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Giegé R. A historical perspective on protein crystallization from 1840 to the present day. FEBS J 2013; 280:6456-97. [DOI: 10.1111/febs.12580] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/30/2013] [Accepted: 09/27/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire; Université de Strasourg et CNRS; France
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2
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Giegé R. Fifty years excitement with science: recollections with and without tRNA. J Biol Chem 2013; 288:6679-87. [PMID: 23325807 DOI: 10.1074/jbc.x113.453894] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Richard Giegé
- Institut de Biologie Moléculaire et Cellulaire, CNRS and Université de Strasbourg, 67084 Strasbourg, France.
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3
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Abstract
Since the year 2000 a number of large RNA three-dimensional structures have been determined by X-ray crystallography. Structures composed of more than 100 nucleotide residues include the signal recognition particle RNA, group I intron, the GlmS ribozyme, RNAseP RNA, and ribosomal RNAs from Haloarcula morismortui, Escherichia coli, Thermus thermophilus, and Deinococcus radiodurans. These large RNAs are constructed from the same secondary and tertiary structural motifs identified in smaller RNAs but appear to have a larger organizational architecture. They are dominated by long continuous interhelical base stacking, tend to segregate into domains, and are planar in overall shape as opposed to their globular protein counterparts. These findings have consequences in RNA folding, intermolecular interaction, and packing, in addition to studies of design and engineering and structure prediction.
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Affiliation(s)
- Stephen R Holbrook
- Structural Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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4
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Abstract
The current state of three-dimensional structure analysis of RNA by x-ray crystallography is summarized. The methods of sample preparation, crystallization, data collection, and structure solution are discussed, followed by a review of the RNA structures that have been determined and of common structural features, and finally, an appraisal of future prospects for x-ray crystal structure analysis of RNA.
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Affiliation(s)
- S R Holbrook
- Structural Biology Division, Lawrence Berkeley National Laboratory, University of California at Berkeley 94720, USA
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5
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Yan X, Xue H, Liu H, Hang J, Wong JT, Zhu G. NMR studies of Bacillus subtilis tRNA(Trp) hyperexpressed in Escherichia coli. Assignment of imino proton signals and determination of thermal stability. J Biol Chem 2000; 275:6712-6. [PMID: 10702225 DOI: 10.1074/jbc.275.10.6712] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
15N-Labeled Bacillus subtilis tRNA(Trp) wild type and a series of mutants were hyperexpressed in Escherichia coli and purified for NMR studies with the use of two-dimensional nuclear Overhauser effect spectroscopy (NOESY) and heteronuclear single quantum correlation (HSQC) and three-dimensional NOESY-HSQC techniques. These made possible chemical shift assignments of imino protons and determination of the thermal stability of the tRNA(Trp) molecules. Almost all of the imino protons in the helical regions and the tertiary base pairs were assigned, except three imino protons of the AU base pairs whose peaks were not clearly observed. Several base triplets found in the crystal structure of tRNA were observed in the present study as well. These studies also revealed two components of tRNA(Trp), which could not be separated by high pressure liquid chromatography, corresponding to s(4)U and U at position 8 of the tRNA(Trp), as indicated by two different sets of peaks for the TpsiC and D arms. The modification at position 8 altered the local conformation of the core region of the tRNA. Thermal unfolding experiments showed that the unfolding process is cooperative in the presence of a high concentration of magnesium ions and that the component corresponding to the s(4)U8 is more stable than the U8 component, thus providing evidence that the thiolation of U8 stabilizes the tertiary structure of tRNA.
