In vivo and in vitro studies of TrpR-DNA interactions.


:The binding of tryptophan repressor (TrpR) to its operators was examined quantitatively using in vitro and in vivo methods. DNA sequence requirements for 1:1 and tandem 2:1 (TrpR:DNA) binding in various sequence contexts were studied. The results indicate that the optimal half-site sequence for recognition by one helix-turn-helix motif of one TrpR dimer is 3'CNTGA5'5'GNACT3', consistent with contacts observed by X-ray diffraction analysis of cocrystalline 1:1 and 2:1 complexes. Half-sites can be paired to form a palindrome either by direct abutment, forming the nucleation site for a tandem 2:1 complex, or with an 8-base-pair spacer, forming a 1:1 target. Dimethylsulfate (DMS) methylation-protection footprinting in vitro of 1:1 and 2:1 complexes formed sequentially on the two unequal half-site pairs of the trpEDCBA operator from Serratia marcescens indicated an obligate hierarchy of site occupancy, with one half-site pair serving as the nucleation site for tandem binding. DMS footprinting of Escherichia coli operators in vivo showed that, over a wide range of intracellular TrpR concentration, the trpEDCBA operator is occupied by three repressor dimers, aroH is occupied by two dimers, and the 1:1 binding mode is used on the trpR operator. The coexistence of these distinct occupancy states implies that changes in protein concentration affect only the fractional occupancy of each operator rather than the binding mode, which is determined by the number of half-site sequences present in the operator region. Cooperativity of tandem complex formation measured by gel retardation using a symmetrized synthetic operator containing identical, optimal sites spaced as in natural operators was found to be modest, implying a maximum coupling free energy of approximately -2 kcal/mol. On other sequences the apparent degree of cooperativity, as well as the apparent affinity, varies with sequence and sequence context in a manner consistent with the structural models and which suggests compensation between affinity and cooperativity as a mechanism that allows tolerance of operator sequence variation.


J Mol Biol


Yang J,Gunasekera A,Lavoie TA,Jin L,Lewis DE,Carey J




Has Abstract


1996-04-26 00:00:00














  • Impact of mutations on the allosteric conformational equilibrium.

    abstract::Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Weinkam P,Chen YC,Pons J,Sali A

    更新日期:2013-02-08 00:00:00

  • In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities.

    abstract::Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mamm...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Czudnochowski N,Wang AL,Finer-Moore J,Stroud RM

    更新日期:2013-10-23 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


    authors: Heiter DF,Lunnen KD,Wilson GG

    更新日期:2005-05-06 00:00:00

  • Molecular determinants for substrate specificity of the ligand-binding protein OpuAC from Bacillus subtilis for the compatible solutes glycine betaine and proline betaine.

    abstract::Compatible solutes play a decisive role in the defense of microorganisms against changes in temperature and increases in osmolarity in their natural habitats. In Bacillus subtilis, the substrate-binding protein (SBP)-dependent ABC-transporter OpuA serves for the uptake of the compatible solutes glycine betaine (GB) an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Horn C,Sohn-Bösser L,Breed J,Welte W,Schmitt L,Bremer E

    更新日期:2006-03-24 00:00:00

  • NMR structure of activated CheY.

    abstract::The CheY protein is the response regulator in bacterial chemotaxis. Phosphorylation of a conserved aspartyl residue induces structural changes that convert the protein from an inactive to an active state. The short half-life of the aspartyl-phosphate has precluded detailed structural analysis of the active protein. Pe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Cho HS,Lee SY,Yan D,Pan X,Parkinson JS,Kustu S,Wemmer DE,Pelton JG

    更新日期:2000-03-31 00:00:00

  • Molecular crowding limits the role of fetal hemoglobin in therapy for sickle cell disease.

    abstract::The dominant assumption central to most treatments for sickle cell anemia has been that replacement of sickle hemoglobin (HbS) by fetal hemoglobin (HbF) would have major clinical benefit. Using laser photolysis, we have measured polymerization kinetics including rates of homogeneous and heterogeneous nucleation on mix...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Rotter M,Aprelev A,Adachi K,Ferrone FA

