coordinates used for the simulations. As such, our
approach should be widely applicable in mapping the conformational
landscape of RNAs via chemical shift-guided molecular dynamics simulations.
The simplicity and demonstrated sensitivity to three-dimensional structure
should also allow our method to be used in chemical shift-based RNA
structure prediction, validation, and refinement.
Collapse
Affiliation(s)
- Aaron T Frank
- Department of Chemistry and Biophysics, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States
| | | | | |
Collapse
|
42
|
Abramov G, Goldbourt A. Nucleotide-type chemical shift assignment of the encapsulated 40 kbp dsDNA in intact bacteriophage T7 by MAS solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2014; 59:219-230. [PMID: 24875850 DOI: 10.1007/s10858-014-9840-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 05/20/2014] [Indexed: 06/03/2023]
Abstract
The icosahedral bacteriophage T7 is a 50 MDa double-stranded DNA (dsDNA) virus that infects Escherichia coli. Although there is substantial information on the physical and morphological properties of T7, structural information, based mostly on Raman spectroscopy and cryo-electron microscopy, is limited. Here, we apply the magic-angle spinning (MAS) solid-state NMR (SSNMR) technique to study a uniformly (13)C and (15)N labeled wild-type T7 phage. We describe the details of the large-scale preparation and purification of an isotopically enriched phage sample under fully hydrated conditions, and show a complete (13)C and a near-complete (15)N nucleotide-type specific assignment of the sugar and base moieties in the 40 kbp dsDNA of T7 using two-dimensional (13)C-(13)C and (15)N-(13)C correlation experiments. The chemical shifts are interpreted as reporters of a B-form conformation of the encapsulated dsDNA. While MAS SSNMR was found to be extremely useful in determining the structures of proteins in native-like environments, its application to nucleic acids has lagged behind, leaving a missing (13)C and (15)N chemical shift database. This work therefore expands the (13)C and (15)N database of real B-form DNA systems, and opens routes to characterize more complex nucleic acid systems by SSNMR.
Collapse
Affiliation(s)
- Gili Abramov
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, 69978, Ramat Aviv, Tel Aviv, Israel
| | | |
Collapse
|
43
|
Alvarado LJ, LeBlanc RM, Longhini AP, Keane SC, Jain N, Yildiz ZF, Tolbert BS, D'Souza VM, Summers MF, Kreutz C, Dayie TK. Regio-selective chemical-enzymatic synthesis of pyrimidine nucleotides facilitates RNA structure and dynamics studies. Chembiochem 2014; 15:1573-7. [PMID: 24954297 DOI: 10.1002/cbic.201402130] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Indexed: 12/16/2022]
Abstract
Isotope labeling has revolutionized NMR studies of small nucleic acids, but to extend this technology to larger RNAs, site-specific labeling tools to expedite NMR structural and dynamics studies are required. Using enzymes from the pentose phosphate pathway, we coupled chemically synthesized uracil nucleobase with specifically (13) C-labeled ribose to synthesize both UTP and CTP in nearly quantitative yields. This chemoenzymatic method affords a cost-effective preparation of labels that are unattainable by current methods. The methodology generates versatile (13) C and (15) N labeling patterns which, when employed with relaxation-optimized NMR spectroscopy, effectively mitigate problems of rapid relaxation that result in low resolution and sensitivity. The methodology is demonstrated with RNAs of various sizes, complexity, and function: the exon splicing silencer 3 (27 nt), iron responsive element (29 nt), Pro-tRNA (76 nt), and HIV-1 core encapsidation signal (155 nt).
Collapse
Affiliation(s)
- Luigi J Alvarado
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, 1115 Biomolecular Sciences Building, College Park, MD 20782 (USA)
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
Conformational changes in nucleic acids play a key role in the way genetic information is stored, transferred, and processed in living cells. Here, we describe new approaches that employ a broad range of experimental data, including NMR-derived chemical shifts and residual dipolar couplings, small-angle X-ray scattering, and computational approaches such as molecular dynamics simulations to determine ensembles of DNA and RNA at atomic resolution. We review the complementary information that can be obtained from diverse sets of data and the various methods that have been developed to combine these data with computational methods to construct ensembles and assess their uncertainty. We conclude by surveying RNA and DNA ensembles determined using these methods, highlighting the unique physical and functional insights obtained so far.
Collapse
Affiliation(s)
- Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109;
| | | | | |
Collapse
|
45
|
Frank AT, Bae SH, Stelzer AC. Prediction of RNA 1H and 13C chemical shifts: a structure based approach. J Phys Chem B 2013; 117:13497-506. [PMID: 24033307 DOI: 10.1021/jp407254m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of NMR-derived chemical shifts in protein structure determination and prediction has received much attention, and, as such, many methods have been developed to predict protein chemical shifts from three-dimensional (3D) coordinates. In contrast, little attention has been paid to predicting chemical shifts from RNA coordinates. Using the random forest machine learning approach, we developed RAMSEY, which is capable of predicting both (1)H and protonated (13)C chemical shifts from RNA coordinates. In this report, we introduce RAMSEY, assess its accuracy, and demonstrate the sensitivity of RAMSEY-predicted chemical shifts to RNA 3D structure.