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Affiliation(s)
- X Yan
- Department of Biochemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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6
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Jeruzalmi D, Steitz TA. Use of organic cosmotropic solutes to crystallize flexible proteins: application to T7 RNA polymerase and its complex with the inhibitor T7 lysozyme. J Mol Biol 1997; 274:748-56. [PMID: 9405156 DOI: 10.1006/jmbi.1997.1366] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have crystallized, using several approaches that may be of general interest, T7 RNA polymerase (T7RP) and the T7 RNA polymerase-T7 lysozyme complex (T7RPL) in forms suitable for structure determination by X-ray crystallography. A series of polyhydric alcohols, sugars, amino and methylamino acids, compounds known to stabilize protein structure, were found to be critical for both crystallization and subsequent improvement of the crystal's diffraction resolution. Moreover, optimal crystallogenesis was achieved through an unconventional "reverse" vapor diffusion sitting drop method that is suitable for proteins that are insoluble at low ionic strength.T7RP has been crystallized in an orthorhombic form (I), space group P222, with cell parameters a=220 A, b=205 A, c=67 A and a monoclinic form (II), space group P21, with cell parameters a=229 A, b=205 A, c=70 A, beta=106 degrees. Crystal form I diffracts X-rays to 3.5 A and form II to 6.0 A. Three and six copies of the polymerase are predicted to be in the asymmetric unit forms I and II, respectively. Three monoclinic crystal forms of the T7RPL complex have been obtained in space group C2. Form I has cell parameters a=320 A, b=93 A, c=229 A, beta=129 degrees, form II has parameters a=293 A, b=93 A, c=68 A, beta=93 degrees, and form III has parameters a=270 A, b=93 A, c=63 A, beta=103 degrees. Crystal form I diffracts synchrotron wiggler radiation to 3.2 A and form III to 2.8 A. Calculations of crystal density imply three or four copies of the complex in form I and one copy in the asymmetric unit of forms II and III.
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Affiliation(s)
- D Jeruzalmi
- Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA
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7
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Holmes CE, Abraham AT, Hecht SM, Florentz C, Giegé R. Fe.bleomycin as a probe of RNA conformation. Nucleic Acids Res 1996; 24:3399-406. [PMID: 8811095 PMCID: PMC146117 DOI: 10.1093/nar/24.17.3399] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.
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Affiliation(s)
- C E Holmes
- Department of Chemistry, University of Virginia, Charlottesville 22901, USA
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8
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Kolchanov NA, Titov II, Vlassova IE, Vlassov VV. Chemical and computer probing of RNA structure. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 53:131-96. [PMID: 8650302 PMCID: PMC7133174 DOI: 10.1016/s0079-6603(08)60144-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ribonucleic acids (RNAs) are one of the most important types of biopolymers. RNAs play key roles in the storage and multiplication of genetic information. They are important in catalysis and RNA splicing and are the most important steps of translation. This chapter describes experimental methods for probing RNA structure and theoretical methods allowing the prediction of thermodynamically favorable RNA folding. These methods are complementary and together they provide a powerful approach to determine the structure of RNAs. The three-dimensional (tertiary) structure of RNA is formed by hydrogen-bonding among functional groups of nucleosides in different regions of the molecule, by coordination of polyvalent cations, and by stacking between the double-stranded regions present in the RNA. The tertiary structures of only some small RNAs have been determined by high-resolution X-ray crystallographic analysis and nuclear magnetic resonance analysis. The most widely used approach for the investigation of RNA structure is chemical and enzymatic probing, in combination with theoretical methods and phylogenetic studies allowing the prediction of variants of RNA folding. Investigations of RNA structures with different enzymatic and chemical probes can provide detailed data allowing the identification of double-stranded regions of the molecules and nucleotides involved in tertiary interactions.
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Affiliation(s)
- N A Kolchanov
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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9
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Abstract
Two new enzymatic probes have been used for structural investigations of native and unmodified transcript tRNA molecules. Both probes were single-strand-specific nucleases isolated from higher plants. The results obtained after enzymatic hydrolysis of tRNAs support the earlier hypothesis that posttranscriptional modifications in tRNA help to stabilize its structure and make it more rigid.
