当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > In vitro selection of small RNAs that bind to Escherichia coli phenylalanyl-tRNA synthetase.

In vitro selection of small RNAs that bind to Escherichia coli phenylalanyl-tRNA synthetase.

Abstract：

:Small RNAs were selected from a highly degenerate library on the basis of their ability to bind tightly to Escherichia coli phenylalanyl-tRNA synthetase (FRS). The 63 nucleotide library consisted of the acceptor stem and portions of the D and T stems of E. coli tRNA(Phe) flanking a 32 nucleotide randomized region. Because FRS binding relies on a correctly folded tRNA substrate, the selected variants from this library were expected to resemble tRNA(Phe) structure. After seven cycles of selection, the RNA library bound to FRS with similar affinity to that of the E. coli tRNA(Phe), but did not show detectable aminoacylation. Fourteen FRS-specific isolates were sequenced and found to contain an anticodon stem-loop including the anticodon triplet of tRNA(Phe). The tight-binding RNAs fell into two classes depending on the location of this step-loop within the sequence. The acceptor stem defined by the non-randomized sequence was also found to be essential for binding. Mutation of two residues within a common hexanucleotide sequence present in one of the classes reduced binding to FRS. Taken together, these results suggest that in order to bind RNAs tightly, FRS requires the simultaneous interaction of the anticodon stem-loop and acceptor stem, and additional sequences needed for proper folding. This approach should assist in the detection of motifs that resemble tRNA, but are too dissimilar to be identified by sequence comparison.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Peterson ET,Pan T,Coleman J,Uhlenbeck OC

doi

10.1006/jmbi.1994.1571

subject

Has Abstract

pub_date

1994-09-23 00:00:00

pages

186-92

issue

3

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(84)71571-3

journal_volume

242

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • The IL-10R2 binding hot spot on IL-22 is located on the N-terminal helix and is dependent on N-linked glycosylation.

    abstract：:IL-22 is a class 2 alpha-helical cytokine involved in the generation of inflammatory responses. These activities require IL-22 to engage the cell surface receptors IL-22R1 and the low-affinity signaling molecule IL-10R2. IL-10R2 also interacts with five other class 2 cytokines: IL-10, IL-26, and the interferon-like cy...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.07.069

    authors： Logsdon NJ,Jones BC,Allman JC,Izotova L,Schwartz B,Pestka S,Walter MR

    更新日期：2004-09-10 00:00:00

  • Effects of rifampicin resistant rpoB mutations on antitermination and interaction with nusA in Escherichia coli.

    abstract：:Rifampicin resistant (Rifr mutations map in the rpoB gene encoding the beta subunit of Escherichia coli RNA polymerase. We have used our collection of 17 sequenced Rifr mutations to investigate the involvement of E. coli RNA polymerase in the antitermination systems enhancing expression of delayed early lambda genes o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90573-6

    authors： Jin DJ,Cashel M,Friedman DI,Nakamura Y,Walter WA,Gross CA

    更新日期：1988-11-20 00:00:00

  • Local and global cooperativity in the human alpha-lactalbumin molten globule.

    abstract：:NMR spectroscopy has been used to follow the urea-induced unfolding of the low pH molten globule states of a single-disulfide variant of human alpha-lactalbumin ([28-111] alpha-LA) and of two mutants, each with a single proline substitution in a helix. [28-111] alpha-LA forms a molten globule very similar to that form...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.02.045

    authors： Quezada CM,Schulman BA,Froggatt JJ,Dobson CM,Redfield C

    更新日期：2004-04-16 00:00:00

  • Cooperative and non-cooperative DNA binding modes of catabolite control protein CcpA from Bacillus megaterium result from sensing two different signals.

    abstract：:Carbon catabolite repression (CCR) of several operons in Bacillus subtilis and Bacillus megaterium is mediated by the cis-acting cre sequence and trans-acting catabolite control protein (CcpA). We describe purification of CcpA from B. megaterium and its interaction with regulatory sequences from the xyl operon. Specif...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0820

    authors： Gösseringer R,Küster E,Galinier A,Deutscher J,Hillen W

    更新日期：1997-03-07 00:00:00

  • Crystallographic characterization of an exocyclic DNA adduct: 3,N4-etheno-2'-deoxycytidine in the dodecamer 5'-CGCGAATTepsilonCGCG-3'.

    abstract：:Exocyclic DNA adducts are formed from metabolites of chemical carcinogens and have also been detected as endogenous lesions in human DNA. The exocyclic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilon dC), positioned opposite deoxyguanosine in the B-form duplex of the dodecanucleotide d(CGCGAATTepsilonCGCG), has been cr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(03)00445-5

    authors： Freisinger E,Fernandes A,Grollman AP,Kisker C

    更新日期：2003-06-13 00:00:00

  • Manipulating conformational equilibria in the lactose permease of Escherichia coli.

