当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae.

Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae.

Abstract：

:Riboswitches are complex folded RNA domains found in noncoding regions of mRNA that regulate gene expression upon small molecule binding. Recently, Breaker and coworkers reported a tandem aptamer riboswitch (VCI-II) that binds glycine cooperatively. Here, we use hydroxyl radical footprinting and small-angle X-ray scattering (SAXS) to study the conformations of this tandem aptamer as a function of Mg(2+) and glycine concentration. We fit a simple three-state thermodynamic model that describes the energetic coupling between magnesium-induced folding and glycine binding. Furthermore, we characterize the structural conformations of each of the three states: In low salt with no magnesium present, the VCI-II construct has an extended overall conformation, presumably representing unfolded structures. Addition of millimolar concentrations of Mg(2+) in the absence of glycine leads to a significant compaction and partial folding as judged by hydroxyl radical protections. In the presence of millimolar Mg(2+) concentrations, the tandem aptamer binds glycine cooperatively. The glycine binding transition involves a further compaction, additional tertiary packing interactions and further uptake of magnesium ions relative to the state in high Mg(2+) but no glycine. Employing density reconstruction algorithms, we obtain low resolution 3-D structures for all three states from the SAXS measurements. These data provide a first glimpse into the structural conformations of the VCI-II aptamer, establish rigorous constraints for further modeling, and provide a framework for future mechanistic studies.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Lipfert J,Das R,Chu VB,Kudaravalli M,Boyd N,Herschlag D,Doniach S

doi

10.1016/j.jmb.2006.10.022

subject

Has Abstract

pub_date

2007-02-02 00:00:00

pages

1393-406

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(06)01360-X

journal_volume

365

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Effect of single DNA lesions on in vitro replication with DNA polymerase III holoenzyme. Comparison with other polymerases.

    abstract：:In the present work, we have studied in vitro replication of N-2-acetylaminofluorene (AAF) or cis-diamminedichloroplatinum II (cis-DDP) single modified DNA templates. We used the holoenzyme (pol III HE) or the alpha subunit of DNA polymerase III, which is involved in SOS mutagenesis, and other DNA polymerases in order...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1125

    authors： Belguise-Valladier P,Maki H,Sekiguchi M,Fuchs RP

    更新日期：1994-02-11 00:00:00

  • Conformational properties of the aggregation precursor state of HypF-N.

    abstract：:The conversion of specific proteins or protein fragments into insoluble, ordered fibrillar aggregates is a fundamental process in protein chemistry, biology, medicine and biotechnology. As this structural conversion seems to be a property shared by many proteins, understanding the mechanism of this process will be of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.04.002

    authors： Campioni S,Mossuto MF,Torrassa S,Calloni G,de Laureto PP,Relini A,Fontana A,Chiti F

    更新日期：2008-06-06 00:00:00

  • The positive transcription elongation factor b is an essential cofactor for the activation of transcription by myocyte enhancer factor 2.

    abstract：:The positive transcription elongation factor b (P-TEFb), composed of cyclin-dependent kinase 9 and cyclin T1, stimulates the elongation of transcription by hyperphosphorylating the C-terminal region of RNA polymerase II. Aberrant activation of P-TEFb results in manifestations of cardiac hypertrophy in mice, suggesting...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.07.017

    authors： Nojima M,Huang Y,Tyagi M,Kao HY,Fujinaga K

    更新日期：2008-10-03 00:00:00

  • Crystallization and preliminary X-ray data for the A-isozyme of O-acetylserine sulfhydrylase from Salmonella typhimurium.

    abstract：:The A-isozyme of O-acetylserine sulfhydrylase, a pyridoxal phosphate-dependent enzyme isolated from Salmonella typhimurium catalyzes the synthesis of L-cysteine from O-acetyl-L-serine and sulfide. The pyridoxal form of the enzyme has been crystallized in two different forms. One form is in the orthorhombic space group...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1358

    authors： Rao GS,Mottonen J,Goldsmith EJ,Cook PF

    更新日期：1993-06-20 00:00:00

  • Thermodynamics of RNA unfolding: stabilization of a ribosomal RNA tertiary structure by thiostrepton and ammonium ion.

