Abstract:
:RNAs are involved in myriad cellular events. In general, RNA function is affected by cellular conditions. For instance, molecular crowding promotes RNA folding through compaction of the RNA. Metabolites generally destabilize RNA secondary structure, which improves RNA folding cooperativity and increases the fraction of functional RNA. Our recent studies demonstrate that cellular concentrations of amino acid-chelated magnesium (aaCM) stimulate RNA folding and catalysis while protecting RNAs from magnesium ion-induced degradation. However, effects of other cellular magnesium ion chelators on RNA function have not been tested. Herein, we report that nucleotide diphosphate-chelated magnesium, which is of intermediate strength, promotes RNA catalysis much like aaCM. Nucleotides are some of the major metabolites in cells and have one to three phosphates, which have increasingly tight binding of magnesium. On the basis of binding calculations, ∼85% ATP, ∼40% ADP, and only 5% AMP are estimated to possess a magnesium ion under cellular conditions of 0.50 mM Mg2+free. We tested the self-cleaving activity of the hammerhead ribozyme in the presence of these chelated magnesium species. Our results indicate that NTP-chelated magnesium and NMP-chelated magnesium do not appreciably stimulate RNA catalysis, whereas NDP-chelated magnesium promotes RNA catalysis up to 6.5-fold. Inspired by NDP, we observed similar stimulatory effects for several other Mg2+ diphosphate-containing metabolites, including UDP-GlcNAC and UDP-Glc; in addition, we found similar effects for a DNAzyme. Thus, rate stimulatory effects are general with respect to the diphosphate and nucleic acid enzyme. These results implicate magnesium-chelated diphosphate metabolites as general facilitators of RNA function inside cells.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Yamagami R,Huang R,Bevilacqua PCdoi
10.1021/acs.biochem.9b00578subject
Has Abstractpub_date
2019-09-24 00:00:00pages
3971-3979issue
38eissn
0006-2960issn
1520-4995journal_volume
58pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::To understand the stabilization, folding, and functional mechanisms of proteins, it is very important to understand the structural and thermodynamic properties of the molten globule state. In this study, the global structure of the acid molten globule state, which we call MG1, of horse cytochrome c at low pH and high ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi101806b
更新日期:2011-04-19 00:00:00
abstract::Stopped-flow total intensity and anisotropy experiments on single tryptophan containing mutants of yeast phosphoglycerate kinase (PGK) located in either the carboxy-terminal domain (W308 and W333), amino-terminal domain (W48 and W122), or "hinge" region (W194 and W399) were performed. The results obtained for single t...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00042a028
更新日期:1995-10-24 00:00:00
abstract::The factors that govern the substrate reactivity and stereoselectivity of phosphotriesterase (PTE) toward organophosphotriesters containing various combinations of methyl, ethyl, isopropyl, and phenyl substituents at the phosphorus center were determined by systematic alterations in the dimensions of the active site. ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi001549d
更新日期:2001-02-06 00:00:00
abstract::Photolyases (PHRs) repair the UV-induced photoproducts, cyclobutane pyrimidine dimer (CPD) or pyrimidine-pyrimidone (6-4) photoproduct [(6-4) PP], restoring normal bases to maintain genetic integrity. CPD and (6-4) PP are repaired by substrate-specific PHRs, CPD PHR and (6-4) PHR, respectively. Flavin adenine dinucleo...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b01111
更新日期:2016-02-02 00:00:00
abstract::The complete primary structure of the major component myoglobin from the Arctic minke whale, Balaenoptera acutorostrata, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequencer. Over 80% of the amino acid sequence was established from the three ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00623a023
更新日期:1977-02-22 00:00:00
abstract::The borrelidin polyketide synthase (PKS) begins with a carboxylated substrate and, unlike typical decarboxylative loading PKSs, retains the carboxy group in the final product. The specificity and tolerance of incorporation of carboxyacyl substrate into type I PKSs have not been explored. Here, we show that the first e...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi500951c
更新日期:2014-09-30 00:00:00
abstract::Members of the ATP-binding cassette (ABC) transporters share the same basic architecture, with a four-core domain made of two transmembrane plus two nucleotide-binding domains. However, a supramolecular organization has been detected in some ABC transporters, which might be relevant to physiological regulation of subs...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0482809
