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Zhitnikova M, Shestopalova A. DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations. J Biomol Struct Dyn 2017; 35:3384-3397. [DOI: 10.1080/07391102.2016.1255259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- M.Y. Zhitnikova
- O. Ya. Usikov Institute for Radiophysics and Electronics, National Academy of Sciences of Ukraine, Acad. Proskury Street, 12 Kharkiv 61085, Ukraine
| | - A.V. Shestopalova
- O. Ya. Usikov Institute for Radiophysics and Electronics, National Academy of Sciences of Ukraine, Acad. Proskury Street, 12 Kharkiv 61085, Ukraine
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2
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Levengood JD, Rollins C, Mishler CHJ, Johnson CA, Miner G, Rajan P, Znosko BM, Tolbert BS. Solution structure of the HIV-1 exon splicing silencer 3. J Mol Biol 2011; 415:680-98. [PMID: 22154809 DOI: 10.1016/j.jmb.2011.11.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 11/17/2011] [Accepted: 11/18/2011] [Indexed: 12/20/2022]
Abstract
Alternative splicing of the human immunodeficiency virus type 1 (HIV-1) genomic RNA is necessary to produce the complete viral protein complement, and aberrations in the splicing pattern impair HIV-1 replication. Genome splicing in HIV-1 is tightly regulated by the dynamic assembly/disassembly of trans host factors with cis RNA control elements. The host protein, heterogeneous nuclear ribonucleoprotein (hnRNP) A1, regulates splicing at several highly conserved HIV-1 3' splice sites by binding 5'-UAG-3' elements embedded within regions containing RNA structure. The physical determinants of hnRNP A1 splice site recognition remain poorly defined in HIV-1, thus precluding a detailed understanding of the molecular basis of the splicing pattern. Here, the three-dimensional structure of the exon splicing silencer 3 (ESS3) from HIV-1 has been determined using NMR spectroscopy. ESS3 adopts a 27-nucleotide hairpin with a 10-bp A-form stem that contains a pH-sensitive A(+)C wobble pair. The seven-nucleotide hairpin loop contains the high-affinity hnRNP-A1-responsive 5'-UAGU-3' element and a proximal 5'-GAU-3' motif. The NMR structure shows that the heptaloop adopts a well-organized conformation stabilized primarily by base stacking interactions reminiscent of a U-turn. The apex of the loop is quasi-symmetric with UA dinucleotide steps from the 5'-GAU-3' and 5'-UAGU-3' motifs stacking on opposite sides of the hairpin. As a step towards understanding the binding mechanism, we performed calorimetric and NMR titrations of several hnRNP A1 subdomains into ESS3. The data show that the UP1 domain forms a high-affinity (K(d)=37.8±1.1 nM) complex with ESS3 via site-specific interactions with the loop.
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Affiliation(s)
- Jeffrey D Levengood
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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3
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Miyazaki Y, Irobalieva RN, Tolbert BS, Smalls-Mantey A, Iyalla K, Loeliger K, D'Souza V, Khant H, Schmid MF, Garcia EL, Telesnitsky A, Chiu W, Summers MF. Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography. J Mol Biol 2010; 404:751-72. [PMID: 20933521 DOI: 10.1016/j.jmb.2010.09.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 09/07/2010] [Accepted: 09/07/2010] [Indexed: 01/11/2023]
Abstract
The 5'-untranslated regions of all gammaretroviruses contain a conserved "double-hairpin motif" (Ψ(CD)) that is required for genome packaging. Both hairpins (SL-C and SL-D) contain GACG tetraloops that, in isolated RNAs, are capable of forming "kissing" interactions stabilized by two intermolecular G-C base pairs. We have determined the three-dimensional structure of the double hairpin from the Moloney murine leukemia virus ([Ψ(CD)](2), 132 nt, 42.8 kDa) using a (2)H-edited NMR-spectroscopy-based approach. This approach enabled the detection of (1)H-(1)H dipolar interactions that were not observed in previous studies of isolated SL-C and SL-D hairpin RNAs using traditional (1)H-(1)H correlated and (1)H-(13)C-edited NMR methods. The hairpins participate in intermolecular cross-kissing interactions (SL-C to SL-D' and SLC' to SL-D) and stack in an end-to-end manner (SL-C to SL-D and SL-C' to SL-D') that gives rise to an elongated overall shape (ca 95 Å×45 Å×25 Å). The global structure was confirmed by cryo-electron tomography (cryo-ET), making [Ψ(CD)](2) simultaneously the smallest RNA to be structurally characterized to date by cryo-ET and among the largest to be determined by NMR. Our findings suggest that, in addition to promoting dimerization, [Ψ(CD)](2) functions as a scaffold that helps initiate virus assembly by exposing a cluster of conserved UCUG elements for binding to the cognate nucleocapsid domains of assembling viral Gag proteins.
