当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Involvement of a stem-loop structure in the location of junction sites in viral RNA recombination.

Involvement of a stem-loop structure in the location of junction sites in viral RNA recombination.

Abstract：

:Recombination between RNAs associated with turnip crinkle virus is thought to occur during plus-strand synthesis at motifs resembling the 5'-ends of genomic, subgenomic and satellite RNAs. Common structural regions encompassing the motifs have been found for major crossover sites on two different minus-strand templates, with junctions preferentially located in a single-stranded region at the 3' base of a hairpin. Base changes, deletions and compensatory alteration constructed in and around the hairpin in the region of the turnip crinkle virus genomic RNA involved in recombination support the importance of the hairpin for normal crossover site selection. This region of the genomic RNA is also important for replication of the viral genomic RNA in plants and protoplasts, suggesting a common link between sequences required for recombination and viral replication.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Carpenter CD,Oh JW,Zhang C,Simon AE

doi

10.1006/jmbi.1994.0050

subject

Has Abstract

pub_date

1995-02-03 00:00:00

pages

608-22

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022283684700507

journal_volume

245

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.

    abstract：:In order to study the effect of internal dynamics on the accuracy of NMR structures in detail, we generated NOE distance data from a long molecular dynamics trajectory of BPTI. Cross-relaxation rates were calculated from the trajectory by analysis of the appropriate proton-proton vector autocorrelation functions. A cr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2323

    authors： Schneider TR,Brünger AT,Nilges M

    更新日期：1999-01-15 00:00:00

  • Ribosomal protein L9: a structure determination by the combined use of X-ray crystallography and NMR spectroscopy.

    abstract：:The structure of protein L9 from the Bacillus stearothernophilus ribosome has been determined at 2.5 A resolution by refinement against single crystal X-ray diffraction data with additional constraints provided by NMR data. This highly elongated protein consists of two domains separated by a nine-turn connecting helix...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0696

    authors： Hoffman DW,Cameron CS,Davies C,White SW,Ramakrishnan V

    更新日期：1996-12-20 00:00:00

  • Structural organization and assembly of flagellar hook protein from Salmonella typhimurium.

    abstract：:The terminal regions of monomeric hook protein from Salmonella typhimurium are known to be highly mobile and exposed to the solvent. Although hook protein exhibits an unusual far-UV circular dichroism spectrum, resembling that of random coil structures, our calorimetric experiments clearly demonstrate that the molecul...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0453

    authors： Vonderviszt F,Závodszky P,Ishimura M,Uedaira H,Namba K

    更新日期：1995-08-25 00:00:00

  • A C-H triplebond O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins.

    abstract：:The serendipitous observation of a C-H cdots, three dots, centered O hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been ex...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00715-5

    authors： Madan Babu M,Kumar Singh S,Balaram P

    更新日期：2002-09-27 00:00:00

  • X-ray diffraction analysis of crystals of bovine platelet factor 4.

    abstract：:Bovine platelet factor 4 has been crystallized by "vapor dilution" in space group P2(1)2(1)2(1), a = 63.7 A, b = 66.7 A, c = 80.5 A, with four molecules, each 9505 Mr, in the asymmetric unit. The crystals diffract X-rays to better than 2.8 A resolution. ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(84)90497-2

    authors： St Charles R,Ciaglowski RE,Walz D,Edwards BF

    更新日期：1984-07-05 00:00:00

  • Evidence for intramolecular processing of prosubtilisin sequestered on a solid support.

    abstract：:Subtilisin E is synthesized in Bacillus subtilis as a preprosubtilisin. The prepeptide is removed by a signal peptidase, and the propeptide is cleaved from the mature protein by the catalytic domain of subtilisin itself in an autocatalytic fashion. A six residue histidine-tag was attached to the C terminus of prosubti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0538

    authors： Volkov A,Jordan F

    更新日期：1996-10-11 00:00:00

  • Solution structure of R-elafin, a specific inhibitor of elastase.