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MESH Headings
- Base Sequence
- Fungi/chemistry
- Molecular Sequence Data
- Nucleic Acid Conformation
- Plants/enzymology
- RNA Processing, Post-Transcriptional
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Ribonucleosides/chemistry
- Single-Strand Specific DNA and RNA Endonucleases/metabolism
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Affiliation(s)
- A Przykorska
- Institute of Biochemistry and Biophysics, PAN, Warshaw, Poland
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10
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Frugier M, Florentz C, Hosseini MW, Lehn JM, Giegé R. Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase. Nucleic Acids Res 1994; 22:2784-90. [PMID: 8052534 PMCID: PMC308248 DOI: 10.1093/nar/22.14.2784] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The influence of nine synthetic polyamines on in vitro transcription with T7 RNA polymerase has been studied. The compounds used were linear or macrocyclic tetra- and hexaamine, varying in their size, shape and number of protonated groups. Their effect was tested on different types of templates, all presenting the T7 RNA promoter in a double-stranded form followed by sequences encoding short transcripts (25 to 35-mers) either on single- or double-stranded synthetic oligodeoxyribonucleotides. All polyamines used stimulate transcription of both types of templates at levels dependent on their size, shape, protonation degree, and concentration. For each compound, an optimal concentration could be defined; above this concentration, transcription inhibition occurred. Highest stimulation (up to 12-fold) was obtained by the largest cyclic compound called [38]N6C10.
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Affiliation(s)
- M Frugier
- UPR Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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11
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Przykorska A, el Adlouni C, Keith G, Szarkowski JW, Dirheimer G. Structural specificity of Rn nuclease I as probed on yeast tRNA(Phe) and tRNA(Asp). Nucleic Acids Res 1992; 20:659-63. [PMID: 1542562 PMCID: PMC312001 DOI: 10.1093/nar/20.4.659] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A single-strand-specific nuclease from rye germ (Rn nuclease I) was characterized as a tool for secondary and tertiary structure investigation of RNAs. To test the procedure, yeast tRNA(Phe) and tRNA(Asp) for which the tertiary structures are known, as well as the 3'-half of tRNA(Asp) were used as substrates. In tRNA(Phe) the nuclease introduced main primary cuts at positions U33 and A35 of the anticodon loop and G18 and G19 of the D loop. No primary cuts were observed within the double stranded stems. In tRNA(Asp) the main cuts occurred at positions U33, G34, U35, C36 of the anticodon loop and G18 and C20:1 positions in the D loop. No cuts were observed in the T loop in intact tRNA(Asp) but strong primary cleavages occurred at positions psi 55, C56, A57 within that loop in the absence of the tertiary interactions between T and D loops (use of 3'-half tRNA(Asp)). These results show that Rn nuclease I is specific for exposed single-stranded regions.
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MESH Headings
- Base Composition
- Base Sequence
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA, Transfer, Asp/chemistry
- RNA, Transfer, Asp/genetics
- RNA, Transfer, Asp/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- Ribonuclease, Pancreatic/metabolism
- Secale
- Substrate Specificity
- Yeasts/genetics
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Affiliation(s)
- A Przykorska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa
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12
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13
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Ruff M, Cavarelli J, Mikol V, Lorber B, Mitschler A, Giege R, Thierry JC, Moras D. A high resolution diffracting crystal form of the complex between yeast tRNAAsp and aspartyl-tRNA synthetase. J Mol Biol 1988; 201:235-6. [PMID: 3047397 DOI: 10.1016/0022-2836(88)90450-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Three new crystal forms of the complex between yeast tRNAAsp and aspartyl-tRNA synthetase have been produced. The best crystals, obtained after modifying both purification and crystallization conditions, belong to space group P2(1)2(1)2(1) and diffract to 2.7 A. Unit cell parameters are a = 210.4 A, b = 145.3 A and c = 86.0 A (1 A = 0.1 nm), with one dimeric enzyme and two tRNA molecules in the asymmetric unit.