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Affiliation(s)
- Yasuyuki Miyazaki
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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4
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Tolbert BS, Miyazaki Y, Barton S, Kinde B, Starck P, Singh R, Bax A, Case DA, Summers MF. Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement. JOURNAL OF BIOMOLECULAR NMR 2010; 47:205-19. [PMID: 20549304 PMCID: PMC2929647 DOI: 10.1007/s10858-010-9424-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2010] [Accepted: 04/20/2010] [Indexed: 05/22/2023]
Abstract
Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by (1)H- (1)H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of isolated A-form RNA helices are sensitive to crystal packing effects, variations among the published X-ray structures are significantly smaller than those observed in NMR structures. Here we show that restraints derived from aromatic (1)H- (13)C residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) can overcome NMR restraint and force field deficiencies and afford structures with helical properties similar to those observed in high-resolution X-ray structures.
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Affiliation(s)
- Blanton S Tolbert
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Yasuyuki Miyazaki
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Shawn Barton
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Benyam Kinde
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Patrice Starck
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Rashmi Singh
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250
| | - Ad Bax
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, MD 208992
| | - David A. Case
- Dept. of Chemistry & Chemical Biology and BioMaPS Institute, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, Phone: (732)-445-5885; Fax: (732)-445-5958;
| | - Michael F Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, phone: (410)-455-2527; fax: (410)-455-1174;
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5
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Howarth JW, Meller J, Solaro RJ, Trewhella J, Rosevear PR. Phosphorylation-dependent conformational transition of the cardiac specific N-extension of troponin I in cardiac troponin. J Mol Biol 2007; 373:706-22. [PMID: 17854829 DOI: 10.1016/j.jmb.2007.08.035] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 08/08/2007] [Accepted: 08/14/2007] [Indexed: 10/22/2022]
Abstract
We present here the solution structure for the bisphosphorylated form of the cardiac N-extension of troponin I (cTnI(1-32)), a region for which there are no previous high-resolution data. Using this structure, the X-ray crystal structure of the cardiac troponin core, and uniform density models of the troponin components derived from neutron contrast variation data, we built atomic models for troponin that show the conformational transition in cardiac troponin induced by bisphosphorylation. In the absence of phosphorylation, our NMR data and sequence analyses indicate a less structured cardiac N-extension with a propensity for a helical region surrounding the phosphorylation motif, followed by a helical C-terminal region (residues 25-30). In this conformation, TnI(1-32) interacts with the N-lobe of cardiac troponin C (cTnC) and thus is positioned to modulate myofilament Ca2+-sensitivity. Bisphosphorylation at Ser23/24 extends the C-terminal helix (residues 21-30) which results in weakening interactions with the N-lobe of cTnC and a re-positioning of the acidic amino terminus of cTnI(1-32) for favorable interactions with basic regions, likely the inhibitory region of cTnI. An extended poly(L-proline)II helix between residues 11 and 19 serves as the rigid linker that aids in re-positioning the amino terminus of cTnI(1-32) upon bisphosphorylation at Ser23/24. We propose that it is these electrostatic interactions between the acidic amino terminus of cTnI(1-32) and the basic inhibitory region of troponin I that induces a bending of cTnI at the end that interacts with cTnC. This model provides a molecular mechanism for the observed changes in cross-bridge kinetics upon TnI phosphorylation.
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Affiliation(s)
- Jack W Howarth
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, Ohio, 45267, USA
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6
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Abstract
Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other SRD features is presented. The SRD is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean square deviation (r.m.s.d.) values between averaged MD and high-resolution X-ray structures of 1-1.4 A. Modest dynamics is observed in the tetraloop, namely, rotation of adenine in its apex and subtle reversible shift of the tetraloop with respect to the adjacent base pair. The deformed flexible region in low-resolution rat X-ray structure is repaired by simulations. The simulations reveal few backbone flips, which do not affect positions of bases and do not indicate a force field imbalance. Non-Watson-Crick base pairs are rigid and mediated by long-residency water molecules while there are several modest cation-binding sites around SRD. In summary, SRD is an unusually stiff rRNA building block. Its intrinsic structural and dynamical signatures seen in simulations are strikingly distinct from other rRNA motifs such as Loop E and Kink-turns.