    abstract：:The solution structure of r-elafin, a specific elastase inhibitor, has been determined using NMR spectroscopy. Characterized by a flat core and a flexible N-terminal extremity, the three-dimensional structure is formed by a central twisted beta-hairpin accompanied by two external segments linked by the proteinase bind...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.0983

    authors： Francart C,Dauchez M,Alix AJ,Lippens G

    更新日期：1997-05-09 00:00:00

  • All-D peptides recognized by an anti-carbohydrate antibody identified from a positional scanning library.

    abstract：:Monoclonal antibodies recognize antigens with high affinity and specificity, but the structural basis for molecular mimicry remains unclear. It is often assumed that cross-reactive antigens share some structural similarity that is specifically recognized by a monoclonal antibody. Recent studies using combinatorial lib...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2137

    authors： Pinilla C,Appel JR,Campbell GD,Buencamino J,Benkirane N,Muller S,Greenspan NS

    更新日期：1998-11-13 00:00:00

  • Secondary structure and temperature-induced unfolding and refolding of ribonuclease T1 in aqueous solution. A Fourier transform infrared spectroscopic study.

    abstract：:The secondary structure of ribonuclease T1 (RNase T1) in aqueous solution and its temperature-induced structural changes have been investigated by Fourier-transform infrared (FT-IR) spectroscopy. 13 to 14% alpha-helix and 32 to 33% beta-sheet were estimated from the resolution-enhanced FT-IR spectra, in agreement with...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1442

    authors： Fabian H,Schultz C,Naumann D,Landt O,Hahn U,Saenger W

    更新日期：1993-08-05 00:00:00

  • Identifying determinants of recombination specificity: construction and characterization of mutant bacteriophage integrases.

    abstract：:The Integrases of bacteriophages lambda and HK022 promote recombination between DNA molecules that carry attachment sites. The two integrases are about 70% identical in sequence and catalyze nearly identical reactions, but recognize different sets of sites. To identify the amino acids that determine this difference in...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0486

    authors： Dorgai L,Yagil E,Weisberg RA

    更新日期：1995-09-15 00:00:00

  • An apparent pause site in the transcription unit of the rabbit alpha-globin gene.

    abstract：:Transcription of the rabbit alpha-globin gene begins primarily at the cap site, although some upstream start sites are also observed. Analysis by RNA polymerase run-on assays in nuclei shows that transcription continues at a high level past the polyadenylation site, after which the polymerase density actually increase...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90011-t

    authors： Vandenbergh DJ,James-Pederson M,Hardison RC

    更新日期：1991-07-20 00:00:00

  • Human cardiac myosin binding protein C: structural flexibility within an extended modular architecture.

    abstract：:New insights into the modular organization and flexibility of the N-terminal half of human cardiac myosin binding protein C (cMyBP-C) and information on the association state of the full-length protein have been deduced from a combined small-angle X-ray scattering (SAXS) and NMR study. SAXS data show that the first fi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.10.029

    authors： Jeffries CM,Lu Y,Hynson RM,Taylor JE,Ballesteros M,Kwan AH,Trewhella J

    更新日期：2011-12-16 00:00:00

  • Evidence for helical unwinding of an RNA substrate by the RNA enzyme RNase P: use of an interstrand disulfide crosslink in substrate.

    abstract：:To gain an understanding of structural changes induced in substrates by Escherichia coli ribonuclease P (RNase P), we have incorporated an interstrand disulfide crosslink proximal to the cleavage site in a model substrate. RNase P is able to process the reduced, non-crosslinked form of this substrate as well as a subs...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3424

    authors： Pomeranz Krummel DA,Kent O,MacMillan AM,Altman S

    更新日期：2000-02-04 00:00:00

  • A clathrin, caveolae, and dynamin-independent endocytic pathway requiring free membrane cholesterol drives HIV-1 internalization and infection in polarized trophoblastic cells.

    abstract：:In human trophoblastic cells, a correlation between early endosomal trafficking of HIV-1 and virus infection was previously documented. However, if HIV-1 is massively internalized in these cells, the endocytic pathway(s) responsible for viral uptake is still undefined. Here we address this vital question. Amongst all ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.03.003

    authors： Vidricaire G,Tremblay MJ

    更新日期：2007-05-18 00:00:00

  • Two-dimensional kinetics of inter-connexin interactions from single-molecule force spectroscopy.