更新日期:2005-03-22 00:00:00
abstract::Alditol oxidase (AldO) from Streptomyces coelicolor A3(2) is a soluble monomeric flavin-dependent oxidase that performs selective oxidation of the terminal primary hydroxyl group of several alditols. Here, we report the crystal structure of the recombinant enzyme in its native state and in complex with both six-carbon...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi701886t
更新日期:2008-01-22 00:00:00
abstract::Human heart short chain L-3-hydroxyacyl-CoA dehydrogenase (SCHAD) catalyzes the oxidation of the hydroxyl group of L-3-hydroxyacyl-CoA to a keto group, concomitant with the reduction of NAD+ to NADH, as part of the beta-oxidation pathway. The homodimeric enzyme has been overexpressed in Escherichia coli, purified to h...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9829027
更新日期:1999-05-04 00:00:00
abstract::Metallo-beta-lactamases are a newly characterized family of zinc enzymes present in several pathogenic strains that represent an emerging clinical threat. Enzymes from different organisms exhibit an outstanding functional diversity, particularly in the metal ion requirements for activity. We have investigated the effe...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi010933n
更新日期:2002-02-12 00:00:00
abstract::kappa-Bungarotoxin (kappa-bgt) is a 66-residue peptide originally purified from snake venom that acts as an antagonist at certain acetylcholine receptors. It is one of four homologous kappa-neurotoxins that are distinguished from the structurally related alpha-neurotoxins by their ability to block the alpha 3-subunit-...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00248a004
更新日期:1994-11-08 00:00:00
abstract::Proton nuclear magnetic resonance and ultraviolet circular dichroism spectroscopy have been used to probe the conformational ensemble of the tandemly repeating tetrapeptide unit of the circumsporozoite coat protein of the malaria parasite Plasmodium falciparum. Peptides based on the Asn-Ala-Asn-Pro and Asn-Pro-Asn-Ala...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00486a008
更新日期:1990-08-28 00:00:00
abstract::Tryptic digestion studies of the human erythrocyte glucose carrier have shown that a reactive and transport-sensitive exofacial sulfhydryl is located in the carboxy-terminal half of the molecule, corresponding to Cys347, Cys421, or Cys429. In the present studies, the erythrocyte glucose carrier labeled on the exofacia...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00497a014
更新日期:1990-11-13 00:00:00
abstract::We have mapped the interface between the two transmembrane alpha-helices in the membrane domain of the Escherichia coli enzyme leader peptidase by analyzing disulfides formed between pairs of cysteine residues introduced near their respective periplasmic ends. The interface is formed primarily from aliphatic amino aci...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00084a020
更新日期:1993-08-24 00:00:00
abstract::Deoxycytidylate (dCMP) hydroxymethylase (CH) catalyzes the formation of 5-(hydroxymethyl)-dCMP, essential for DNA synthesis in phage T4, from dCMP and methylenetetrahydrofolate (CH2THF). The nucleotide analog 5-fluorodeoxuridylate (FdUMP) stoichiometrically inactivates CH by formation of a covalent complex containing ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00248a014
更新日期:1994-11-08 00:00:00
abstract::The conformations of three peptide models of the one-disulfide and fully reduced forms of apamin were characterized by using nuclear magnetic resonance (NMR) spectroscopy. Apa-2 contains the native disulfide bond between Cys3 and Cys15 in apamin with the other two cysteines replaced by alanines. Apa-1 contains the nat...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00183a031
更新日期:1994-05-03 00:00:00
abstract::Maduropeptin (MDP) is a recently isolated antitumor antibiotic, consisting of an enediyne-containing chromophore embedded in a highly acidic protein. This holoantibiotic damages duplex DNA in vitro, producing a mixture of single- and double-strand breaks at selected sites. The chromophore, isolated as the methanol add...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00036a035
更新日期:1995-09-12 00:00:00
abstract::Site-directed mutants of human carbonic anhydrase III were used to examine the role of Thr-199 and its interaction with Phe-198 in the catalyzed hydration of CO2. Threonine-199 is a hydrogen bond acceptor for the zinc-bound water, and Phe-198 forms part of the hydrophobic side of the active-site cavity of carbonic anh...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00082a004
更新日期:1993-08-10 00:00:00
