Abstract:
:The human double-stranded RNA- (dsRNA) activated protein kinase (PKR) has a dsRNA-binding domain (dsRBD) that contains two tandem copies of the dsRNA-binding motif (dsRBM). The minimal-length polypeptide required to bind dsRNA contains both dsRBMs, as determined by mobility-shift and filter-binding assays. Mobility-shift experiments indicate binding requires a minimum of 16 base pairs of dsRNA, while a minimal-length site for saturation of longer RNAs is 11 base pairs. Bulge defects in the helix disfavor binding, and single-stranded tails do not strongly influence the dsRNA length requirement. These polypeptides do not bind an RNA-DNA hybrid duplex or dsDNA as judged by either mobility-shift or competition experiments, suggesting 2'-OH contacts on both strands of the duplex stabilize binding. Related experiments on chimeric duplexes in which specific sets of 2'-OHs are substituted with 2'-H or 2'-OCH3 reveal that the 2'-OHs required for binding are located along the entire 11 basepair site. These results are supported by Fe(II) EDTA footprinting experiments that show protein-dependent protection of the minor groove of dsRNA. The dependence of dsRNA-protein binding on salt concentration suggests that only one ionic contact is made between the protein and dsRNA phosphate backbone and that at physiological salt concentrations 90% of the free energy of binding is nonelectrostatic. Thus, the specificity of PKR for dsRNA over RNA-DNA hybrids and dsDNA is largely due to molecular recognition of a network of 2'-OHs involving both strands of dsRNA and present along the entire 11 base-pair site.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Bevilacqua PC,Cech TRdoi
10.1021/bi9607259subject
Has Abstractpub_date
1996-08-06 00:00:00pages
9983-94issue
31eissn
0006-2960issn
1520-4995pii
bi9607259journal_volume
35pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::SopE and SopE2 are delivered by the Salmonella type III secretion system into eukaryotic cells to promote cell invasion. SopE and SopE2 are potent guanine nucleotide exchange factors (GEFs) for Rho GTPases Cdc42 and Rac1 and constitute a novel class of Rho GEFs. Although the sequence of SopE-like GEFs is not at all ho...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0490744
更新日期:2004-09-28 00:00:00
abstract::An expression plasmid encoding the extracellular portion of the human tumor necrosis factor (TNF) type 1 receptor (TNF-R1) was constructed and used to generate a stable cell line secreting soluble TNF-R1 (sTNF-R1). The sTNF-R1 was purified, and its biochemical properties and its interactions with human TNF-alpha were ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00119a023
更新日期:1992-02-04 00:00:00
abstract::We have investigated the loss of histone H1 from chromatin [D'Anna, J. A., Gurley, L. R., & Tobey, R. A. (1982) Biochemistry 21, 3991-4001] and the structure of chromatin from Chinese hamster (line CHO) cells blocked in early S phase by sequential use of isoleucine deprivation G1 block and 1 mM hydroxyurea (HU) blocka...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00293a027
更新日期:1983-11-22 00:00:00
abstract::The kcat and Km values for the bovine heart low molecular weight phosphotyrosyl protein phosphatase catalyzed hydrolysis of 16 aryl phosphate monoesters and of five alkyl phosphate monoesters having the structure Ar(CH2)nOPO3H2 (n = 1-5) were measured at pH 5.0 and 37 degrees C. With the exception of alpha-naphthyl ph...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00101a006
更新日期:1991-09-17 00:00:00
abstract::Steric constraints in the retinal binding pocket of sensory rhodopsin I (SR-I) are analyzed by studying effects of sample temperature and retinal analogs. The flash-induced yield of the earliest detected intermediate S610, which corresponds to the K intermediate in the bacteriorhodopsin (BR) photocycle, decreases belo...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00089a044
更新日期:1993-09-28 00:00:00
abstract::The head of the P22 bacteriophage is interrupted by a unique dodecameric portal vertex that serves as a conduit for the entrance and exit of the DNA. Here, the in vitro unfolding/refolding processes of the portal protein of P22 were investigated at different temperatures (1, 25, and 37 degrees C) through the use of ur...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700006d
更新日期:2007-06-26 00:00:00
abstract::The two key structural features of alpha 2-macroglobulin (alpha 2M) involved in inhibitory caging of proteases are the thiol ester and the bait region. This paper examines the environment of the hydrolyzed thiol ester in methylamine-treated human alpha 2M and the separation between the bait region and the thiol ester ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00408a036
更新日期:1988-04-19 00:00:00
