A branched pathway in the early stage of transcription by Escherichia coli RNA polymerase.


:The time-course of synthesis of long and short (abortive) transcripts by Escherichia coli RNA polymerase was investigated under single round conditions in vitro. The synthesis of long RNA initiated at the lambda PR (with an altered leader sequence) or at the lacUV5 promoter was completed within five minutes, but abortive transcripts were continuously synthesized for at least 20 minutes. The results indicate the presence of transcription complexes that are capable only of abortive synthesis, and not of productive elongation. Consistently, only one in four of the RNA polymerase molecules that initially associated with the lambda PR promoter synthesized long RNA. The enzyme reisolated from productive complexes synthesized both long and abortive transcripts, behaving just like the original enzyme. This suggests that RNA polymerase is homogeneous with respect to its ability to synthesize the two types of product. Overall, the results indicate that many transcription complexes can be irreversibly trapped in vitro in an abortive cycle.


J Mol Biol


Kubori T,Shimamoto N




Has Abstract


1996-03-01 00:00:00














  • The conserved asparagine in the HNH motif serves an important structural role in metal finger endonucleases.

    abstract::The HNH motif is a small nucleic acid binding and cleavage module, widespread in metal finger endonucleases in all life kingdoms. Here we studied a non-specific endonuclease, the nuclease domain of ColE7 (N-ColE7), to decipher the role of the conserved asparagine and histidine residues in the HNH motif. We found, usin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Huang H,Yuan HS

    更新日期:2007-05-04 00:00:00

  • Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.

    abstract::HIV-1 (human immunodeficiency virus type 1) protease (PR) and its mutants are important antiviral drug targets. The PR flap region is critical for binding substrates or inhibitors and catalytic activity. Hence, mutations of flap residues frequently contribute to reduced susceptibility to PR inhibitors in drug-resistan...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Liu F,Kovalevsky AY,Tie Y,Ghosh AK,Harrison RW,Weber IT

    更新日期:2008-08-01 00:00:00

  • Conserved hydrophobic clusters on the surface of the Caf1A usher C-terminal domain are important for F1 antigen assembly.

    abstract::The outer membrane usher protein Caf1A of the plague pathogen Yersinia pestis is responsible for the assembly of a major surface antigen, the F1 capsule. The F1 capsule is mainly formed by thin linear polymers of Caf1 (capsular antigen fraction 1) protein subunits. The Caf1A usher promotes polymerization of subunits a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Dubnovitsky AP,Duck Z,Kersley JE,Härd T,MacIntyre S,Knight SD

    更新日期:2010-10-22 00:00:00

  • RNA-dependent folding and stabilization of C5 protein during assembly of the E. coli RNase P holoenzyme.

    abstract::The pre-tRNA processing enzyme ribonuclease P is a ribonucleoprotein. In Escherichia coli assembly of the holoenzyme involves binding of the small (119 amino acid residue) C5 protein to the much larger (377 nucleotide) P RNA subunit. The RNA subunit makes the majority of contacts to the pre-tRNA substrate and contains...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Guo X,Campbell FE,Sun L,Christian EL,Anderson VE,Harris ME

    更新日期:2006-06-30 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


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

    更新日期:1995-06-16 00:00:00

  • Diffusing and colliding: the atomic level folding/unfolding pathway of a small helical protein.

    abstract::Proteins with ultra-fast folding/unfolding kinetics are excellent candidates for study by molecular dynamics. Here, we describe such simulations of a three helix bundle protein, the engrailed homeodomain (En-HD), which folds via the diffusion-collision model. The unfolding pathway of En-HD was characterized by seven s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: DeMarco ML,Alonso DO,Daggett V

    更新日期:2004-08-20 00:00:00

  • Accommodation of amino acid insertions in an alpha-helix of T4 lysozyme. Structural and thermodynamic analysis.