    abstract：:A mechanism proposed for lactose/H(+) symport by the lactose permease of Escherichia coli indicates that lactose permease is protonated prior to ligand binding. Moreover, in the ground state, the symported H(+) is shared between His322 (helix X) and Glu269 (helix VIII), while Glu325 (helix X) is charge-paired with Arg...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5289

    authors： Weinglass AB,Sondej M,Kaback HR

    更新日期：2002-01-25 00:00:00

  • The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution.

    abstract：:The crystal structure of dihydrodipicolinate synthase from E. coli was determined by multiple isomorphous replacement methods. The structure was refined at a resolution of 2.5 A and the final R-factor is 19.6% for 32,190 reflections between 10.0 A and 2.5 A and F > 2 sigma (F). The crystallographic asymmetric unit con...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.0078

    authors： Mirwaldt C,Korndörfer I,Huber R

    更新日期：1995-02-10 00:00:00

  • Effect of Mg(2+) and Na(+) on the nucleic acid chaperone activity of HIV-1 nucleocapsid protein: implications for reverse transcription.

    abstract：:The human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) is an essential protein for retroviral replication. Among its numerous functions, NC is a nucleic acid (NA) chaperone protein that catalyzes NA rearrangements leading to the formation of thermodynamically more stable conformations. In vitro, NC ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.12.073

    authors： Vo MN,Barany G,Rouzina I,Musier-Forsyth K

    更新日期：2009-02-27 00:00:00

  • Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces.

    abstract：:Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of nine group II introns in maize chloroplasts. CRS2 functions in the context of splicing complexes that include one of two CRS2-associated factors (CAF1 and CAF2). The CRS2-CAF1 and CRS2-CAF2 complexes are required for the splici...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.10.032

    authors： Ostheimer GJ,Hadjivassiliou H,Kloer DP,Barkan A,Matthews BW

    更新日期：2005-01-07 00:00:00

  • Myosin isoform determines the conformational dynamics and cooperativity of actin filaments in the strongly bound actomyosin complex.

    abstract：:We used transient phosphorescence anisotropy to detect the microsecond rotational dynamics of erythrosin-iodoacetamide-labeled actin strongly bound to single-headed fragments of muscle myosin subfragment 1 (S1) and non-muscle myosin V (MV). The conformational dynamics of actin filaments in solution are markedly influe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.11.063

    authors： Prochniewicz E,Chin HF,Henn A,Hannemann DE,Olivares AO,Thomas DD,De La Cruz EM

    更新日期：2010-02-26 00:00:00

  • RecA protein assisted selection reveals a low fidelity of recognition of homology in a duplex DNA by an oligonucleotide.

    abstract：:We have developed an in vitro selection procedure to elucidate the specificity of RecA assisted oligonucleotide recognition of double stranded DNA. The procedure was based on formation of a synaptic complex between an oligonucleotide-RecA filament and a supercoiled plasmid bearing a homologous partially degenerate reg...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1164

    authors： Malkov VA,Sastry L,Camerini-Otero RD

    更新日期：1997-08-15 00:00:00

  • Combining EPR with fluorescence spectroscopy to monitor conformational changes at the myosin nucleotide pocket.

    abstract：:We used spin-labeled nucleotide analogs and fluorescence spectroscopy to monitor conformational changes at the nucleotide-binding site of wild-type Dictyostelium discoideum (WT) myosin and a construct containing a single tryptophan at position F239 near the switch 1 loop. Electron paramagnetic resonance (EPR) spectros...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.12.035

    authors： Naber N,Málnási-Csizmadia A,Purcell TJ,Cooke R,Pate E

    更新日期：2010-03-05 00:00:00

  • Properties of supercoiled DNA in gel electrophoresis. The V-like dependence of mobility on topological constraint. DNA-matrix interactions.

    abstract：:The dependence of the electrophoretic mobility of small DNA rings on topological constraint was investigated in acrylamide or agarose gels as a function of DNA size (from approximately 350 to 1400 base-pairs), gel concentration and nucleotide sequence. Under appropriate adjustment between the size of the DNA and the g...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90282-2

    authors： Zivanovic Y,Goulet I,Prunell A

    更新日期：1986-12-05 00:00:00

  • Deletion analysis of the che operon in the archaeon Halobacterium salinarium.