    abstract：:Gap junction channels are intercellular channels that form by docking the extracellular loops of connexin protein subunits. While the structure and function of gap junctions as intercellular channels have been characterized using different techniques, the physics of the inter-connexin interaction remain unknown. Moreo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.07.013

    authors： Rico F,Oshima A,Hinterdorfer P,Fujiyoshi Y,Scheuring S

    更新日期：2011-09-09 00:00:00

  • Toward Decoding Bioelectric Events in Xenopus Embryogenesis: New Methodology for Tracking Interplay Between Calcium and Resting Potentials In Vivo.

    abstract：:Although chemical signaling during embryogenesis is readily addressed by a plethora of available techniques, the developmental functions of ionic signaling are still poorly understood. It is increasingly realized that bioelectric events in nonneural cells are critical for pattern regulation, but their study has been h...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.10.029

    authors： McMillen P,Novak R,Levin M

    更新日期：2020-01-17 00:00:00

  • Hemoglobin allostery: new views on old players.

    abstract：:Proteins are dynamic molecular machines whose structure and function are modulated by environmental perturbations and natural selection. Allosteric regulation, discovered in 1963 as a novel molecular mechanism of enzymatic adaptation [Monod, Changeux & Jacob (1963). J. Mol. Biol.6, 306-329], seems to be the leit motiv...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.12.018

    authors： Miele AE,Bellelli A,Brunori M

    更新日期：2013-05-13 00:00:00

  • Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs.

    abstract：:Interactions of transmembrane helices play a crucial role in the folding and oligomerisation of integral membrane proteins. In order to uncover novel sequence motifs mediating these interactions, we randomised one face of a transmembrane helix with a set of non-polar or moderately polar amino acids. Those sequences ca...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.09.056

    authors： Unterreitmeier S,Fuchs A,Schäffler T,Heym RG,Frishman D,Langosch D

    更新日期：2007-11-30 00:00:00

  • PhhR binds to target sequences at different distances with respect to RNA polymerase in order to activate transcription.

    abstract：:The NtrC-family PhhR protein of Pseudomonas putida is involved in the control of the metabolism of aromatic amino acids, and it is a dual regulatory protein. When PhhR acts as an activator, it stimulates transcription from its cognate promoters with RNA polymerase/sigma(70) rather than with sigma(54), as is the case f...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.09.045

    authors： Herrera MC,Krell T,Zhang X,Ramos JL

    更新日期：2009-12-04 00:00:00

  • Limited proteolysis unmasks specific DNA-binding of the murine RNA polymerase I-specific transcription termination factor TTFI.

    abstract：:Previously we have shown that nuclear extracts from mouse cells contain a heterogeneous group of polypeptides (p65, p80, p90, p100) which form distinct DNA-protein complexes on the 18 base-pair sequence element (termed Sal-box), which constitutes the murine rDNA transcription termination signal. These distinct protein...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90213-4

    authors： Smid A,Finsterer M,Grummt I

    更新日期：1992-10-05 00:00:00

  • A thiol labelling competition experiment as a probe for sidechain packing in the kinetic folding intermediate of N-PGK.

    abstract：:Protein folding is directed by the sequence of sidechains along the polypeptide backbone, but despite this the developement of sidechain interactions during folding is not well understood. Here, the thiol-active reagent, dithio-nitrobenzoic acid (DTNB), is used to probe the exposure of the cysteine sidechain thiols in...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.09.014

    authors： Cliff MJ,Alizadeh T,Jelinska C,Craven CJ,Staniforth RA,Waltho JP

    更新日期：2006-12-08 00:00:00

  • Solution state NMR structure and dynamics of KpOmpA, a 210 residue transmembrane domain possessing a high potential for immunological applications.

    abstract：:The three-dimensional structure of the outer membrane protein A from Klebsiella pneumoniae transmembrane domain was determined by NMR.This protein induces specific humoral and cytotoxic responses, and is a potent carrier protein. This is one of the largest integral membrane proteins(210 residues) for which nearly comp...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.10.021

    authors： Renault M,Saurel O,Czaplicki J,Demange P,Gervais V,Löhr F,Réat V,Piotto M,Milon A

    更新日期：2009-01-09 00:00:00

  • Splicing of a cap-proximal human Papillomavirus 16 E6E7 intron promotes E7 expression, but can be restrained by distance of the intron from its RNA 5' cap.