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MESH Headings
- Animals
- Base Pairing
- Binding Sites
- Carbohydrates/chemistry
- Cations/chemistry
- Computer Simulation
- Crystallography, X-Ray
- Endoribonucleases/metabolism
- Escherichia coli/genetics
- Fungal Proteins/metabolism
- Hydrogen Bonding
- Models, Molecular
- Nucleic Acid Conformation
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/metabolism
- RNA, Ribosomal, 28S/chemistry
- RNA, Ribosomal, 28S/metabolism
- Rats
- Ricin/metabolism
- Water/chemistry
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Affiliation(s)
- Nad'a Špačková
- Institute of Biophysics, Academy of Sciences of the Czech RepublicKrálovopolská 135, 612 65 Brno, Czech Republic
- To whom correspondence should be addressed. Tel: +420 541 517 109; Fax: +420 541 212 179;
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech RepublicKrálovopolská 135, 612 65 Brno, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech RepublicFlemingovo náměstí 2, 166 10 Prague 6, Czech Republic
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7
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D'Souza V, Dey A, Habib D, Summers MF. NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus. J Mol Biol 2004; 337:427-42. [PMID: 15003457 DOI: 10.1016/j.jmb.2004.01.037] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Revised: 01/19/2004] [Accepted: 01/20/2004] [Indexed: 10/26/2022]
Abstract
The full length, positive-strand genome of the Moloney Murine Leukemia Virus contains a "core encapsidation signal" that is essential for efficient genome packaging during virus assembly. We have determined the structure of a 101-nucleotide RNA that contains this signal (called mPsi) using a novel isotope-edited NMR approach. The method is robust and should be generally applicable to larger RNAs. mPsi folds into three stem loops, two of which (SL-C and SL-D) co-stack to form an extended helix. The third stem loop (SL-B) is connected to SL-C by a flexible, four-nucleotide linker. The structure contains five mismatched base-pairs, an unusual C.CG base-triple platform, and a novel "A-minor K-turn," in which unpaired adenosine bases A340 and A341 of a GGAA bulge pack in the minor groove of a proximal stem, and a bulged distal uridine (U319) forms a hydrogen bond with the phosphodiester of A341. Phylogenetic analyses indicate that these essential structural elements are conserved among the murine C-type retroviruses.
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Affiliation(s)
- Victoria D'Souza
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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8
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Correll CC, Beneken J, Plantinga MJ, Lubbers M, Chan YL. The common and the distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure. Nucleic Acids Res 2003; 31:6806-18. [PMID: 14627814 PMCID: PMC290275 DOI: 10.1093/nar/gkg908] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Revised: 10/15/2003] [Accepted: 10/15/2003] [Indexed: 11/13/2022] Open
Abstract
Bulged-G motifs are ubiquitous internal RNA loops that provide specific recognition sites for proteins and RNAs. To establish the common and distinctive features of the motif we determined the structures of three variants and compared them with related structures. The variants are 27-nt mimics of the sarcin/ricin loop (SRL) from Escherichia coli 23S ribosomal RNA that is an essential part of the binding site for elongation factors (EFs). The wild-type SRL has now been determined at 1.04 A resolution, supplementing data obtained before at 1.11 A and allowing the first calculation of coordinate error for an RNA motif. The other two structures, having a viable (C2658U*G2663A) or a lethal mutation (C2658G*G2663C), were determined at 1.75 and 2.25 A resolution, respectively. Comparisons reveal that bulged-G motifs have a common hydration and geometry, with flexible junctions at flanking structural elements. Six conserved nucleotides preserve the fold of the motif; the remaining seven to nine vary in sequence and alter contacts in both grooves. Differences between accessible functional groups of the lethal mutation and those of the viable mutation and wild-type SRL may account for the impaired elongation factor binding to ribosomes with the C2658G*G2663C mutation and may underlie the lethal phenotype.
