Detection of Escherichia coli ribosome binding at translation initiation sites in the absence of tRNA.

Abstract:

:Binary complexes between messenger RNA and E. coli ribosomes were examined. A ribosome-mRNA binary complex on T4 gene 32 mRNA withstood inhibition by antibodies against ribosomal protein S1. Anti-S1 blocks ternary complex formation, as measured by "extension inhibition" or "toeprinting" analysis, only when preincubated with ribosomes prior to mRNA addition and not when anti-S1 was added after preincubation of ribosomes and mRNA. The ribosome was directly localized in a binary complex on two translation initiation sites by toeprinting analysis. In the absence of tRNA the ribosome halted cDNA synthesis by reverse transcriptase close to the Shine and Dalgarno sequence. Binary complex formation was inhibited by an oligodeoxynucleotide competitor of the Shine and Dalgarno sequence.

journal_name

J Mol Biol

authors

Hartz D,McPheeters DS,Green L,Gold L

doi

10.1016/0022-2836(91)90876-8

subject

Has Abstract

pub_date

1991-03-05 00:00:00

pages

99-105

issue

1

eissn

0022-2836

issn

1089-8638

pii

0022-2836(91)90876-8

journal_volume

218

pub_type

杂志文章
  • Crystal structure of Bacillus sp. GL1 xanthan lyase complexed with a substrate: insights into the enzyme reaction mechanism.

    abstract::Bacillus sp. GL1 xanthan lyase, a member of polysaccharide lyase family 8 (PL-8), acts exolytically on the side-chains of pentasaccharide-repeating polysaccharide xanthan and cleaves the glycosidic bond between glucuronic acid (GlcUA) and pyruvylated mannose (PyrMan) through a beta-elimination reaction. To clarify the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.05.055

    authors: Maruyama Y,Hashimoto W,Mikami B,Murata K

    更新日期:2005-07-29 00:00:00

  • A critical assessment of putative gatekeeper interactions in the villin headpiece helical subdomain.

    abstract::The helical subdomain of the villin headpiece (HP36) is one of the smallest naturally occurring proteins that folds cooperatively. Its small size, rapid folding, and simple three-helix topology have made it an extraordinary popular model system for computational, theoretical, and experimental studies of protein foldin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.070

    authors: Xiao S,Raleigh DP

    更新日期:2010-08-13 00:00:00

  • Recognition of protein substrates by the prolyl isomerase trigger factor is independent of proline residues.

    abstract::The trigger factor is associated with bacterial ribosomes and catalyzes proline-limited protein folding reactions. Its folding activity is very high and conserved in evolution, as shown for the homologous enzymes from Escherichia coli and Mycoplasma genitalium. The folding protein substrate (a variant of ribonuclease ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1604

    authors: Scholz C,Mücke M,Rape M,Pecht A,Pahl A,Bang H,Schmid FX

    更新日期:1998-04-03 00:00:00

  • Extensive methylation of a part of the CpG island located 3.0-4.5 kbp upstream to the chicken alpha-globin gene cluster may contribute to silencing the globin genes in non-erythroid cells.

    abstract::Here, we show that in the chicken genome, the domain of alpha-globin genes is preceded by a CpG island of which the downstream part ( approximately 0.65 kbp) is heavily methylated in lymphoid cells; it is either non-methylated or undermethylated in erythroid cells. Recombinant plasmids were constructed with the corres...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3775

    authors: Razin SV,Ioudinkova ES,Scherrer K

    更新日期:2000-06-16 00:00:00

  • Innate immune response to arenaviral infection: a focus on the highly pathogenic New World hemorrhagic arenaviruses.

    abstract::Arenaviruses are enveloped, negative-stranded RNA viruses that belong to the family Arenaviridae. This diverse family can be further classified into OW (Old World) and NW (New World) arenaviruses based on their antigenicity, phylogeny, and geographical distribution. Many of the NW arenaviruses are highly pathogenic vi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2013.09.028

    authors: Koma T,Huang C,Kolokoltsova OA,Brasier AR,Paessler S

    更新日期:2013-12-13 00:00:00

  • Structural and functional analyses of beta-glucosidase 3B from Thermotoga neapolitana: a thermostable three-domain representative of glycoside hydrolase 3.