abstract::Measurement of x-ray scattering at very small angles by solutions of myosin subfragment 1 (S1) yields a radius of gyration of 3.24 nm (mean) +/- 0.03 nm (standard error for N = 9). If S1 is assumed to be ellipsoid of revolution, of uniform electron density, with a molecular weight of 1.15 X 10(5) and a partial specifi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00605a009
更新日期:1978-06-13 00:00:00
abstract::The heteronemertine worm Cerebratulus lacteus produces a family of three structurally homologous proteins that function as direct lytic factors for a variety of cells [Kem, W. R., & Blumenthal, K. M. (1978) J. Biol. Chem. 253, 5752-5757]. It is demonstrated herein that the hemolytic activity of the most abundant varia...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00261a007
更新日期:1982-08-31 00:00:00
abstract::Notwithstanding the relevance of their biological function, slow motions in proteins, beyond the microsecond range, are still poorly understood and often elusive. We propose that acrylamide quenching of Trp phosphorescence of deeply buried residues, when extended over the entire accessible range of lifetime measuremen...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9009659
更新日期:2009-08-11 00:00:00
abstract::Serine hydroxymethyltransferase and C1-tetrahydrofolate synthase catalyze four reactions which convert formate and glycine to serine. The one-carbon carrier in these reactions if tetrahydropteroylglutamate which is regenerated in the coupled reaction and thus can be used in catalytic concentrations with respect to ser...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00450a028
更新日期:1989-11-28 00:00:00
abstract::Recent studies of DNA hairpin loops have shown considerable dependence of the stability on the sequence of the loop [Senior, M., Jones, R. A., & Breslauer, K. J. (1988a) Proc. Natl. Acad. Sci. U.S.A. 85, 6242-6246; Xodo, L. E., Manzini, G., Quadrifoglio, F., van der Marel, G., & van Boom, J. H. (1989) Biochimie 71, 79...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00181a026
更新日期:1994-04-19 00:00:00
abstract::A peptide consisting of the first 21 residues of human myelin basic protein (MBP) was synthesized. The N-terminal alanine of portions was blocked in separate experiments with alkyl carboxylates varying in size from 2 to 10 carbon atoms. The effects of these different alkyl carboxylates at the N-terminus on the seconda...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00180a008
更新日期:1994-04-12 00:00:00
abstract::For three prokaryotic enzymes of the xanthine oxidase family, namely quinoline 2-oxidoreductase, quinaldine 4-oxidase, and isoquinoline 1-oxidoreductase, the electron transfer centers were investigated by electron paramagnetic resonance. The enzymes are containing a molybdenum-molybdopterin cytosine dinucleotide cofac...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi970581d
更新日期:1997-08-12 00:00:00
abstract::We have examined in detail the kinetics of binding of the serpin alpha 2-antiplasmin to the serine proteases alpha-chymotrypsin and plasmin. These represent model systems for serpin binding. We find, in contrast to earlier published results with alpha 2-antiplasmin and plasmin, that binding is reversible, and slow bin...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00218a014
更新日期:1991-01-29 00:00:00
abstract::The aspartate receptors of Escherichia coli and Salmonella typhimurium which mediate chemotactic responsiveness to aspartate have 79% amino acid sequence identity but exhibited apparently quite different aspartate binding plots. The Scatchard plot of the Salmonella receptor was concave upward whereas the E. coli recep...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00169a002
更新日期:1994-01-25 00:00:00
abstract::Deposition of misfolded alpha-synuclein is a critical factor in several neurodegenerative disorders. Filamentous alpha-synuclein is the major component of Lewy bodies and Lewy neurites, the intracellular inclusions in the dopaminergic neurons of the substantia nigra, which are considered the pathological hallmark of P...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi034938r
更新日期:2004-03-23 00:00:00
abstract::The pH dependence of the 13C chemical shifts of the side-chain carboxyl carbons of all Asp and Glu residues in the reduced and oxidized states of human thioredoxin and in a mixed disulfide complex of human thioredoxin with a target peptide from the transcription factor NF kappa B has been investigated by multidimensio...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi952299h
更新日期:1996-01-09 00:00:00
abstract::Two dioxygenases (ARD and ARD') were cloned from Klebsiella pneumoniae that catalyze different oxidative decomposition reactions of an advanced aci-reductone intermediate, CH(3)SCH(2)CH(2)COCH(OH)=CH(OH) (I), in the methionine salvage pathway. The two enzymes are remarkable in that they have the same polypeptide seque...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi010110y