    abstract：:Human papillomavirus 16 (HPV16) E6E7 pre-mRNA is bicistronic and has an intron in the E6 coding region with one 5' splice site and two alternative 3' splice sites, which produce E6(*)I and E6(*)II, respectively. If this intron remains unspliced, the resulting E6E7 mRNA expresses oncogenic E6. We found for the first ti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.02.023

    authors： Zheng ZM,Tao M,Yamanegi K,Bodaghi S,Xiao W

    更新日期：2004-04-09 00:00:00

  • Monomer/dimer ratios of replication protein modulate the DNA strand-opening in a replication origin.

    abstract：:DNA opening is an essential step in the initiation of replication via the Cairns mode of replication. The opening reaction was investigated in a gamma ori system by using hyperactive variants of plasmid R6K-encoded initiator protein, pi. Reactivity to KMnO4 (indicative of opening) within gamma ori DNA occurred in both...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4426

    authors： Krüger R,Konieczny I,Filutowicz M

    更新日期：2001-03-09 00:00:00

  • Somatic insertions and deletions shape the human antibody repertoire.

    abstract：:We have sequenced the heavy and light chain genes from 365 IgG(+) B cells and found that 24 (6.5 %) contain somatically introduced insertions or deletions. These insertions and deletions are clustered at "hot-spots" in the antigen-binding site and frequently result in the creation of new combinations of canonical loop...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3289

    authors： de Wildt RM,van Venrooij WJ,Winter G,Hoet RM,Tomlinson IM

    更新日期：1999-12-03 00:00:00

  • The geometry of interactions between catalytic residues and their substrates.

    abstract：:The process of deducing the catalytic mechanism of an enzyme from its structure is highly complex and requires extensive experimental work to validate a proposed mechanism. As one step towards improving the reliability of this process, we have gathered statistics describing the typical geometry of catalytic residues w...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.03.055

    authors： Torrance JW,Holliday GL,Mitchell JB,Thornton JM

    更新日期：2007-06-15 00:00:00

  • Characterization of the structure and the amyloidogenic properties of the Josephin domain of the polyglutamine-containing protein ataxin-3.

    abstract：:Expansion of the polyglutamine (polyQ) region in the protein ataxin-3 is associated with spinocerebellar ataxia type 3, an inherited neurodegenerative disorder that belongs to the family of polyQ diseases. Increasing evidence indicates that protein aggregation and fibre formation play an important role in these pathol...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.09.065

    authors： Masino L,Nicastro G,Menon RP,Dal Piaz F,Calder L,Pastore A

    更新日期：2004-12-03 00:00:00

  • Ligand-induced conformational rearrangements promote interaction between the Escherichia coli enterobactin biosynthetic proteins EntE and EntB.

    abstract：:Siderophores are small-molecule iron chelators that many bacteria synthesize and secrete in order to survive in iron-depleted environments. Biosynthesis of enterobactin, the Escherichia coli catecholate siderophore, requires adenylation of 2,3-dihydroxybenzoic acid (2,3-DHB) by the cytoplasmic enzyme EntE. The DHB-AMP...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.08.036

    authors： Khalil S,Pawelek PD

    更新日期：2009-10-30 00:00:00

  • The protein synthesis inhibitors, oxazolidinones and chloramphenicol, cause extensive translational inaccuracy in vivo.

    abstract：:The oxazolidinone family is a new class of synthetic antibiotics that bind to the bacterial 50S ribosomal subunit. Two members of the family, linezolid and XA043, were examined for their effects on translational fidelity using a lacZ reporter gene in vivo. Both promoted highly significant frameshifting and nonsense su...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00784-2

    authors： Thompson J,O'Connor M,Mills JA,Dahlberg AE

    更新日期：2002-09-13 00:00:00

  • Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation.

    abstract：:We have developed a formalism and a computational method for analyzing the potential functional consequences of non-synonymous single nucleotide polymorphisms. Our approach uses a structural model and phylogenetic information to derive a selection of structure and sequence-based features serving as indicators of an am...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4510

    authors： Chasman D,Adams RM

    更新日期：2001-03-23 00:00:00