    abstract::Based on sequence and phylogenetic analyses, glycoside hydrolase (GH) family 3 can be divided into several clusters that differ in the length of their primary sequences. However, structural data on representatives of GH3 are still scarce, since only three of their structures are known and only one of them has been tho...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.01.072

    authors: Pozzo T,Pasten JL,Karlsson EN,Logan DT

    更新日期:2010-04-02 00:00:00

  • Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor.

    abstract::The structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor was determined in the presence of coenzyme NAD+ at 1.88 A resolution with a final R-factor of 0.175. The structure refinement was carried out on the basis of the structure of holo-GAPDH at 2.0 A resoluti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2628

    authors: Song SY,Xu YB,Lin ZJ,Tsou CL

    更新日期:1999-04-09 00:00:00

  • Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains.

    abstract::Carbohydrate-binding polypeptides, including carbohydrate-binding modules (CBMs) from polysaccharidases, and lectins, are widespread in nature. Whilst CBMs are classically considered distinct from lectins, in that they are found appended to polysaccharide-degrading enzymes, this distinction is blurring. The crystal st...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00152-9

    authors: Boraston AB,Notenboom V,Warren RA,Kilburn DG,Rose DR,Davies G

    更新日期:2003-03-28 00:00:00

  • FlgB, FlgC, FlgF and FlgG. A family of structurally related proteins in the flagellar basal body of Salmonella typhimurium.

    abstract::The flagellar basal body of Salmonella typhimurium consists of four rings surrounding a rod. The rod, which is believed to transmit motor rotation to the filament, is not well characterized in terms of its structure and composition. FlgG is known to lie within the distal portion of the rod, in the region where it is s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90365-S

    authors: Homma M,Kutsukake K,Hasebe M,Iino T,Macnab RM

    更新日期:1990-01-20 00:00:00

  • Pseudo 2-fold symmetry in the copper-binding domain of arthropodan haemocyanins. Possible implications for the evolution of oxygen transport proteins.

    abstract::Investigation of the copper-binding centre of Panulirus interruptus haemocyanin led to the discovery of a pseudo 2-fold axis relating two helical pairs surrounding and co-ordinating the two copper ions. The pseudo 2-fold symmetry relating one helical pair, co-ordinating Cu-A, to the second helical pair co-ordinating C...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90499-3

    authors: Volbeda A,Hol WG

    更新日期:1989-04-05 00:00:00

  • Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI.

    abstract::The restriction enzyme R.BbvCI cleaves duplex DNA within a seven base-pair asymmetric recognition sequence, thus: CCTCAGC/GCTGAGG-->CC--TCAGC/GC--TGAGG. We show that R.BbvCI comprises two different subunits, R(1) and R(2); that each subunit contains a catalytic site for DNA strand hydrolysis; and that these sites act ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.02.034

    authors: Heiter DF,Lunnen KD,Wilson GG

    更新日期:2005-05-06 00:00:00

  • Segmental flexibility and head-head interaction in scallop myosin. A study using saturation transfer electron paramagnetic resonance spectroscopy.

    abstract::Saturation transfer electron paramagnetic resonance spectroscopy was used to investigate the rotational motion of the head domains of native and desensitized scallop myosin and its proteolytic subfragments. Scallop myosin was spin-labelled with 4-(2-iodoacetamido)-2,2,6,6-tetramethylpiperidinooxyl, which reacted with ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(83)90090-6

    authors: Wells C,Bagshaw CR

    更新日期:1983-02-15 00:00:00

  • The importance of G.A hydrogen bonding in the metal ion- and protein-induced folding of a kink turn RNA.

    abstract::The kink turn (K-turn) is a common motif in RNA structure, found in many RNA species important in translation, RNA modification and splicing, and the control of gene expression. In general the K-turn comprises a three nucleotide bulge followed by trans sugar-Hoogsteen G.A pairs. The RNA adopts a tightly kinked conform...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.05.052

    authors: Turner B,Lilley DM

    更新日期:2008-08-29 00:00:00

  • Structure determination of the three disulfide bond isomers of alpha-conotoxin GI: a model for the role of disulfide bonds in structural stability.