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Affiliation(s)
- M Ruff
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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Ehresmann C, Baudin F, Mougel M, Romby P, Ebel JP, Ehresmann B. Probing the structure of RNAs in solution. Nucleic Acids Res 1987; 15:9109-28. [PMID: 2446263 PMCID: PMC306456 DOI: 10.1093/nar/15.22.9109] [Citation(s) in RCA: 583] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
During these last years, a powerful methodology has been developed to study the secondary and tertiary structure of RNA molecules either free or engaged in complex with proteins. This method allows to test the reactivity of every nucleotide towards chemical or enzymatic probes. The detection of the modified nucleotides and RNase cleavages can be conducted by two different paths which are oriented both by the length of the studied RNA and by the nature of the probes used. The first one uses end-labeled RNA molecule and allows to detect only scissions in the RNA chain. The second approach is based on primer extension by reverse transcriptase and detects stops of transcription at modified or cleaved nucleotides. The synthesized cDNA fragments are then sized by electrophoresis on polyacrylamide:urea gels. In this paper, the various structure probes used so far are described, and their utilization is discussed.
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Affiliation(s)
- C Ehresmann
- Laboratoire de Biochimie, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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Romby P, Giegé R, Houssier C, Grosjean H. Anticodon-anticodon interactions in solution. Studies of the self-association of yeast or Escherichia coli tRNAAsp and of their interactions with Escherichia coli tRNAVal. J Mol Biol 1985; 184:107-118. [PMID: 2411934 DOI: 10.1016/0022-2836(85)90047-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The temperature-jump method was used to measure the thermodynamic and kinetic parameters of the yeast tRNAAsp (anticodon GUC) duplex, which involves a U/U mismatch in the middle position of the quasi self-complementary anticodon, and of the yeast tRNAAsp (GUC)-Escherichia coli tRNAVal (GAC) complex, in which the tRNAs have complementary anticodons. The existence of the tRNAAsp duplex involving GUC-GUC interactions as evidenced in the crystal structure has now been demonstrated in solution. However, the value of its association constant (Kass = 10(4)M-1 at 0 degrees C) is characteristic of a rather weak complex, when compared with that between tRNAAsp and tRNAVal (Kass = 4 X 10(6) M-1 at 0 degrees C), the effect being essentially linked to differences in the rate constant for dissociation. tRNAAsp split in the anticodon by T1 ribonuclease gives no relaxation signal, indicating that the effects observed with intact tRNA were entirely due to anticodon interactions. No duplex formation was observed with other tRNAs having quasi self-complementary GNC anticodons (where N is C, A or G), such as E. coli tRNAGly (GCC), E. coli tRNAVal (GAC) or E. coli tRNAAla (GGC). This is compatible with the idea that, probably as in the crystal structure, a short double helix is formed in solution between the two GUC anticodons. Because of steric effects, such a complex formation would be hindered if a cytosine, adenine or guanine residue were located in the middle position of the anticodon. Escherichia coli tRNAAsp possessing a modified G residue, the Q base, at the first position of the anticodon, showed a weaker self-association than yeast tRNAAsp but its complex with E. coli tRNAVal was found to be only 1.5 times less stable than that between yeast tRNAAsp and E. coli tRNAVal. Temperature-jump experiments conducted under conditions mimicking those used for the crystallization of yeast tRNAAsp (in the presence of 1.6 M-ammonium sulphate and 3mM-spermine) revealed an important stabilization of the yeast and E. coli tRNAAsp duplexes or of their complexes with E. coli tRNAVal. The effect is due exclusively to ammonium sulphate; it is entropy driven and its influence is reflected on the association rate constant; no influence on the dissociation rate constant was observed. For all tRNA-tRNA complexes, the melting temperature upon addition of ammonium sulphate was considerably increased. This study permits the definition of solution conditions in which tRNAs with appropriate anticodons exist mainly as anticodon-anticodon dimers.