    abstract：:RNAs with interesting secondary and tertiary structures tend to melt in several broad and overlapping transitions over a wide temperature range, and it has been consequently difficult to resolve the thermodynamics of individual unfolding steps. In the case that a ligand selectively binds a single folded state of the R...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0291

    authors： Draper DE,Xing Y,Laing LG

    更新日期：1995-06-02 00:00:00

  • Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis.

    abstract：:A normal mode and energy minimization of ras p21 is used to determine the flexibility of the protein and the origin of the conformational differences between GTP and GDP-bound forms. To preserve the integrity of the structures, a hydration shell of water molecules was included as part of the system. Certain low-freque...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1313

    authors： Ma J,Karplus M

    更新日期：1997-11-21 00:00:00

  • Direct interaction of 14-3-3ζ with ezrin promotes cell migration by regulating the formation of membrane ruffle.

    abstract：:14-3-3 proteins have been shown to regulate the actin cytoskeleton remodeling, cell adhesion and migration. In this study, we identified ezrin, a cross-linker between plasma membrane and actin cytoskeleton, as a novel 14-3-3ζ interacting partner. The direct interaction between 14-3-3ζ and ezrin was validated in the ce...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.06.021

    authors： Chen M,Liu T,Xu L,Gao X,Liu X,Wang C,He Q,Zhang G,Liu L

    更新日期：2014-09-09 00:00:00

  • Structural and biophysical characterization of the Syk activation switch.

    abstract：:Syk is an essential non-receptor tyrosine kinase in intracellular immunological signaling, and the control of Syk kinase function is considered as a valuable target for pharmacological intervention in autoimmune or inflammation diseases. Upon immune receptor stimulation, the kinase activity of Syk is regulated by bind...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.11.007

    authors： Grädler U,Schwarz D,Dresing V,Musil D,Bomke J,Frech M,Greiner H,Jäkel S,Rysiok T,Müller-Pompalla D,Wegener A

    更新日期：2013-01-23 00:00:00

  • Cadherin superfamily proteins in Caenorhabditis elegans and Drosophila melanogaster.

    abstract：:The ability to form selective cell-cell adhesions is an essential property of metazoan cells. Members of the cadherin superfamily are important regulators of this process in both vertebrates and invertebrates. With the advent of genome sequencing projects, determination of the full repertoire of cadherins available to...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4361

    authors： Hill E,Broadbent ID,Chothia C,Pettitt J

    更新日期：2001-02-02 00:00:00

  • Extending the accuracy limits of prediction for side-chain conformations.

    abstract：:Current techniques for the prediction of side-chain conformations on a fixed backbone have an accuracy limit of about 1.0-1.5 A rmsd for core residues. We have carried out a detailed and systematic analysis of the factors that influence the prediction of side-chain conformation and, on this basis, have succeeded in ex...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4865

    authors： Xiang Z,Honig B

    更新日期：2001-08-10 00:00:00

  • Signal sequences containing multiple aromatic residues.

    abstract：:Using homopolymeric units of either phenylalanine or tryptophan to replace the natural core segment of the Escherichia coli alkaline phosphatase signal peptide, the hydrophobicity requirements for protein export and processing were further explored. The mutant signal peptide containing polyphenylalanine functioned at ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90577-7

    authors： Rusch SL,Kendall DA

    更新日期：1992-03-05 00:00:00

  • A New Type of Circular RNA derived from Nonconventional Introns in Nuclear Genes of Euglenids.

    abstract：:Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringin...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.166758

    authors： Gumińska N,Zakryś B,Milanowski R

    更新日期：2021-02-05 00:00:00

  • The mechanism of loading of the FLP recombinase onto its DNA target sequence.

    abstract：:The FLP recombinase interacts with its target sequence with the formation of three distinct DNA-protein complexes. The first complex leaves neither a DNase footprint nor is the DNA protected from methylation by dimethyl sulfate. We have found, however, that the FLP protein is bound predominantly to only one of the thr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90576-1

    authors： Beatty LG,Sadowski PD

    更新日期：1988-11-20 00:00:00

  • RNA binding, packaging and polymerase activities of the different incomplete polymerase complex particles of dsRNA bacteriophage phi 6.