    abstract::The three possible disulfide bonded isomers of alpha-conotoxin GI have been selectively synthesised and their structures determined by 1H NMR spectroscopy. alpha-Conotoxin GI derives from the venom of Conus geographus and is a useful neuropharmacological tool as it selectively binds to the nicotinic acetylcholine rece...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1701

    authors: Gehrmann J,Alewood PF,Craik DJ

    更新日期:1998-05-01 00:00:00

  • Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate.

    abstract::The folding/unfolding pathway of barnase has been studied extensively using the protein engineering method, which has provided indirect structural information for the transition state and the major folding intermediate. To further characterize the structural properties of the intermediate, we have simulated the therma...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1484

    authors: Li A,Daggett V

    更新日期:1998-01-30 00:00:00

  • Decay of rplN and lacZ mRNA in Escherichia coli.

    abstract::To examine the previously proposed retroregulation model of spc mRNA degradation, two strains of Escherichia coli B/r were used; one has wild-type spc and lac operons and the other has a lac operon deletion, a wild-type spc operon, and a Pspc-rplN-lacZ fusion operon lacking the normal control sites of the spc operon (...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2710

    authors: Liang ST,Ehrenberg M,Dennis P,Bremer H

    更新日期:1999-05-14 00:00:00

  • Crystallization and preliminary X-ray analysis of the monoclonal anti-tumor antibody BR96 and its complex with the Lewis Y determinant.

    abstract::The monoclonal anti-tumor antibody BR96 binds a tetrasaccharide, Lewis y (Le(y)), in vitro and recognizes a Le(y)-bearing or Le(y)-related tumor-associated antigen in vivo. The Fab of the murine monoclonal antibody, mBR96 (IgG3, kappa), and the Fab' of its human chimera, cBR96 (IgG1, kappa), and their complexes with L...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(05)80044-0

    authors: Chang CY,Jeffrey PD,Bajorath J,Hellström I,Hellström KE,Sheriff S

    更新日期:1994-01-07 00:00:00

  • Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein-Protein Interfaces.

    abstract::Building on the substantial progress that has been made in using free energy perturbation (FEP) methods to predict the relative binding affinities of small molecule ligands to proteins, we have previously shown that results of similar quality can be obtained in predicting the effect of mutations on the binding affinit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.02.003

    authors: Clark AJ,Negron C,Hauser K,Sun M,Wang L,Abel R,Friesner RA

    更新日期:2019-03-29 00:00:00

  • Structure of cryptic lambda prophages.

    abstract::When Escherichia coli cells lysogenic for bacteriophage lambda are induced with ultraviolet light, cells carrying cryptic lambda prophages are occasionally found among the apparently cured survivors. The lambda variant crypticogen (lambda crg) carries an insertion of the transposable element IS2, which increases the f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90289-0

    authors: Redfield RJ,Campbell AM

    更新日期:1987-12-05 00:00:00

  • Growth rate-dependent control, feedback regulation and steady-state mRNA levels of the threonyl-tRNA synthetase gene of Escherichia coli.

    abstract::The expression of the gene thrS encoding threonyl-tRNA synthetase is under the control of two apparently different regulatory loops: translational feedback regulation and growth rate-dependent control. The translational feedback regulation is due to the binding of threonyl-tRNA synthetase to a site located in the lead...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0445

    authors: Comer MM,Dondon J,Graffe M,Yarchuk O,Springer M

    更新日期:1996-08-16 00:00:00

  • Function of His185 in Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase.

    abstract::Aquifex aeolicus 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) catalyzes the condensation of arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) by favoring the activation of a water molecule coordinated to the active-site metal ion. Cys11, His185, Glu222 and Asp233 are the other metal ligands. Wild...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)01096-3

    authors: Wang J,Duewel HS,Stuckey JA,Woodard RW,Gatti DL

    更新日期:2002-11-22 00:00:00

  • Effect of the Asn52----Ile mutation on the redox potential of yeast cytochrome c. Theory and experiment.