Collapse
Affiliation(s)
- Aaron T Frank
- Nymirum , 3510 West Liberty Road, Ann Arbor, Michigan 48103, United States
| | | | | |
Collapse
|
46
|
Kwok CK, Lam SL. NMR proton chemical shift prediction of T·T mismatches in B-DNA duplexes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 234:184-9. [PMID: 23892104 DOI: 10.1016/j.jmr.2013.06.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 06/24/2013] [Accepted: 06/28/2013] [Indexed: 05/15/2023]
Abstract
A proton chemical shift prediction scheme for B-DNA duplexes containing a T·T mismatch has been established. The scheme employs a set of T·T mismatch triplet chemical shift values, 5'- and 3'-correction factors extracted from reference sequences, and also the B-DNA chemical shift values predicted by Altona et al. The prediction scheme was tested by eight B-DNA duplexes containing T·T mismatches. Based on 560 sets of predicted and experimental proton chemical shift values, the overall prediction accuracy for non-labile protons was determined to be 0.07 ppm with an excellent correlation coefficient of 0.9996. In addition, the prediction accuracy for 96 sets of labile protons was found to be 0.22 ppm with a correlation coefficient of 0.9961. The prediction scheme developed herein can facilitate resonance assignments of B-DNA duplexes containing T·T mismatches and be generalized for the chemical shift prediction of other DNA mismatches. Our chemical shift data will also be useful for establishing structure-chemical shift information in B-DNA containing mismatches.
Collapse
Affiliation(s)
- Chun Kit Kwok
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | | |
Collapse
|
47
|
Aeschbacher T, Schmidt E, Blatter M, Maris C, Duss O, Allain FHT, Güntert P, Schubert M. Automated and assisted RNA resonance assignment using NMR chemical shift statistics. Nucleic Acids Res 2013; 41:e172. [PMID: 23921634 PMCID: PMC3794610 DOI: 10.1093/nar/gkt665] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The three-dimensional structure determination of RNAs by NMR spectroscopy relies on chemical shift assignment, which still constitutes a bottleneck. In order to develop more efficient assignment strategies, we analysed relationships between sequence and 1H and 13C chemical shifts. Statistics of resonances from regularly Watson–Crick base-paired RNA revealed highly characteristic chemical shift clusters. We developed two approaches using these statistics for chemical shift assignment of double-stranded RNA (dsRNA): a manual approach that yields starting points for resonance assignment and simplifies decision trees and an automated approach based on the recently introduced automated resonance assignment algorithm FLYA. Both strategies require only unlabeled RNAs and three 2D spectra for assigning the H2/C2, H5/C5, H6/C6, H8/C8 and H1′/C1′ chemical shifts. The manual approach proved to be efficient and robust when applied to the experimental data of RNAs with a size between 20 nt and 42 nt. The more advanced automated assignment approach was successfully applied to four stem-loop RNAs and a 42 nt siRNA, assigning 92–100% of the resonances from dsRNA regions correctly. This is the first automated approach for chemical shift assignment of non-exchangeable protons of RNA and their corresponding 13C resonances, which provides an important step toward automated structure determination of RNAs.
Collapse
Affiliation(s)
- Thomas Aeschbacher
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland, Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, 60438 Frankfurt am Main, Germany and Graduate School of Science and Engineering, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | | | | | | | | | | | | | | |
Collapse
|
48
|
|
49
|
Salmon L, Bascom G, Andricioaei I, Al-Hashimi HM. A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed. J Am Chem Soc 2013; 135:5457-66. [PMID: 23473378 DOI: 10.1021/ja400920w] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to modulate alignment and measure multiple independent sets of NMR residual dipolar couplings (RDCs) has made it possible to characterize internal motions in proteins at atomic resolution and with time scale sensitivity ranging from picoseconds up to milliseconds. The application of such methods to the study of RNA dynamics, however, remains fundamentally limited by the inability to modulate alignment and by strong couplings between internal and overall motions that complicate the quantitative interpretation of RDCs. Here, we address this problem by showing that RNA alignment can be generally modulated, in a controlled manner, by variable elongation of A-form helices and that the information contained within the measured RDCs can be extracted even in the presence of strong couplings between motions and overall alignment via structure-based prediction of alignment. Using this approach, four RDC data sets, and a broad conformational pool obtained from a 8.2 μs molecular dynamics simulation, we successfully construct and validate an atomic resolution ensemble of human immunodeficiency virus type I transactivation response element RNA. This ensemble reveals local motions in and around the bulge involving changes in stacking and hydrogen-bonding interactions, which are undetectable by traditional spin relaxation and drive global changes in interhelical orientation. This new approach broadens the scope of using RDCs in characterizing the dynamics of nucleic acids.
Collapse
Affiliation(s)
- Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | | | | |
Collapse
|