    abstract：:Halobacterium salinarium is a chemo- and phototactic archaeon whose signal transduction pathway includes the classical two-component system made up of CheA and CheY. Deletion analysis of the che operon in H. salinarium has been undertaken. Following the removal of the entire operon, the importance of each of the four ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0267

    authors： Rudolph J,Oesterhelt D

    更新日期：1996-05-17 00:00:00

  • Identifying functionally important conformational changes in proteins: activation of the yeast α-factor receptor Ste2p.

    abstract：:We have developed a procedure in which disulfide cross-links are used to identify regions of proteins that undergo functionally important intramolecular motion. The approach was applied to the identification of disulfide bonds that stabilize the active state of the yeast α-mating pheromone receptor Ste2p, a member of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.02.024

    authors： Taslimi A,Mathew E,Celić A,Wessel S,Dumont ME

    更新日期：2012-05-18 00:00:00

  • Fibrinogen structure in projection at 18 A resolution. Electron density by co-ordinated cryo-electron microscopy and X-ray crystallography.

    abstract：:Electron microscope images of frozen-hydrated crystals of a proteolytically modified fibrinogen show excellent preservation of the structure. An electron density map of the key centric projection of the crystal at 18 A resolution has been obtained by combining the phases derived from cryo-electron microscopy with X-ra...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90739-s

    authors： Rao SP,Poojary MD,Elliott BW Jr,Melanson LA,Oriel B,Cohen C

    更新日期：1991-11-05 00:00:00

  • Identity elements required for enzymatic formation of N2,N2-dimethylguanosine from N2-monomethylated derivative and its possible role in avoiding alternative conformations in archaeal tRNA.

    abstract：:Here, we have investigated the specificity of purified recombinant tRNA:m(2)(2)G10 methyltransferase of Pyrococcus abyssi ((Pab)Trm-m(2)(2)G10 enzyme). This archaeal enzyme catalyses mono- and dimethylation of the N(2)-exocyclic amino group of guanine at position 10 of several tRNA species. Our results indicate that o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.12.087

    authors： Urbonavicius J,Armengaud J,Grosjean H

    更新日期：2006-03-24 00:00:00

  • Molecular symmetry of the ClpP component of the ATP-dependent Clp protease, an Escherichia coli homolog of 20 S proteasome.

    abstract：:The ClpP component Clp protease from Escherichia coli has been crystallized and examined by X-ray crystallography and self-rotation function calculations. The crystal belongs to the monoclinic space group P2(1) with unit cell dimensions of a = 196.9 A, b = 104.3 A, c = 162.4 A and beta = 98.3 degrees. The X-ray diffra...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0499

    authors： Shin DH,Lee CS,Chung CH,Suh SW

    更新日期：1996-09-20 00:00:00

  • Construction of new ligand binding sites in proteins of known structure. I. Computer-aided modeling of sites with pre-defined geometry.

    abstract：:We have devised a molecular model building computer program (DEZYMER) which builds new ligand binding sites into a protein of known three-dimensional structure. It alters only the sequence and the side-chain structure of the protein, leaving the protein backbone fold intact by definition. The program searches for a co...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90510-d

    authors： Hellinga HW,Richards FM

    更新日期：1991-12-05 00:00:00

  • The conformational properties of the Glc3Man unit suggest conformational biasing within the chaperone-assisted glycoprotein folding pathway.

    abstract：:A major puzzle is: are all glycoproteins routed through the ER calnexin pathway irrespective of whether this is required for their correct folding? Calnexin recognizes the terminal Glcalpha1-3Manalpha linkage, formed by trimming of the Glcalpha1-2Glcalpha1-3Glcalpha1-3Manalpha (Glc3Man) unit in Glc3Man9GlcNAc2. Differ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.01.043

    authors： Mackeen MM,Almond A,Deschamps M,Cumpstey I,Fairbanks AJ,Tsang C,Rudd PM,Butters TD,Dwek RA,Wormald MR

    更新日期：2009-03-27 00:00:00

  • X-ray crystal structure of a non-crystalline cellulose-specific carbohydrate-binding module: CBM28.

    abstract：:Natural cellulose exists as a composite of different forms, which have historically been broadly characterized as "crystalline" or "amorphous". The recognition of both of these forms of cellulose by the carbohydrate-binding modules (CBM) of microbial glycoside hydrolases is central to natural and efficient biotechnolo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.03.069

    authors： Jamal S,Nurizzo D,Boraston AB,Davies GJ

    更新日期：2004-05-28 00:00:00

  • Nucleation and polymerization of sickle hemoglobin with Leu beta 88 substituted by Ala.