    abstract：:phi 6 is an enveloped dsRNA bacterial virus. Its segmented genome resides inside the virion associated polymerase complex which is formed by four proteins (P1, P2, P4 and P7) encoded by the viral L segment. Complete and incomplete polymerase complex particles can be produced using cDNA copies of this largest genome se...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0317

    authors： Juuti JT,Bamford DH

    更新日期：1995-06-09 00:00:00

  • Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering.

    abstract：:A systematic classification of beta-hairpin structures which takes into account the polypeptide chain length and hydrogen bonding between the two antiparallel beta-strands is described. We have used this classification of beta-hairpin structures and their specific sequence pattern to derive rules which demonstrate its...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90583-4

    authors： Sibanda BL,Blundell TL,Thornton JM

    更新日期：1989-04-20 00:00:00

  • Distinct functions of N and C-terminal domains of GreA, an Escherichia coli transcript cleavage factor.

    abstract：:The prokaryotic transcription factors GreA and GreB are involved in the regulation of transcript elongation by RNA polymerase (RNAP). Their known activities include suppression of transcription arrest, enhancement of transcription fidelity, and facilitation of the transition from abortive initiation to productive elon...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1545

    authors： Koulich D,Nikiforov V,Borukhov S

    更新日期：1998-02-20 00:00:00

  • Structure and binding determinants of the recombinant kringle-2 domain of human plasminogen to an internal peptide from a group A Streptococcal surface protein.

    abstract：:The X-ray crystal structure of a complex of a modified recombinant kringle-2 domain of human plasminogen, K2Pg[C4G/E56D/L72Y] (mK2Pg), containing an upregulated lysine-binding site, bound to a functional 30 residue internal peptide (VEK-30) from an M-type protein of a group A Streptococcus surface protein, has been de...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4646

    authors： Rios-Steiner JL,Schenone M,Mochalkin I,Tulinsky A,Castellino FJ

    更新日期：2001-05-11 00:00:00

  • X-ray diffraction studies of 14-filament models of deoxygenated sickle cell hemoglobin fibers. Models based on electron micrograph reconstructions.

    abstract：:The transforms of a large number of models of deoxygenated sickle hemoglobin fibers, related to that derived from image reconstruction of electron micrographs, have been calculated and compared with X-ray diffraction data of 15 A resolution. The model of the fiber, determined from the reconstructed image, is a helix c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90172-x

    authors： Rosen LS,Magdoff-Fairchild B

    更新日期：1985-06-25 00:00:00

  • The effect of regulatory Ca2+ on the in situ structures of troponin C and troponin I: a neutron scattering study.

    abstract：:The effects of regulatory amounts of Ca2+ on the in situ structures of troponin C (TnC) and troponin I (TnI) in whole troponin have been investigated by neutron scattering. In separate difference experiments, 97% deuterated TnC and TnI within whole troponin were studied +/-Ca2+ in 41.6% 2H2O buffers in which protonate...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.1965

    authors： Stone DB,Timmins PA,Schneider DK,Krylova I,Ramos CH,Reinach FC,Mendelson RA

    更新日期：1998-08-28 00:00:00

  • Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase.

    abstract：:The Escherichia coli T4 bacteriophage uses two glycosyltransferases to glucosylate and thus protect its DNA: the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). They glucosylate 5-hydroxymethyl cytosine (5-HMC) bases of duplex DNA using UDP-glucose as the sugar donor to form...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.07.007

    authors： Larivière L,Sommer N,Moréra S

    更新日期：2005-09-09 00:00:00

  • The structure of Xis reveals the basis for filament formation and insight into DNA bending within a mycobacteriophage intasome.

    abstract：:The recombination directionality factor, Xis, is a DNA bending protein that determines the outcome of integrase-mediated site-specific recombination by redesign of higher-order protein-DNA architectures. Although the attachment site DNA of mycobacteriophage Pukovnik is likely to contain four sites for Xis binding, Xis...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2013.10.002

    authors： Singh S,Plaks JG,Homa NJ,Amrich CG,Héroux A,Hatfull GF,VanDemark AP

    更新日期：2014-01-23 00:00:00

  • A direct estimation of the context effect on the efficiency of termination.

    abstract：:An in vitro assay in which terminating Escherichia coli ribosomes with different stop signals in the A-site compete for a limited amount of a release factor (RF1 or RF2) has been used to estimate the relative termination efficiencies at stop codons with different adjacent downstream nucleotides. The assay allows direc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2220

    authors： Pavlov MY,Freistroffer DV,Dincbas V,MacDougall J,Buckingham RH,Ehrenberg M