    abstract::One to four alanines were inserted by site-directed mutagenesis at three different locations within the alpha-helix comprising residues 39 to 50 in bacteriophage T4 lysozyme. All insertion mutants were correctly folded and catalytically active although the insertions led to a thermal destabilization by 1.1 to 4.2 kcal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Heinz DW,Baase WA,Zhang XJ,Blaber M,Dahlquist FW,Matthews BW

    更新日期:1994-02-25 00:00:00

  • Defining functional regions of the IS903 transposase.

    abstract::The insertion sequence IS903 encodes a 307 amino acid residue protein, transposase, that is essential for transposition. It is a multi-functional DNA-binding protein that specifically recognizes the 18 bp inverted repeats at the ends of the element and also recognizes DNa non-specifically when it captures a target sit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Tavakoli NP,DeVost J,Derbyshire KM

    更新日期:1997-12-12 00:00:00

  • Tryptophan supports interaction of transmembrane helices.

    abstract::Interactions of transmembrane helices play an important role in folding and oligomerization of integral membrane proteins. The interfacial residues of these helices frequently correspond to heptad repeat motifs. In order to uncover novel mechanisms underlying these interactions, we randomised a heptad repeat pattern w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ridder A,Skupjen P,Unterreitmeier S,Langosch D

    更新日期:2005-12-09 00:00:00

  • Three-dimensional structure of a cloning vector. X-ray diffraction studies of filamentous bacteriophage M13 at 7 A resolution.

    abstract::Filamentous bacteriophage M13 is a single-stranded DNA phage about 65 A in diameter and 9300 A long. X-ray diffraction studies of magnetically oriented fibers of native, mercury and iodine-labeled phage particles have been used to determine the arrangement of the major coat protein, the gene 8 product, in the virion. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Glucksman MJ,Bhattacharjee S,Makowski L

    更新日期:1992-07-20 00:00:00

  • Myosin binding surface on actin probed by hydroxyl radical footprinting and site-directed labels.

    abstract::Actin and myosin are the two main proteins required for cell motility and muscle contraction. The structure of their strongly bound complex-rigor state-is a key for delineating the functional mechanism of actomyosin motor. Current knowledge of that complex is based on models obtained from the docking of known atomic s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Oztug Durer ZA,Kamal JK,Benchaar S,Chance MR,Reisler E

    更新日期:2011-11-25 00:00:00

  • Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI.

    abstract::Sequence-specific interactions between proteins and DNA are essential for a variety of biological functions. The (cytosine-C5)-methyltransferase from HhaI (M.HhaI) specifically modifies the second base in GCGC sequences, employing a base flipping mechanism to access the target base being chemically modified. The mecha...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Huang N,MacKerell AD Jr

    更新日期:2005-01-14 00:00:00

  • Disulfide mutants of barnase. II: Changes in structure and local stability identified by hydrogen exchange.

    abstract::The hydrogen exchange behaviour of two stabilised disulfide mutants of barnase has been examined using NMR H/2H exchange measurements. The choice of experimental conditions is crucial in experiments to study the effects of mutations on local and global stability and dynamic behaviour of proteins. If exchange condition...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Clarke J,Hounslow AM,Fersht AR

    更新日期:1995-10-27 00:00:00

  • Role of the salt-bridge between switch-1 and switch-2 of Dictyostelium myosin.

    abstract::Motifs N2 and N3, also referred to as switch-1 and switch-2, form part of the active site of molecular motors such as myosins and kinesins. In the case of myosin, N3 is thought to act as a gamma-phosphate sensor and moves almost 6 A relative to N2 during the catalysed turnover of ATP, opening and closing the active si...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Furch M,Fujita-Becker S,Geeves MA,Holmes KC,Manstein DJ

    更新日期:1999-07-16 00:00:00

  • Weak and strong states of kinesin and ncd.

    abstract::Kinesin superfamily molecular motors step along microtubules (MTs) via a cycle of conformational changes which is coupled to ATP turnover. To probe the coupling mechanism, we titrated the effects of various nucleotides on MT binding by two superfamily members; MT plus-end-directed kinesin and MT minus-end-directed non...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Crevel IM,Lockhart A,Cross RA