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MESH Headings
- Animals
- Base Sequence
- Crystallization
- Crystallography, X-Ray
- Escherichia coli/genetics
- Genes, Essential/genetics
- Genes, Lethal/genetics
- Models, Molecular
- Mutation/genetics
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- Rats
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Affiliation(s)
- Carl C Correll
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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9
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Auffinger P, Bielecki L, Westhof E. The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. CHEMISTRY & BIOLOGY 2003; 10:551-61. [PMID: 12837388 DOI: 10.1016/s1074-5521(03)00121-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Molecular dynamics simulations have been used to investigate the binding of Mg(2+) ions to the deep groove of the eubacterial 5S rRNA loop E. The simulations suggest that long-lived and specific water-mediated interactions established between the hydrated ions and the RNA atoms lining up the binding sites contribute to the stabilization of this motif. The Mg(2+) binding specificity is modulated by two factors: (i) a required electrostatic complementarity and (ii) a structural correspondence between the hydrated ion and its binding pocket that can be estimated by its degree of dehydration and the resulting number and lifetime of the intervening water-mediated contacts. Two distinct binding modes for pentahydrated Mg(2+) ions that result in a significant freezing of the tumbling motions of the ions are described, and mechanistic details related to the stabilization of nucleic acids by divalent ions are provided.
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Affiliation(s)
- Pascal Auffinger
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations et Simulations des Acides Nucléiques, UPR 9002, 15 rue René Descartes, 67084 Cedex, Strasbourg, France.
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10
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Correll CC, Swinger K. Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution. RNA (NEW YORK, N.Y.) 2003; 9:355-63. [PMID: 12592009 PMCID: PMC1370402 DOI: 10.1261/rna.2147803] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2002] [Accepted: 11/12/2002] [Indexed: 05/18/2023]
Abstract
GNRA tetraloops (N is A, C, G, or U; R is A or G) are basic building blocks of RNA structure that often interact with proteins or other RNA structural elements. Understanding sequence-dependent structural variation among different GNRA tetraloops is an important step toward elucidating the molecular basis of specific GNRA tetraloop recognition by proteins and RNAs. Details of the geometry and hydration of this motif have been based on high-resolution crystallographic structures of the GRRA subset of tetraloops; less is known about the GYRA subset (Y is C or U). We report here the structure of a GUAA tetraloop determined to 1.4 A resolution to better define these details and any distinctive features of GYRA tetraloops. The tetraloop is part of a 27-nt structure that mimics the universal sarcin/ricin loop from Escherichia coli 23S ribosomal RNA in which a GUAA tetraloop replaces the conserved GAGA tetraloop. The adenosines of the GUAA tetraloop form an intermolecular contact that is a commonplace RNA tertiary interaction called an A-minor motif. This is the first structure to reveal in great detail the geometry and hydration of a GUAA tetraloop and an A-minor motif. Comparison of tetraloop structures shows a common backbone geometry for each of the eight possible tetraloop sequences and suggests a common hydration. After backbone atom superposition, equivalent bases from different tetraloops unexpectedly depart from coplanarity by as much as 48 degrees. This variation displaces the functional groups of tetraloops implicated in protein and RNA binding, providing a recognition feature.
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MESH Headings
- Crystallography, X-Ray
- Models, Molecular
- Mutation
- Nucleic Acid Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
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Affiliation(s)
- Carl C Correll
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.
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11
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Vallurupalli P, Moore PB. The solution structure of the loop E region of the 5S rRNA from spinach chloroplasts. J Mol Biol 2003; 325:843-56. [PMID: 12527295 DOI: 10.1016/s0022-2836(02)01270-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A structure has been obtained for the loop E region of the 5S rRNA from Spinacia oleracia chloroplast ribosomes using residual dipolar coupling data as well as NOE, J coupling and chemical shift information. Even though the loop E sequence of this chloroplast 5S rRNA differs from that of Escherichia coli loop E at approximately 40% of its positions, its conformation is remarkably similar to that of E.coli loop E. Consistent with this conclusion, ribosomal protein L25 from E.coli, which binds to the loop E region of both intact E.coli 5S rRNA and to oligonucleotides containing that sequence, also binds to the chloroplast-derived oligonucleotide discussed here.