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17
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Abstract
The structure of yeast transfer RNA aspartic acid has been refined in one crystal form to 3 A resolution using the restrained least-squares method of Hendrickson and Konnert and real-space fitting using the FRODO program of Jones. The final crystallographic discrepancy index R is 23.5% for 4585 reflections with magnitudes twice their standard deviations between 10 and 3 A. With lower occupancies for some residues of the D-loop, the phosphate U1, and the base U33, the R-factor is 22.3%. The adaptation of the restrained least-squares program for nucleic acids and the progress of the refinement are described. The conformations are analysed with respect to stereochemistry and folding of the backbone. The contacts and hydrogen bonds of the secondary structure are compared with those of yeast tRNAPhe. The presence of only four bases in the variable loop, instead of five as in yeast tRNAPhe, leads to a rotation of residue 48 and a lateral movement of residue 46. These two rearrangements induce different environments for [U8 . . . A14] . . . A21 as well as for A9 and G45. Otherwise, all tertiary contacts observed in yeast tRNAPhe are present in yeast tRNAAsp, except for the absence of hydrogen-bonding between G18 of the D-loop and C56 of the T-loop. The presence of anticodon triplet pairing leads to a distribution of temperature factors different from that observed in yeast tRNAPhe with a stabilization of the AC stem-and-loop and a destabilization of the T and D-loops. We are inclined to suggest that the labilization of the interactions between the T and D-loops is a consequence of the interaction of the anticodon triplets of symmetry-related molecules through hydrogen bonding, which mimics the interaction between the anticodon and its cognate codon on the messenger RNA.
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18
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Lorber B, Giegé R. High-performance liquid chromatographic analysis of crystals of tRNA, aminoacyl-tRNA synthetase, and their complex. Anal Biochem 1985; 146:402-4. [PMID: 3896023 DOI: 10.1016/0003-2697(85)90558-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
High-performance liquid chromatography on an ion exchanger column was successfully used for a rapid biochemical analysis of crystals of yeast tRNAAsp and aspartyl-tRNA synthetase as well as cocrystals formed by the synthetase and the tRNA.
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20
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Dock AC, Lorber B, Moras D, Pixa G, Thierry JC, Giégé R. Crystallization of transfer ribonucleic acids. Biochimie 1984; 66:179-201. [PMID: 6204693 DOI: 10.1016/0300-9084(84)90063-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A compilation of crystallization experiments of tRNAs published in literature as well as original results are given and discussed in this paper. Up to now 17 different tRNA species originating from Escherichia coli and from the yeast Saccharomyces cerevisiae have been crystallized. All structural tRNA families are represented, namely the tRNAs with large or small extra-loops and among them the initiator tRNAs. The tRNAs with small variable loops (4 to 5 nucleotides), e.g. tRNAAsp and tRNAPhe, yield the best diffracting crystals. Crystalline polymorphism is a common feature; about 100 different crystal forms have been observed, but only 6 among them enabled structure determination studies by X-ray diffraction. Crystallization strongly depends upon experimental parameters such as the presence of polyamines and magnesium as well as upon the purity and the molecular integrity of the tRNAs. Crystals are usually obtained by vapour diffusion methods using salts (e.g. ammonium sulfate), organic solvents (e.g. isopropanol, dioxane or 2-methyl-2,4-pentane diol) or polyethylene glycol as precipitants. A methodological strategy for crystallyzing new tRNA species is described.