    更新日期：1998-12-04 00:00:00

  • A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.

    abstract：:The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that both P. A base-pairs are of the wobble type. This result appears inc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2080

    authors： Schuerman GS,Van Meervelt L,Loakes D,Brown DM,Kong Thoo Lin P,Moore MH,Salisbury SA

    更新日期：1998-10-09 00:00:00

  • Control of expression of the Tn10-encoded tetracycline resistance operon. II. Interaction of RNA polymerase and TET repressor with the tet operon regulatory region.

    abstract：:The promoter and operator sequences of the Tn10-encoded tetracycline resistance operon are determined in vitro by transcription studies of purified DNA restriction fragments, protection of guanosine from methylation by dimethylsulphate, and DNase I footprinting employing the purified TET repressor protein. In vitro tr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(84)80037-6

    authors： Hillen W,Schollmeier K,Gatz C

    更新日期：1984-01-15 00:00:00

  • Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement.

    abstract：:Bulges are common structural motifs in RNA secondary structure and are thought to play important roles in RNA-protein and RNA-drug interactions. Adenosine bases are the most commonly occurring unpaired base in double helical RNA secondary structures. The solution conformation and dynamics of a 25-nucleotide RNA duplex...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3931

    authors： Thiviyanathan V,Guliaev AB,Leontis NB,Gorenstein DG

    更新日期：2000-07-28 00:00:00

  • Infecting bacteriophage mu DNA forms a circular DNA-protein complex.

    abstract：:Upon superinfection of immune (lysogenic) cells with bacteriophage Mu, a form of Mu DNA accumulates that sediments about twice as fast as the linear phage DNA marker in neutral sucrose gradients. This form is also detected upon infection of sensitive cells with Mu. We have purified it and examined its physical nature....

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(83)80343-x

    authors： Harshey RM,Bukhari AI

    更新日期：1983-06-25 00:00:00

  • Effect of pseudorepeat rearrangement on alpha-synuclein misfolding, vesicle binding, and micelle binding.

    abstract：:The pathological and physiological hallmarks of the protein alpha-synuclein (aS) are its misfolding into cytotoxic aggregates and its binding to synaptic vesicles, respectively. Both events are mediated by seven 11-residue amphiphilic pseudorepeats and, most generally, involve a transition from intrinsically unstructu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.05.058

    authors： Rao JN,Kim YE,Park LS,Ulmer TS

    更新日期：2009-07-17 00:00:00

  • Kinetic role of a meta-stable native-like two-disulphide species in the folding transition of bovine pancreatic trypsin inhibitor.

    abstract：:The properties have been determined of a recently identified form of bovine pancreatic trypsin inhibitor, with only two of the three disulphide bonds of the native protein, but possessing a native-like conformation. The kinetics of refolding of the reduced inhibitor were re-measured to elucidate the kinetic role in fo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(84)90077-9

    authors： Creighton TE,Goldenberg DP

    更新日期：1984-11-05 00:00:00

  • An autonomously replicating sequence of pSRI plasmid is effective in two yeast species, Zygosaccharomyces rouxii and Saccharomyces cerevisiae.

    abstract：:The autonomously replicating sequences (ARSs) of pSR1, a cryptic circular DNA plasmid detected in a strain of Zygosaccharomyces rouxii, were delimited by subcloning and deletion analysis and by the isolation of nucleotide substitution mutations. A 30 base-pair (bp) sequence from inverted repeat 1 (IR1) and presumably ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90242-8

    authors： Araki H,Oshima Y

    更新日期：1989-06-20 00:00:00

  • Mathematical modeling of the effects of the signal recognition particle on translation and translocation of proteins across the endoplasmic reticulum membrane.

    abstract：:The kinetics of the signal recognition particle(SRP)-mediated process of protein translocation across the endoplasmic reticulum membrane was studied by mathematical modeling and complementary experiments. The following results were obtained. (1) A model according to which SRP directs the ribosome, rather than the mRNA...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90186-0

    authors： Rapoport TA,Heinrich R,Walter P,Schulmeister T

    更新日期：1987-06-05 00:00:00