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12
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Mauffret O, Tevanian G, Fermandjian S. Residual dipolar coupling constants and structure determination of large DNA duplexes. JOURNAL OF BIOMOLECULAR NMR 2002; 24:317-328. [PMID: 12522296 DOI: 10.1023/a:1021645131882] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Several NMR works have shown that long-range information provided by residual dipolar couplings (RDCs) significantly improve the global structure definition of RNAs and DNAs. Most of these are based on the use of a large set of RDCs, the collect of which requires samples labeled with (13)C, (15)N, and sometimes, (2)H. Here, we carried out torsion-angle dynamics simulations on a non-self complementary DNA fragment of 17 base-pairs, d(GGAAAATATCTAGCAGT).(ACTGCTAGAGATTTTCC). This reproduces the U5 LTR distal end of the HIV-1 cDNA that contains the enzyme integrase binding site. Simulations aimed at evaluating the impact of RDCs on the structure definition of long oligonucleotides, were performed in incorporating (i) nOe-distances at both < 4.5 A and < 5 A; (ii) a small set of (13)C-(1)H RDCs, easily detectable at the natural abundance, and (iii) a larger set of RDCs only accessible through the (13)C labeling of DNAs. Agreement between a target structure and a simulated structure was measured in terms of precision and accuracy. Results allowed to define conditions in which accurate DNA structures can be determined. We confirmed the strong impact of RDCs on the structure determination, and, above all, we found that a small set of RDC constraints (ca. 50) detectable at the natural abundance is sufficient to accurately derive the global and local DNA duplex structures when used in conjunction with nOe-distances < 5 A.
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Affiliation(s)
- Olivier Mauffret
- Département de Biologie et Pharmacologie Structurales, UMR 8532 CNRS, Institut Gustave-Roussy, 94800 Villejuif, France
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13
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Abstract
The CHARMM27 all-atom force field for nucleic acids represents a highly optimized model for investigations of nucleic acids via empirical force field calculations. The force field satisfactorily treats the A, B, and Z forms of DNA as well as RNA, and it also useful for nucleosides and nucleotides. In addition, it is compatible with the CHARMM force fields for proteins and lipids, allowing for simulation studies of heterogeneous systems.
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Affiliation(s)
- A D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 N. Pine Street, Baltimore, MD 21201, USA.
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14
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Milecki J. Specific labelling of nucleosides and nucleotides with13C and15N. J Labelled Comp Radiopharm 2002. [DOI: 10.1002/jlcr.553] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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15
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Burkhardt C, Zacharias M. Modelling ion binding to AA platform motifs in RNA: a continuum solvent study including conformational adaptation. Nucleic Acids Res 2001; 29:3910-8. [PMID: 11574672 PMCID: PMC60250 DOI: 10.1093/nar/29.19.3910] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Binding of monovalent and divalent cations to two adenine-adenine platform structures from the Tetrahymena group I intron ribozyme has been studied using continuum solvent models based on the generalised Born and the finite-difference Poisson-Boltzmann approaches. The adenine-adenine platform RNA motif forms an experimentally characterised monovalent ion binding site important for ribozyme folding and function. Qualitative agreement between calculated and experimental ion placements and binding selectivity was obtained. The inclusion of solvation effects turned out to be important to obtain low energy structures and ion binding placements in agreement with the experiment. The calculations indicate that differences in solvation of the isolated ions contribute to the calculated ion binding preference. However, Coulomb attraction and van der Waals interactions due to ion size differences and RNA conformational adaptation also influence the calculated ion binding affinity. The calculated alkali ion binding selectivity for both platforms followed the order K(+) > Na(+) > Rb(+) > Cs(+) > Li(+) (Eisenman series VI) in the case of allowing RNA conformational relaxation during docking. With rigid RNA an Eisenman series V was obtained (K(+) > Rb(+) > Na(+) > Cs(+) > Li(+)). Systematic energy minimisation docking simulations starting from several hundred initial placements of potassium ions on the surface of platform containing RNA fragments identified a coordination geometry in agreement with the experiment as the lowest energy binding site. The approach could be helpful to identify putative ion binding sites in nucleic acid structures determined at low resolution or with experimental methods that do not allow identification of ion binding sites.