    更新日期:1996-03-22 00:00:00

  • Fluid and condensed ApoA-I/phospholipid monolayers provide insights into ApoA-I membrane insertion.

    abstract::Apolipoprotein A-I (ApoA-I) is a protein implicated in the solubilization of lipids and cholesterol from cellular membranes. The study of ApoA-I in phospholipid (PL) monolayers brings relevant information about ApoA-I/PL interactions. We investigated the influence of PL charge and acyl chain organization on the intera...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Chièze L,Bolanos-Garcia VM,Pinot M,Desbat B,Renault A,Beaufils S,Vié V

    更新日期:2011-07-01 00:00:00

  • Relationship of DNA structure to internal dynamics: correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)(2) and d(CGCTAGCG)(2) with (13)C order parameters implies conformational coupling in dinucleotide units.

    abstract::The coupling between the conformational properties of double-stranded DNA and its internal dynamics has been examined. The solution structures of the isomeric DNA oligomers d(GCGTACGC)(2) (UM) and d(CGCTAGCG)(2) (CTSYM) were determined with (1)H NMR spectroscopy by utilizing distance restraints from total relaxation m...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Isaacs RJ,Spielmann HP

    更新日期:2001-03-23 00:00:00

  • Functional analysis of the glucocorticoid regulatory elements present in the mouse mammary tumor virus long terminal repeat. A synthetic distal binding site can replace the proximal binding domain.

    abstract::Transcription of mouse mammary tumor virus DNA is stimulated by steroid hormones. The DNA sequences involved in this regulation are located in the viral long terminal repeat between positions -200 and -50 with respect to the transcription initiation site. In this region four, one distal and three proximal, in vitro bi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kühnel B,Buetti E,Diggelmann H

    更新日期:1986-08-05 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


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

    更新日期:2002-09-27 00:00:00

  • Ion-coupling determinants of Na+-driven and H+-driven flagellar motors.

    abstract::The bacterial flagellar motor is a tiny molecular machine that uses a transmembrane flux of H(+) or Na(+) ions to drive flagellar rotation. In proton-driven motors, the membrane proteins MotA and MotB interact via their transmembrane regions to form a proton channel. The sodium-driven motors that power the polar flage...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Asai Y,Yakushi T,Kawagishi I,Homma M

    更新日期:2003-03-21 00:00:00

  • Structural basis of interaction between urokinase-type plasminogen activator and its receptor.

    abstract::Recent studies indicate that binding of the urokinase-type plasminogen activator (uPA) to its high-affinity receptor (uPAR) orchestrates uPAR interactions with other cellular components that play a pivotal role in diverse (patho-)physiological processes, including wound healing, angiogenesis, inflammation, and cancer ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Barinka C,Parry G,Callahan J,Shaw DE,Kuo A,Bdeir K,Cines DB,Mazar A,Lubkowski J

    更新日期:2006-10-20 00:00:00

  • The 29.9 kDa subunit of mitochondrial complex I is involved in the enzyme active/de-active transitions.

    abstract::Mitochondrial respiratory chain complex I undergoes transitions from active to de-activated forms. We have investigated the phenomenon in sub-mitochondrial particles from Neurospora crassa wild-type and a null-mutant lacking the 29.9 kDa nuclear-coded subunit of complex I. Based on enzymatic activities, genetic crosse...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ushakova AV,Duarte M,Vinogradov AD,Videira A

    更新日期:2005-08-12 00:00:00

  • Crystallization of porcine liver ribonuclease inhibitor a member of the family of proteins containing leucine-rich repeats.

    abstract::Single crystals of the RNase inhibitor from porcine liver have been obtained from 30 to 34% saturated ammonium sulphate solutions at pH 6.0 to 7.2, containing 20 mM dithiothreitol, at room temperature over a period of two to three weeks. Because the inhibitor contains 30 1/2-cystinyl residues, all of which occur in th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Neumann U,Hofsteenge J,Arkema AH,Dijkstra BW