    更新日期:2005-04-15 00:00:00

  • Crystal structure of the C-terminal domain of S.cerevisiae eIF5.

    abstract::eIF5, a GTPase-activating protein (GAP) specific for eIF2, plays a critical role in pre-initiation complex assembly and correct AUG selection during eukaryotic translation initiation. eIF5 is involved in the formation of the multifactor complex (MFC), an important intermediate of the 43S pre-initiation complex. The C-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Wei Z,Xue Y,Xu H,Gong W

    更新日期:2006-05-26 00:00:00

  • Immunoaffinity enrichment coupled to quantitative mass spectrometry reveals ubiquitin-mediated signaling events.

    abstract::Ubiquitination is one of the most prevalent posttranslational modifications in eukaryotic cells, with functional importance in protein degradation, subcellular localization and signal transduction pathways. Immunoaffinity enrichment coupled with quantitative mass spectrometry enables the in-depth characterization of p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Yu K,Phu L,Varfolomeev E,Bustos D,Vucic D,Kirkpatrick DS

    更新日期:2015-06-05 00:00:00

  • Two slow stages in refolding of bovine carbonic anhydrase B are due to proline isomerization.

    abstract::Kinetics of refolding of bovine carbonic anhydrase B have been studied by the "double-jump" technique (i.e. the dependence of protein refolding on delay time in the unfolded state after fast unfolding). It is shown that two stages (the slow with a relaxation time of t1/2 approximately equal to 120 s and the superslow ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Semisotnov GV,Uversky VN,Sokolovsky IV,Gutin AM,Razgulyaev OI,Rodionova NA

    更新日期:1990-06-05 00:00:00

  • Novel Insights into Cell Entry of Emerging Human Pathogenic Arenaviruses.

    abstract::Viral hemorrhagic fevers caused by emerging RNA viruses of the Arenavirus family are among the most devastating human diseases. Climate change, global trade, and increasing urbanization promote the emergence and re-emergence of these human pathogenic viruses. Emerging pathogenic arenaviruses are of zoonotic origin and...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Fedeli C,Moreno H,Kunz S

    更新日期:2018-06-22 00:00:00

  • Structure of alpha-chymotrypsin refined at 1.68 A resolution.

    abstract::Diffraction data for alpha-chymotrypsin crystals at -10 degrees C were measured at 1.68 A resolution and refined by restrained structure-factor least-squares refinement. The two independent chymotrypsin molecules in the crystallographic asymmetric unit were refined independently. The overall structure of alpha-chymotr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Tsukada H,Blow DM

    更新日期:1985-08-20 00:00:00

  • Geometry of the flagellar motor in the cytoplasmic membrane of Salmonella typhimurium as determined by stereo-photogrammetry of quick-freeze deep-etch replica images.

    abstract::The precise geometry of the flagellar basal structure anchored in the cytoplasmic membrane was determined by digital stereo-photogrammetry of the images captured by quick-freeze deep-etch replica electron microscopy. In order to examine the structure on the periplasmic side of the membrane, we analyzed the MS ring com...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Katayama E,Shiraishi T,Oosawa K,Baba N,Aizawa S

    更新日期:1996-01-26 00:00:00

  • Fast Translation within the First 45 Codons Decreases mRNA Stability and Increases Premature Transcription Termination in E. coli.

    abstract::We show here that the specific use of fast or slowly translated codons in the early coding region of a gene may influence both the mRNA stability and premature transcription termination. We first inserted a pair of nearly identical 42-base-pair (bp)-long sequences into codon 3 of the Escherichia coli lacZ gene. The on...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Pedersen S,Terkelsen TB,Eriksen M,Hauge MK,Lund CC,Sneppen K,Mitarai N

    更新日期:2019-03-15 00:00:00

  • Functional structures of the recA protein found by chimera analysis.