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Affiliation(s)
- C Burkhardt
- AG Theoretische Biophysik, Institut für Molekulare Biotechnologie, Beutenbergstrasse 11, D-07745 Jena, Germany
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16
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Huber PW, Rife JP, Moore PB. The structure of helix III in Xenopus oocyte 5 S rRNA: an RNA stem containing a two-nucleotide bulge. J Mol Biol 2001; 312:823-32. [PMID: 11575935 DOI: 10.1006/jmbi.2001.4966] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The solution structure of an oligonucleotide containing the helix III sequence from Xenopus oocyte 5 S rRNA has been determined by NMR spectroscopy. Helix III includes two unpaired adenosine residues, flanked on either side by G:C base-pairs, that are required for binding of ribosomal protein L5. The consensus conformation of helix III in the context provided by this oligonucleotide has the two adenosine residues located in the minor groove and stacked upon the 3' flanking guanosine residue, consistent with biochemical studies of free 5 S rRNA in solution. A distinct break in stacking that occurs between the first adenosine residue of the bulge and the flanking 5' guanosine residue exposes the base of the adenosine residue in the minor groove and the base of the guanosine residue in the major groove. The major groove of the helix is widened at the site of the unpaired nucleotides and the helix is substantially bent; nonetheless, the G:C base-pairs flanking the bulge are intact. The data indicate that there may be conformational heterogeneity centered in the bulge region. The corresponding adenosine residues in the Haloarcula marismortui 50 S ribosomal subunit form a dinucleotide platform, which is quite different from the motif seen in solution. Thus, the conformation of helix III probably changes when 5 S rRNA is incorporated into the ribosome.
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Affiliation(s)
- P W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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Zhou H, Vermeulen A, Jucker FM, Pardi A. Incorporating residual dipolar couplings into the NMR solution structure determination of nucleic acids. Biopolymers 2001; 52:168-80. [PMID: 11295749 DOI: 10.1002/1097-0282(1999)52:4<168::aid-bip1002>3.0.co;2-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
NMR solution structures of nucleic acids are generally less well defined than similar-sized proteins. Most NMR structures of nucleic acids are defined only by short-range interactions, such as intrabase-pair or sequential nuclear Overhauser effects (NOEs), and J-coupling constants, and there are no long-range structural data on the tertiary structure. Residual dipolar couplings represent an extremely valuable source of distance and angle information for macromolecules but they average to zero in isotropic solutions. With the recent advent of general methods for partial alignment of macromolecules in solution, residual dipolar couplings are rapidly becoming indispensable constraints for solution NMR structural studies. These residual dipolar couplings give long-range global structural information and thus complement the strictly local structural data obtained from standard NOE and torsion angle constraints. Such global structural data are especially important in nucleic acids due to the more elongated, less-globular structure of many DNAs and RNAs. Here we review recent progress in application of residual dipolar couplings to structural studies of nucleic acids. We also present results showing how refinement procedures affect the final solution structures of nucleic acids.
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Affiliation(s)
- H Zhou
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA
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18
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Warren JJ, Moore PB. Application of dipolar coupling data to the refinement of the solution structure of the sarcin-ricin loop RNA. JOURNAL OF BIOMOLECULAR NMR 2001; 20:311-323. [PMID: 11563555 DOI: 10.1023/a:1011214214552] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Residual dipolar couplings can provide the long-range information that most NMR solution structures lack. The use of such data in protein structure determinations is now fairly routine, but even though these data should be much more useful for nucleic acids, their application to nucleic acid structure determination is still in its infancy. Here we present a method for producing accurate, dipolar-refined structures of nucleic acids that is more efficient than those used previously, and apply it to E73, a 29 nucleotide RNA that includes the sarcin-ricin loop from rat 28S rRNA. The results enable us to address the differences between the crystal structure of E73 and the solution structure proposed for it previously.
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Affiliation(s)
- J J Warren
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8107, USA
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Bosch D, Foloppe N, Pastor N, Pardo L, Campillo M. Calibrating nucleic acids torsional energetics in force-field: insights from model compounds. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(00)00685-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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20
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Schneider C, Brandl M, Sühnel J. Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex. J Mol Biol 2001; 305:659-67. [PMID: 11162082 DOI: 10.1006/jmbi.2000.4338] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A 4 ns molecular dynamics simulation of an RNA duplex (r-GGACUUCGGUCC)(2 )in solution with Na+ and Cl- as counterions was performed. The X-ray structure of this duplex includes two water-mediated uracil-cytosine pairs. In contrast to the other base-pairs in the duplex the water-mediated pairs switch between different conformations. One conformation corresponds to the geometry of the water-mediated UC pairs in the duplex X-ray structure with water acting both as hydrogen-bond donor and acceptor. Another conformation is close to that of a water-mediated UC base-pair found in the X-ray structure of the 23 S rRNA sarcin/ricin domain. In this case the oxygen of the water molecule is linked to two-base donor sites. For a very short time also a direct UC base-pair and a further conformation that is similar to the one found in the RNA duplex structure but exhibits an increased H3(U)...N3(C) distance is observed. Water molecules with unusually long residence times are involved in the water-mediated conformations. These results indicate that the dynamic behaviour of the water-mediated UC base-pairs differs from that of the duplex Watson-Crick and non-canonical guanine-uracil pairs with two or three direct hydrogen bonds. The conformational variability and increased flexibility has to be taken into account when considering these base-pairs as RNA building blocks and as recognition motifs.