    abstract：:We have measured the solubility, and the rates of homogeneous and heterogeneous nucleation on sickle hemoglobin (HbS beta 6 Glu-->Val) additionally modified by site-directed mutagenesis to possess Ala rather than Leu at beta 88, which forms part of the receptor site for beta 6 Val in the sickle polymer. The solubility...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0749

    authors： Cao Z,Liao D,Mirchev R,Martin de Llano JJ,Himanen JP,Manning JM,Ferrone FA

    更新日期：1997-02-07 00:00:00

  • Structure and fluctuations of bacteriorhodopsin in the purple membrane: a molecular dynamics study.

    abstract：:Molecular dynamics simulations on bacteriorhodopsin were performed starting from the model structure described by Henderson et al. The simulations were gradually improved by first treating a monomer in vacuum and then adding further monomers, lipids, and water to finally simulate a unit cell of the hexagonal lattice o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0361

    authors： Edholm O,Berger O,Jähnig F

    更新日期：1995-06-30 00:00:00

  • Three-dimensional crystals of Ca2+-ATPase from sarcoplasmic reticulum: merging electron diffraction tilt series and imaging the (h, k, 0) projection.

    abstract：:Electron crystallography offers an increasingly viable alternative to X-ray crystallography for structure determination, especially for membrane proteins. The methodology has been developed and successfully applied to 2D crystals; however, well-ordered thin, 3D crystals are often produced during crystallization trials...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2283

    authors： Shi D,Lewis MR,Young HS,Stokes DL

    更新日期：1998-12-18 00:00:00

  • Short peptides act as inducers, anti-inducers and corepressors of Tet repressor.

    abstract：:Protein allostery plays a pivotal role in many regulatory processes. Prominent examples are cell-surface receptors, which allosterically transmit ligand-generated signals to their cytoplasmic domains, or bacterial transcription factors, which alternate between a free conformation and a DNA-bound conformation in respon...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.12.009

    authors： Goeke D,Kaspar D,Stoeckle C,Grubmüller S,Berens C,Klotzsche M,Hillen W

    更新日期：2012-02-10 00:00:00

  • Foundations and Emerging Paradigms for Computing in Living Cells.

    abstract：:Genetic circuits, composed of complex networks of interacting molecular machines, enable living systems to sense their dynamic environments, perform computation on the inputs, and formulate appropriate outputs. By rewiring and expanding these circuits with novel parts and modules, synthetic biologists have adapted liv...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.02.018

    authors： Ma KC,Perli SD,Lu TK

    更新日期：2016-02-27 00:00:00

  • Influence of Internal DNA Pressure on Stability and Infectivity of Phage λ.

    abstract：:Viruses must remain infectious while in harsh extracellular environments. An important aspect of viral particle stability for double-stranded DNA viruses is the energetically unfavorable state of the tightly confined DNA chain within the virus capsid creating pressures of tens of atmospheres. Here, we study the influe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2015.07.023

    authors： Bauer DW,Evilevitch A

    更新日期：2015-10-09 00:00:00

  • Molecular framework of steroid/retinoid discrimination in 17beta-hydroxysteroid dehydrogenase type 1 and photoreceptor-associated retinol dehydrogenase.

    abstract：:Steroids and retinoids are signaling molecules that control a variety of physiological processes. 17beta-Hydroxysteroid dehydrogenase type 1 (17beta-HSD1) catalyzes the reduction of estrone to estradiol, supplying biologically active estrogen-regulating sex-specific differentiation. Photoreceptor-associated retinol de...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.04.002

    authors： Haller F,Moman E,Hartmann RW,Adamski J,Mindnich R

    更新日期：2010-06-04 00:00:00

  • A novel C-terminal homologue of Aha1 co-chaperone binds to heat shock protein 90 and stimulates its ATPase activity in Entamoeba histolytica.

    abstract：:Cytosolic heat shock protein 90 (Hsp90) has been shown to be essential for many infectious pathogens and is considered a potential target for drug development. In this study, we have carried out biochemical characterization of Hsp90 from a poorly studied protozoan parasite of clinical importance, Entamoeba histolytica...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.01.008

    authors： Singh M,Shah V,Tatu U

    更新日期：2014-04-17 00:00:00

  • The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes.

    abstract：:Structure determination of complex molecular machines requires a combination of an increasing number of experimental methods with highly specialized software geared toward each data source to properly handle the gathered data. Recently, we introduced the two software packages PowerFit and DisVis. These combine high-re...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.11.032

    authors： van Zundert GC,Trellet M,Schaarschmidt J,Kurkcuoglu Z,David M,Verlato M,Rosato A,Bonvin AM

    更新日期：2017-02-03 00:00:00