    更新日期:1993-05-20 00:00:00

  • Mapping the stability determinants of bacterial tyrosyl transfer RNA synthetases by an experimental evolutionary approach.

    abstract::The tyrosyl-tRNA synthetases from Bacillus stearothermophilus (Bst-TyrTS) and Escherichia coli (Eco-TyrTS) are 56% identical in amino acid sequence. To map and characterize the set of interactions that makes Bst-TyrTS more stable than Eco-TyrTS, a family of nine hybrid proteins was constructed between the two enzymes....

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Guez-Ivanier V,Hermann M,Baldwin D,Bedouelle H

    更新日期:1993-11-05 00:00:00

  • Distribution of surface-exposed and non-accessible amino acid sequences among the two major structural domains of the S-layer protein of Aeromonas salmonicida.

    abstract::The tetragonally arranged crystalline surface protein array (A-layer) of the fish pathogenic bacterium Aeromonas salmonicida is a virulence factor. Circular dichroism studies in the presence or absence of 0.1% sodium dodecyl sulfate showed that the secondary structure of A-protein, and its 39,439 molecular weight amin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Doig P,McCubbin WD,Kay CM,Trust TJ

    更新日期:1993-10-20 00:00:00

  • Distinct Roles of Mic12 and Mic27 in the Mitochondrial Contact Site and Cristae Organizing System.

    abstract::The mitochondrial inner membrane consists of two morphologically distinct domains, the inner boundary membrane and large invaginations termed cristae. Narrow membrane structures, the crista junctions, link these two domains. Maintenance of this elaborate architecture depends on the evolutionarily conserved mitochondri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Zerbes RM,Höß P,Pfanner N,van der Laan M,Bohnert M

    更新日期:2016-04-24 00:00:00

  • Structure-based design of a second-generation Lyme disease vaccine based on a C-terminal fragment of Borrelia burgdorferi OspA.

    abstract::Here, we describe a structure-based approach to reduce the size of an antigen protein for a subunit vaccine. Our method consists of (i) determining the three-dimensional structure of an antigen, (ii) identifying protective epitopes, (iii) generation of an antigen fragment that contains the protective epitope, and (iv)...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Koide S,Yang X,Huang X,Dunn JJ,Luft BJ

    更新日期:2005-07-08 00:00:00

  • Xenopus poly(A) binding protein: functional domains in RNA binding and protein-protein interaction.

    abstract::Subsets of the four RNA binding domains (RBD 1 to 4) in the Xenopus poly-adenylate binding protein (PABP) have distinct affinities and specificities for RNA. RBDs 1 plus 2 exhibit RNA affinity and selectivity equal to the wild-type (WT) protein. RBDs 3 plus 4 have distinct selectivity and about ten-fold reduced affini...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kühn U,Pieler T

    更新日期:1996-02-16 00:00:00

  • Ensemble Modeling and Intracellular Aggregation of an Engineered Immunoglobulin-Like Domain.

    abstract::The production of recombinant proteins in Escherichia coli frequently results in the formation of insoluble protein aggregates called inclusion bodies (IBs). The determinants of IB formation remain poorly understood and are of much interest for biotechnological and research applications, as well as offering insight in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Trainor K,Gingras Z,Shillingford C,Malakian H,Gosselin M,Lipovšek D,Meiering EM

    更新日期:2016-03-27 00:00:00

  • Intrahelical hydrogen bonding of serine, threonine and cysteine residues within alpha-helices and its relevance to membrane-bound proteins.

    abstract::A survey of known protein structures reveals that approximately 70% of serine residues and at least 85% (potentially 100%) of threonine residues in helices make hydrogen bonds to carbonyl oxygen atoms in the preceding turn of the helix. The high frequency of intrahelical hydrogen bonding is of particular significance ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Gray TM,Matthews BW

    更新日期:1984-05-05 00:00:00