更新日期:2001-05-29 00:00:00
abstract::The solution structure of the dicerium(III) complex of the N-terminal domain of calmodulin (Ce2-TR1C hereafter) has been solved employing paramagnetic T1 relaxation enhancements and pseudocontact shifts introduced by the Ce3+ ions, together with conventional NOE constraints. The use of pseudocontact shift constraints ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi971022+
更新日期:1997-09-30 00:00:00
abstract::The increase of the proton motive force mediated by bacteriorhodopsin is compared to the intracellular ATP concentration under steady-state illumination. The membrane potential was measured via the accumulation of the lipophilic ion [14C]triphenylmethylphosphonium and the pH gradient via the accumulation of the weak a...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00561a012
更新日期:1980-09-30 00:00:00
abstract::Conformations of (R)-alpha-(N6-adenyl)styrene oxide adducts at positions X6 in d(CGGACXAGAAG).d(CTTCTTGTCCG) and X7 in d(CGGACAXGAAG).d(CTTCTTGTCCG), incorporating codons 60, 61 (underlined), and 62 of the human n-ras protooncogene, were refined from 1H NMR data. These were the R(61,2) and R(61,3) adducts. Chemical sh...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00043a008
更新日期:1995-10-31 00:00:00
abstract::The properties of neuronal nitric oxide synthase containing one tetrahydrobiopterin (BH4) per dimer [nNOS(BH4+)] were compared to those of the BH4-free enzyme [nNOS(BH4-)]. The stimulation by BH4 of the formation of L-citrulline at the expense of H2O2 production unambiguously demonstrated that BH4 is essential in coup...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi961931j
更新日期:1996-12-24 00:00:00
abstract::Members of the PP1 family of protein phosphatases achieve functional diversity through numerous and varied protein-protein interactions. In mammals, there are four PP1 isoforms, the ubiquitously expressed PPP1CA, PPP1CB, and PPP1CC1, and the testis specific splice isoform PPP1CC2. When the mouse Ppp1cc gene is deleted...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi3010158
更新日期:2012-12-04 00:00:00
abstract::Raman spectra of the parallel-stranded duplex formed from the deoxyoligonucleotides 5'-d-[(A)10TAATTTTAAATATTT]-3' (D1) and 5'-d[(T)10ATTAAAATTTATAAA]-3' (D2) in H2O and D2O have been acquired. The spectra of the parallel-stranded DNA are then compared to the spectra of the antiparallel double helix formed from the de...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00226a012
更新日期:1991-03-26 00:00:00
abstract::The pre-steady-state kinetics of the trichodiene synthase reaction were investigated by rapid chemical quench methods. The single-turnover rate was found to be 3.5-3.8 s-1, a rate 40 times faster than the steady-state catalytic rate (kcat = 0.09 s-1) for trichodiene synthase-catalyzed conversion of farnesyl diphosphat...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi963018o
更新日期:1997-07-08 00:00:00
abstract::Information on the secondary structure and interactions of RNA is important to understand the biological function of RNA as well as in applying RNA as a tool for therapeutic purposes. Recently, the isoenergetic microarray mapping method was developed to improve the prediction of RNA secondary structure. Herein, for th...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi200463p
更新日期:2011-09-06 00:00:00
abstract::The misfolding of amyloid beta (Aβ) is one of the predominant hallmarks in the pathology of Alzheimer's disease (AD). In this study, we showed that the formation of the Aβ ion channel on the membrane depended on the cholesterol concentration. From a mechanical aspect, we found that cholesterol levels affected the stab...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.9b00968
更新日期:2020-03-03 00:00:00
abstract::The bacterial DNA cytosine methyltransferase M.HhaI sequence-specifically modifies DNA in an S-adenosylmethionine dependent reaction. The enzyme stabilizes the target cytosine (GCGC) into an extrahelical position, with a concomitant large movement of an active site loop involving residues 80-99. We used multidimension...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi602662e
更新日期:2007-06-19 00:00:00
abstract::Backbone amide dynamics of the Escherichia coli tryptophan repressor protein (WT-TrpR) and two functionally distinct variants, L75F-TrpR and A77V-TrpR, in their holo (l-tryptophan corepressor-bound) form have been characterized using (15)N nuclear magnetic resonance (NMR) relaxation. The three proteins possess very si...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi200389k
更新日期:2011-06-14 00:00:00