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21
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Lorber B, Kern D, Dietrich A, Gangloff J, Ebel JP, Giegé R. Large scale purification and structural properties of yeast aspartyl-tRNA synthetase. Biochem Biophys Res Commun 1983; 117:259-67. [PMID: 6362667 DOI: 10.1016/0006-291x(83)91569-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A large scale purification procedure of baker's yeast aspartyl-tRNA synthetase is described which yields more than 200 mg pure protein starting from 30 Kg of wet commercial cells. The synthetase is an alpha 2 dimer of Mr = 125,000 +/- 5,000 which can be crystallized (J. Mol. Biol. 138, 1980, 129-135). The enzyme has an elongated shape with a Stokes radius of 50 A and a frictional ratio of 1.5. The synthetase has a tendency to aggregate but methods are described where this effect is overcome.
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22
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Moras D, Lorber B, Romby P, Ebel JP, Giegé R, Lewit-Bentley A, Roth M. Yeast tRNAAsp-aspartyl-tRNA synthetase: the crystalline complex. J Biomol Struct Dyn 1983; 1:209-23. [PMID: 6401112 DOI: 10.1080/07391102.1983.10507435] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Aspartyl-tRNA synthetase from yeast, a dimer of molecular weight 125,000 and its cognate tRNA (Mr = 24,160) were co-crystallized using ammonium sulfate as precipitant agent. The presence in the crystals of both components in the two-to-one stoichiometric ratio was demonstrated by electrophoresis, biological activity assays and crystallographic data. Crystals belong to the cubic space group I432 with cell parameter of 354 A and one complex particle per asymmetric unit. The solvent content of about 78% is favorable for a low resolution structural investigation. By exchanging H2O for D2O in mother liquors, advantage can be taken from contrast variation techniques with neutron radiations. Diffraction data to 20 A resolution were measured at five different contrasts, two of them being close to the theoretical matching point of RNA and protein in the presence of ammonium sulfate. The experimental extinction of the diffracted signal was observed to be close to 36% D2O, significantly different from the predicted value of 41%. The phenomenon can be explained by the existence of a large interface region between the two tRNAs and the enzyme. These parts of the molecules are hidden from the solvent and their protons are less easily exchangeable. Accessibility studies toward chemicals of tRNAAsp in solution and in the presence of synthetase are in agreement with such a model.
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Affiliation(s)
- D Moras
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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23
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Abstract
The stereochemistry and the dynamics of two loops of yeast tRNA-asp, the thymine loop and the anticodon loop, are compared in the hope of a better understanding of the relationships between loop sequence and loop topology. Both loops are seven residues long and both present sharp turns after the second residue, U33 and psi 55, stabilized by hydrogen bonds between N3-H of the pyrimidine and the phosphates of C36 and A58 and stacking interactions of the pyrimidine ring with the phosphates of U35 and A57, respectively. In the thymine loop, the two purines following C56, A57 and A58, open up to leave space for the intercalation of the first invariant guanine residue of the D-loop, while the two pyrimidine bases, which follow A58, turn away from the stacking pattern of the thymine arm and stack instead with the last base pair of the dihydrouridine arm A15-U48. In the anticodon loop, however, the bases G34 to C38 form an helical stack in continuity with the anticodon stem on the 3'-end. At the same time C36 forms Watson-Crick hydrogen bonds with G34 of a twofold symmetrically related molecule. The anticodon-anticodon base pairing interactions between symmetrically-related molecules are stabilized by stacking with the modified base G37 on both sides of the triplet. Some comparisons are made with the structure of yeast tRNA-phe and some implications about the structure of mitochondrial tRNAs are discussed.