    abstract::We developed a novel genetic method for finding functional regions of a protein by the analysis of chimeras formed between homologous proteins. Sets of chimeric genes were made by intramolecular homologous recombination in a linearized plasmid DNA carrying both recA genes of Escherichia coli and Pseudomonas aeruginosa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ogawa T,Shinohara A,Ogawa H,Tomizawa J

    更新日期:1992-08-05 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

  • Light-regulated catalysis by an RNA-cleaving deoxyribozyme.

    abstract::We describe light-induced switches for the catalytic activity of the small, RNA-cleaving 8-17 deoxyribozyme (DNAzyme), based on photochemically induced cis-trans isomerization of azobenzene (Az) moieties covalently tethered at various locations within the DNAzyme. Prior studies have shown that trans-azobenzene is able...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Liu Y,Sen D

    更新日期:2004-08-20 00:00:00

  • Recruiting Zn2+ to mediate potent, specific inhibition of serine proteases.

    abstract::As regulators of ubiquitous biological processes, serine proteases can cause disease states when inappropriately expressed or regulated, and are thus rational targets for inhibition by drugs. Recently we described a new inhibition mechanism applicable for the development of potent, selective small molecule serine prot...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Katz BA,Luong C

    更新日期:1999-09-24 00:00:00

  • Coupling of protein assembly and DNA binding: biotin repressor dimerization precedes biotin operator binding.

    abstract::The kinetics of coupling of protein dimerization and DNA binding have been investigated in the biotin repressor system. Two repressor monomers bind to the 40 base-pair biotin operator sequence. In previous analyses of equilibrium-binding data the weak dimerization of the repressor has justified using a model in which ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Streaker ED,Beckett D

    更新日期:2003-01-31 00:00:00

  • Structure of the Drosophila projectin protein: isoforms and implication for projectin filament assembly.

    abstract::The protein composition of the various muscle types in Drosophila melanogaster has been studied quite thoroughly and the analysis has revealed many differences involving the usage of muscle specific isoforms of a given protein, as well as the presence of proteins restricted to one muscle type. Drosophila projectin, th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Daley J,Southgate R,Ayme-Southgate A

    更新日期:1998-05-29 00:00:00

  • Mitochondrial respiratory chain supercomplexes are destabilized in Barth Syndrome patients.

    abstract::Mutations in the human TAZ gene are associated with Barth Syndrome, an often fatal X-linked disorder that presents with cardiomyopathy and neutropenia. The TAZ gene encodes Tafazzin, a putative phospholipid acyltranferase that is involved in the remodeling of cardiolipin, a phospholipid unique to the inner mitochondri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: McKenzie M,Lazarou M,Thorburn DR,Ryan MT

    更新日期:2006-08-18 00:00:00

  • Refined crystallographic structure of Pseudomonas aeruginosa exotoxin A and its implications for the molecular mechanism of toxicity.

    abstract::Exotoxin A of Pseudomonas aeruginosa asserts its cellular toxicity through ADP-ribosylation of translation elongation factor 2, predicated on binding to specific cell surface receptors and intracellular trafficking via a complex pathway that ultimately results in translocation of an enzymatic activity into the cytopla...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Wedekind JE,Trame CB,Dorywalska M,Koehl P,Raschke TM,McKee M,FitzGerald D,Collier RJ,McKay DB

    更新日期:2001-12-07 00:00:00

  • An examination of the electrostatic interactions between the N-terminal tail of the Brome Mosaic Virus coat protein and encapsidated RNAs.

    abstract::The coat protein of positive-stranded RNA viruses often contains a positively charged tail that extends toward the center of the capsid and interacts with the viral genome. Electrostatic interaction between the tail and the RNA has been postulated as a major force in virus assembly and stabilization. The goal of this ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ni P,Wang Z,Ma X,Das NC,Sokol P,Chiu W,Dragnea B,Hagan M,Kao CC

    更新日期:2012-06-22 00:00:00

  • A shortened form of the Tetrahymena thermophila group I intron can catalyze the complete splicing reaction in trans.

    abstract::The group I intron from Tetrahymena thermophila is able to catalyze its own excision from a precursor RNA. The intron recognizes the splice sites through an intron-encoded sequence called the internal guide sequence, or IGS. The 5' and 3' exons are thought to align on the IGS and form a pseudoknot structure consisting...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Sargueil B,Tanner NK