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Affiliation(s)
- C Schneider
- Biocomputing, Institut für Molekulare Biotechnologie Postfach, 100813 D-07708 Jena, Germany
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Abstract
Computer simulation methods are increasingly being used to study possible conformations and dynamics of structural motifs in RNA. Recent results of molecular dynamics simulations and continum solvent studies of RNA structures and RNA-ligand complexes show promising agreement with experimental data. Combined with the ongoing progress in the experimental characterization of RNA structure and thermodynamics, these computational approaches can help to better understand the mechanism of RNA structure formation and the binding of ligands.
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Affiliation(s)
- M Zacharias
- AG Theoretische Biophysik, Institut für Molekulare Biotechnologie, Jena, D-07745, Germany.
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23
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Foloppe N, MacKerell, Jr. AD. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 2000. [DOI: 10.1002/(sici)1096-987x(20000130)21:2<86::aid-jcc2>3.0.co;2-g] [Citation(s) in RCA: 1273] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Foloppe N, MacKerell, Jr. AD. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 2000. [DOI: 10.1002/(sici)1096-987x(20000130)21:2%3c86::aid-jcc2%3e3.0.co;2-g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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25
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Foloppe N, MacKerell AD. Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics. J Phys Chem B 1999. [DOI: 10.1021/jp992716q] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicolas Foloppe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
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Correll CC, Wool IG, Munishkin A. The two faces of the Escherichia coli 23 S rRNA sarcin/ricin domain: the structure at 1.11 A resolution. J Mol Biol 1999; 292:275-87. [PMID: 10493875 DOI: 10.1006/jmbi.1999.3072] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The sarcin/ricin domain of 23 S - 28 S ribosomal RNA is essential for protein synthesis because it forms a critical part of the binding site for elongation factors. A crystal structure of an RNA of 27 nucleotides that mimics the domain in Escherichia coli 23 S rRNA was determined at 1.11 A resolution. The domain folds into a hairpin distorted by four non-canonical base-pairs and one base triple. The fold is stabilized by cross-strand and intra-stand stacking; no intramolecular stabilizing metal ions are observed. This is the first structure to reveal in great detail the geometry and the hydration of two common motifs that are conserved in this rRNA domain, a GAGA tetraloop and a G-bulged cross-strand A stack. Differences in the region connecting these motifs to the stem in the E. coli and in the rat sarcin/ricin domains may contribute to the species-specific binding of elongation factors. Correlation of nucleotide protection data with the structure indicates that the domain has two surfaces. One surface is accessible, lies primarily in the major groove, and is likely to bind the elongation factors. The second lies primarily in the minor groove, and is likely to be buried in the ribosome. This minor groove surface includes the Watson-Crick faces of the cytosine bases in the unusual A2654.C2666 and U2653.C2667 water-mediated base-pairs.
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Affiliation(s)
- C C Correll
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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Kypr J, Chládková J, Zimulová M, Vorlícková M. Aqueous trifluorethanol solutions simulate the environment of DNA in the crystalline state. Nucleic Acids Res 1999; 27:3466-73. [PMID: 10446234 PMCID: PMC148588 DOI: 10.1093/nar/27.17.3466] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We took 28 fragments of DNA whose crystal structures were known and used CD spectroscopy to search for conditions stabilising the crystal structures in solution. All 28 fragments switched into their crystal structures in 60-80% aqueous trifluorethanol (TFE) to indicate that the crystals affected the conformation of DNA like the concentrated TFE. The fragments crystallising in the B-form also underwent cooperative TFE-induced changes that took place within the wide family of B-form structures, suggesting that the aqueous and crystal B-forms differed as well. Spermine and magnesium or calcium cations, which were contained in the crystallisation buffers, promoted or suppressed the TFE-induced changes of several fragments to indicate that the crystallisation agents can decide which of the possible structures is adopted by the DNA fragment in the crystal.
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Affiliation(s)
- J Kypr
- Academy of Sciences of the Czech Republic, Institute of Biophysics, Královopolská 135, CZ-61265 Brno, Czech Republic
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