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Affiliation(s)
- E Westhof
- Institut de Biologie Moleculaire et Cellulaire, Centre National de la Recherche Scientifique, Strasbourg, France
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24
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Lorber B, Giegé R, Ebel JP, Berthet C, Thierry JC, Moras D. Crystallization of a tRNA . aminoacyl-tRNA synthetase complex. Characterization and first crystallographic data. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(20)82082-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Giegé R, Lorber B, Ebel JP, Moras D, Thierry JC, Jacrot B, Zaccai G. Formation of a catalytically active complex between tRNAAsp and aspartyl-tRNA synthetase from yeast in high concentrations of ammonium sulphate. Biochimie 1982; 64:357-62. [PMID: 7049254 DOI: 10.1016/s0300-9084(82)80440-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The interactions of yeast tRNAAsp with cognate aspartyl-tRNA synthetase have been studied in high concentrations of either sodium chloride or ammonium sulphate by fluorescence titration and small-angle neutron scattering. In solutions containing more than 1M NaCl no complex is formed and enzymatic activity is abolished. In strong contrast, however, the physical measurements showed the formation of a two-to-one tRNA-enzyme complex, with high affinity, in 1.6 M (NH4)2SO4. Aminoacylation assays under the same salt conditions showed the enzymatic fixation of aspartic acid to tRNAAsp to occur at an appreciable rate. The present study emphasizes that the effects of salts on protein-nucleic acid interactions do not depend only on ionic strength but also on the nature of the salt. This study has allowed a rational approach to the crystallisation of a functional tRNAAsp-aspartyl-tRNA synthetase complex (Giegé, Lorber, Ebel, Thierry and Moras (1980) C.R. Acad. Sci. Paris, série D, 291, 393-396).
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Zelwer C, Risler JL, Brunie S. Crystal structure of Escherichia coli methionyl-tRNA synthetase at 2.5 A resolution. J Mol Biol 1982; 155:63-81. [PMID: 7042987 DOI: 10.1016/0022-2836(82)90492-2] [Citation(s) in RCA: 122] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Hélène C, Lancelot G. Interactions between functional groups in protein-nucleic acid associations. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1982; 39:1-68. [PMID: 6175011 DOI: 10.1016/0079-6107(83)90013-5] [Citation(s) in RCA: 181] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Roy S, Redfield AG. Nuclear Overhauser effect study and assignment of D stem and reverse-Hoogsteen base pair proton resonances in yeast tRNAAsp. Nucleic Acids Res 1981; 9:7073-83. [PMID: 6278454 PMCID: PMC327663 DOI: 10.1093/nar/9.24.7073] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Nuclear Overhauser effects (NOEs) in yeast tRNAAsp were found for all four GU and G psi base pairs. NOEs of both reverse-Hoogsteen pairs were identified by comparison with a purine C8 deuterated sample. Several NOEs involving these resonances were also found which are clearly between single protons on adjacent base pairs. These interbase NOEs, combined with the assumption of reasonable similarity between the structure of yeast tRNAAsp and that of yeast tRNAPhe, lead to unambiguous assignment of many resonances including all the ring NH and C2 protons in the D stem. The stability of the stem at 28 degrees C, as recently deduced by Moras et al (Nature 288 669-674), from x-ray diffraction is confirmed. Assignments of the ring NH resonances of T54-A58 and of a G psi pair are made for the first time.
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Moras D, Comarmond MB, Fischer J, Weiss R, Thierry JC, Ebel JP, Giegé R. Crystal structure of yeast tRNAAsp. Nature 1980; 288:669-74. [PMID: 7005687 DOI: 10.1038/288669a0] [Citation(s) in RCA: 212] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Two independent, three-dimensional structures of yeast tRNAAsp, mainly differing by the conformation of the D loop, have been obtained from a multiple isomorphous replacement (MIR) X-ray analysis at 3.5-A resolution. The folding of the ribose-phosphate backbone is similar to that found for tRNAPhe; major differences concern the relative positioning of the acceptor and anticodon stems, and the conformation of the loops in the two molecules. Crystal packing involves self-complementary GUC anticodon interactions.
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Dietrich A, Giege R, Comarmond MB, Thierry JC, Moras D. Crystallographic studies on the aspartyl-tRNA synthetase-tRNAAsp system from yeast. The crystalline aminoacyl-tRNA synthetase. J Mol Biol 1980; 138:129-35. [PMID: 6997491 DOI: 10.1016/s0022-2836(80)80008-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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