    更新日期:1993-10-20 00:00:00

  • Peroxisome proliferator-activated receptor alpha controls hepatic heme biosynthesis through ALAS1.

    abstract::Heme is an essential prosthetic group of proteins involved in oxygen transport, energy metabolism and nitric oxide production. ALAS1 (5-aminolevulinate synthase) is the rate-limiting enzyme in heme synthesis in the liver and is highly regulated to adapt to the metabolic demand of the hepatocyte. In the present study, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,收录出版


    authors: Degenhardt T,Väisänen S,Rakhshandehroo M,Kersten S,Carlberg C

    更新日期:2009-05-01 00:00:00

  • Ancylostoma ceylanicum excretory-secretory protein 2 adopts a netrin-like fold and defines a novel family of nematode proteins.

    abstract::Hookworms are human parasites that have devastating effects on global health, particularly in underdeveloped countries. Ancylostoma ceylanicum infects humans and animals, making it a useful model organism to study disease pathogenesis. A. ceylanicum excretory-secretory protein 2 (AceES-2), a highly immunoreactive mole...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kucera K,Harrison LM,Cappello M,Modis Y

    更新日期:2011-04-22 00:00:00

  • Symmetry and chirality in topoisomerase II-DNA crossover recognition.

    abstract::Several experimental data support the notion that the recognition of DNA crossovers play an important role in the multiple functions of topoisomerase II. Here, a theoretical analysis of the possible modes of assembly of yeast topoisomerase II with right and left-handed tight DNA crossovers is performed, using the crys...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,meta分析


    authors: Timsit Y,Duplantier B,Jannink G,Sikorav JL

    更新日期:1998-12-18 00:00:00

  • The crystal and molecular structure of the Rhizomucor miehei triacylglyceride lipase at 1.9 A resolution.

    abstract::The crystal and molecular structure of a triacylglyceride lipase (EC from the fungus Rhizomucor miehei was analyzed using X-ray single crystal diffraction data to 1.9 A resolution. The structure was refined to an R-factor of 0.169 for all available data. The details of the molecular architecture and the cryst...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Derewenda ZS,Derewenda U,Dodson GG

    更新日期:1992-10-05 00:00:00

  • Accomodation of S-cis-tamoxifen-N(2)-guanine adduct within a bent and widened DNA minor groove.

    abstract::The non-steroidal anti-estrogen tamoxifen [TAM] has been in clinical use over the last two decades as a potent adjunct chemotherapeutic agent for treatment of breast cancer. It has also been given prophylactically to women with a strong family history of breast cancer. However, tamoxifen treatment has also been associ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Shimotakahara S,Gorin A,Kolbanovskiy A,Kettani A,Hingerty BE,Amin S,Broyde S,Geacintov N,Patel DJ

    更新日期:2000-09-15 00:00:00

  • Structural basis of HIV-1 activation by NF-kappaB--a higher-order complex of p50:RelA bound to the HIV-1 LTR.

    abstract::The activation and latency of human immunodeficiency virus type 1 (HIV-1) are tightly controlled by the transcriptional activity of its long terminal repeat (LTR) region. The LTR is regulated by viral proteins as well as host factors, including the nuclear factor kappaB (NF-kappaB) that becomes activated in virus-infe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Stroud JC,Oltman A,Han A,Bates DL,Chen L

    更新日期:2009-10-16 00:00:00

  • Intimate view of a kinetic protein folding intermediate: residue-resolved structure, interactions, stability, folding and unfolding rates, homogeneity.

    abstract::A cytochrome c kinetic folding intermediate was studied by hydrogen exchange (HX) pulse labeling. Advances in the technique and analysis made it possible to define the structured and unstructured regions, equilibrium stability, and kinetic opening and closing rates, all at an amino acid-resolved level. The entire N-te...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Krishna MM,Lin Y,Mayne L,Englander SW

    更新日期:2003-11-28 00:00:00