abstract::The dependence of the activity of bovine Cu,Zn superoxide dismutase on pH and ionic strength was extensively investigated in the ranges of pH 7.4-pH 12.3 and of ionic strength of 0.02-0.25 M. The results obtained indicate that two positively charged groups having pK values of approximately 10.1 and 10.8 are involved i...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00385a043
更新日期:1987-06-02 00:00:00
abstract::Human telomeric DNA consists of tandem repeats of the DNA sequence d(GGGTTA). Oligodeoxynucleotide telomere models such as d[A(GGGTTA)(3)GGG] (Tel22) fold in a cation-dependent manner into quadruplex structures consisting of stacked G-quartets linked by d(TTA) loops. NMR has shown that in Na(+) solutions Tel22 forms a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi901357r
更新日期:2010-01-12 00:00:00
abstract::In the cyanobacterium Anabaena, the precursor to tRNA(Leu) has a 249-nucleotide group I intron inserted between the wobble and second bases of the anticodon; the intron self-splices during transcription in vitro [Xu, M. Q., Kathe, S. D., Goodrich-Blair, H., Nierzwicki-Bauer, S. A., & Shub, D. A. (1990) Science 250, 15...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00082a016
更新日期:1993-08-10 00:00:00
abstract::By limited proteolysis of a type kappa immunoglobulin light chain (Oku) with clostripain, both the VL and CL fragments were obtained with a high yield. The unfolding and refolding by guanidine hydrochloride of light chain Oku and its VL and CL fragments were studied at pH 7.5 and 25 degrees C with circular dichroism a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00393a015
更新日期:1987-09-22 00:00:00
abstract::Thermodynamics of 39 oligonucleotides with internal G.T mismatches dissolved in 1 M NaCl were determined from UV absorbance versus temperature profiles. These data were combined with literature values of six sequences to derive parameters for 10 linearly independent trimer and tetramer sequences with G.T mismatches an...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi962590c
更新日期:1997-08-26 00:00:00
abstract::Acetylcholinesterase (AChE) contains a narrow and deep active site gorge with two sites of ligand binding, an acylation site (or A-site) at the base of the gorge and a peripheral site (or P-site) near the gorge entrance. The P-site contributes to catalytic efficiency by transiently binding substrates on their way to t...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi8015197
更新日期:2008-12-09 00:00:00
abstract::5-HT(2A) serotonin receptors represent the principal molecular targets for LSD-like hallucinogens and atypical antipsychotic drugs. It has been proposed that a dysregulation of 5-HT(2A) receptor-mediated signaling may contribute to the pathogenesis of schizophrenia and related diseases. A major mechanism for the atten...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi035061z
更新日期:2003-09-16 00:00:00
abstract::The ATPase activity of the (Ca2+-Mg2+)-ATPase reconstituted into bilayers of phosphatidylcholines depends on the fatty acyl chain length of the phospholipids. It is shown that the fluorescence response to Ca2+ of the ATPase modified with fluorescein isothiocyanate is also dependent on phospholipid structure and is int...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00371a043
更新日期:1986-11-18 00:00:00
abstract::Osteopontin (OPN) is an acidic hydrophilic glycophosphoprotein that was first identified as a major sialoprotein in bones. It functions as a cell attachment protein displaying a RGD cell adhesion sequence and as a cytokine that signals through integrin and CD44 cell adhesion molecules. OPN is also implicated in human ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi200291e
更新日期:2011-07-12 00:00:00
abstract::c-Jun and c-Fos belong to the bZIP class of transcriptional activator proteins, many of which have been implicated in the neoplastic transformation of cells. We are interested in engineering dominant-negative leucine zipper (LZ) peptides as a means of sequestering these proteins in vivo in order to suppress their tran...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi952817o
更新日期:1996-07-16 00:00:00
abstract::Aspartate-beta-semialdehyde dehydrogenase (ASADH) lies at the first branch point in the biosynthetic pathway through which bacteria, fungi, and the higher plants synthesize amino acids, including lysine and methionine and the cell wall component diaminopimelate from aspartate. Blocks in this biosynthetic pathway, whic...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi015713o
更新日期:2001-12-04 00:00:00
abstract::Covalent labeling of the canine renal parathyroid hormone receptor with [125I]bPTH(1-34) reveals several major binding components that display characteristics consistent with a physiologically relevant adenylate cyclase linked receptor. Through the use of the specific glycosidases neuraminidase and endoglycosidase F a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00398a044
更新日期:1987-12-01 00:00:00