    abstract::Theoretical methods for correlation of sequence changes and redox potential of electron transport proteins are examined using the Asn52----Ile mutation in cytochrome c as a test case. The first approach uses the protein dipoles Langevin dipoles (PDLD) method and the high resolution X-ray structures of the native and t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90546-v

    authors: Langen R,Brayer GD,Berghuis AM,McLendon G,Sherman F,Warshel A

    更新日期:1992-04-05 00:00:00

  • Mechanism of strand cleavage and exchange in the Cre-lox site-specific recombination system.

    abstract::The bacteriophage P1 recombinase Cre mediates site-specific recombination between loxP sites. The loxP site consists of two 13 base-pair inverted repeats separated by an eight base-pair spacer region. When DNA containing the loxP site is incubated with Cre, specific cleavages occur within the spacer region, creating a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90224-4

    authors: Hoess RH,Abremski K

    更新日期:1985-02-05 00:00:00

  • A far-upstream Oct-1 motif regulates cytokine-induced transcription of the human inducible nitric oxide synthase gene.

    abstract::Transcriptional regulation of the human inducible nitric oxide synthase (hiNOS) gene is highly complex and requires an orchestrated flow of positive and negative transcription factors that bind to specific cis-acting upstream response elements. Very little specific information exists about the far-upstream region of t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.05.036

    authors: Park KS,Guo Z,Shao L,Du Q,Geller DA

    更新日期:2009-07-24 00:00:00

  • Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength.

    abstract::The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA that resides in the HDV genome and regulates its replication. The native fold of the ribozyme is complex, having two pseudoknots. Earlier work implicated four non-native pairings in slowing pseudoknot formation: Alt 1, Alt 2, Alt 3, and Alt P1. The goal o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.05.071

    authors: Brown TS,Chadalavada DM,Bevilacqua PC

    更新日期:2004-08-13 00:00:00

  • FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties.

    abstract::FUGUE, a program for recognizing distant homologues by sequence-structure comparison (http://www-cryst.bioc.cam.ac.uk/fugue/), has three key features. (1) Improved environment-specific substitution tables. Substitutions of an amino acid in a protein structure are constrained by its local structural environment, which ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4762

    authors: Shi J,Blundell TL,Mizuguchi K

    更新日期:2001-06-29 00:00:00

  • Infrared dichroism of twisted beta-sheet barrels. The structure of E. coli outer membrane proteins.

    abstract::The infrared dichroic ratios of the amide bands from oriented beta-barrels yield an experimental value for the mean orientation, beta, of the beta-strands, relative to the barrel axis. For a barrel of n strands, this then gives the shear number, S, that characterizes the stagger of the beta-sheet. Combining values of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3557

    authors: Marsh D

    更新日期:2000-03-31 00:00:00

  • Conformational changes in phosphoglucose isomerase induced by ligand binding.

    abstract::Phosphoglucose isomerase (PGI; EC 5.3.1.9) is the second enzyme in glycolysis, where it catalyzes the isomerization of D-glucose-6-phosphate to D-fructose-6-phosphate. It is the same protein as autocrine motility factor, differentiation and maturation mediator, and neuroleukin. Here, we report a new X-ray crystal stru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00892-6

    authors: Arsenieva D,Jeffery CJ

    更新日期:2002-10-11 00:00:00

  • Improving profile HMM discrimination by adapting transition probabilities.

    abstract::Profile hidden Markov models (HMMs) are used to model protein families and for detecting evolutionary relationships between proteins. Such a profile HMM is typically constructed from a multiple alignment of a set of related sequences. Transition probability parameters in an HMM are used to model insertions and deletio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.03.023

    authors: Wistrand M,Sonnhammer EL

    更新日期:2004-05-07 00:00:00

  • Crystal structure of Escherichia coli QOR quinone oxidoreductase complexed with NADPH.

    abstract::The crystal structure of the homodimer of quinone oxidoreductase from Escherichia coli has been determined using the multiple isomorphous replacement method at 2.2 A resolution and refined to an R-factor of 14.1% The crystallographic asymmetric unit contains one functional dimer with the two subunits being related by ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0337

    authors: Thorn JM,Barton JD,Dixon NE,Ollis DL,Edwards KJ

    更新日期:1995-06-16 00:00:00