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1 eit at a level less than that with wild-type tRNA(Phe).
2 bind observably to the nonsubstrate E. coli tRNA(Phe).
3 rystal structure of the fully modified yeast tRNA(Phe).
4 e show that ThiI binds to unmodified E. coli tRNA(Phe).
5 on for understanding Mg(2+) binding to yeast tRNA(Phe).
6 e X-ray crystallographic structures of yeast tRNA(Phe).
7 he cognate tRNA(His) but not with noncognate tRNA(Phe).
8 a U-turn found within the anticodon loop of tRNA(Phe).
9 d adjacent to the anticodon in undermodified tRNA(Phe).
10 transferred alanine, serine, and glycine to tRNA(Phe).
11 slow phases similar to those for natural Phe-tRNA(Phe).
12 tRNA, but still 2-fold less than natural Phe-tRNA(Phe).
13 the side chain of the esterified Phe of Phe-tRNA(Phe).
14 etases (PheRS) that hydrolyze mischarged Tyr-tRNA(Phe).
15 maritima RNase P holoenzyme in complex with tRNA(Phe).
16 zed canonical counterpart, yeast cytoplasmic tRNA(Phe).
17 ne 37 in both mitochondrial tRNA(Met)(f) and tRNA(Phe).
18 for hydrolysis of the noncognate product Tyr-tRNA(Phe).
19 editing of the misaminoacylated species Tyr-tRNA(Phe).
20 psi32 on the anticodon stem-loop from E.coli tRNA(Phe).
21 abolished both cis and trans editing of Tyr-tRNA(Phe).
22 ough hydrolysis of tyrosyl-adenylate and Tyr-tRNA(Phe).
23 has a reduced affinity for mitochondrial Phe-tRNA(Phe).
24 l-modified anticodon stem-loops from E. coli tRNA(Phe).
25 e crystal structure of the full-length yeast tRNAPhe.
26 om those seen for other tRNAs exemplified by tRNAPhe.
27 unit known to interact with the anticodon of tRNAPhe.
28 editing pathway that targets non-cognate Tyr-tRNAPhe.
29 on/peroxidation at position 37 of eukaryotic tRNAPhe.
30 n of HIV-1 with a PBS complementary to yeast tRNAPhe.
31 erved base pairs in the tertiary core of Phe-tRNA(Phe), 18-55 and 19-56, on rate and equilibrium cons
32 of PheRS editing caused accumulation of Tyr-tRNAPhe (5%), but not deacylated tRNAPhe during amino ac
33 arger than the corresponding angle for yeast tRNAPhe (70-80 degrees) under the same ionic conditions.
34 t position 73 of YFA2, a derivative of yeast tRNA(Phe), a single tRNA body was misacylated with 13 di
35 Na+] buffer at low temperature, native yeast tRNAPhe adopts tertiary structure in the absence of Mg2+
36 this modification into the scaffold of yeast tRNA(Phe) also resulted in blocked immunostimulation.
37 s and trans editing and could synthesize Tyr-tRNA(Phe), an activity enhanced in active site variants
39 for 30 in vitro synthesized T-arm mutants of tRNAPhe and 37 mutants of the 17-mer analog of the T-arm
40 show that NC destabilizes the folded form of tRNAPhe and by extension, other complex RNAs, in tertiar
42 ups in the crystal structure of native yeast tRNAPhe and that the modifications do not significantly
44 scale, the fluctuations calculated for yeast tRNAPhe and tRNAAsp in the free state, and for tRNAGln c
45 r which crystallographic data are available: tRNA(phe) and 5S rRNA from Escherichia coli, the P4-P6 d
48 ide wyosine characteristic of position 37 in tRNA(Phe) and known previously only in eukarya, plus two
49 ach other and to that of an unmodified yeast tRNA(Phe) and native yeast tRNA(Phe), as determined by l
50 We find that both a T7 transcript of yeast tRNA(Phe) and natively extracted total bovine liver mt-t
51 fied anticodon stem-loop of Escherichia coli tRNA(Phe) and suggests that this hairpin has a 3 nt loop
52 hydrogen bonds in a co-crystal structure of tRNA(Phe) and T. aquaticus EF-Tu, while the fifth 2' hyd
53 NAs at 37 degrees C: the 76 nucleotide yeast tRNA(Phe) and the 255 nucleotide catalytic domain of the
55 ylpyridyl)porphine were used to characterize tRNA(Phe) and the human immunodeficiency virus type-I Re
56 y, crystal structures of DusC complexes with tRNA(Phe) and tRNA(Trp) show that Dus subfamilies that s
57 alpha-subunit monomer that does not edit Tyr-tRNA(Phe), and a comparable transacting activity does no
58 re force as compared to the complex with Phe-tRNA(Phe), and the resultant force was the same for both
59 bstrate tRNA species, like, tRNA (Thr)(GGT), tRNA(Phe), and tRNA (Ala)(TGC), bind the enzyme with sim
60 USD4 binds 16S mt-rRNA, mt-tRNA(Met), and mt-tRNA(Phe), and we demonstrate that it is responsible for
62 the stability of the anticodon arm of yeast-tRNAphe, and to the magnesium core of the Tetrahymena gr
63 ucleotide loop by the purine-rich unmodified tRNA(Phe) anticodon arm suggests that other anticodon se
64 ational flexibility, structures of the yeast tRNA(Phe) anticodon stem and loop (ASL(Phe)) with natura
66 bosomes with TMR-Met-tRNAMetf or TMR-Met-Phe-tRNAPhe are immobilized on mica and observed by fluoresc
67 ata demonstrate that only mt-tRNA(Val) or mt-tRNA(Phe) are found in the mitoribosomes of five differe
68 uncertain, the m values for the duplexes and tRNA(Phe) are proportional to the amount of the surface
69 onformational properties of unmodified yeast tRNAPhe as a function of ionic strength, [Mg2+], and tem
70 (psHIV-Phe), which relies on exogenous yeast tRNA(Phe) as reverse transcription primer, was used to i
72 unmodified yeast tRNA(Phe) and native yeast tRNA(Phe), as determined by lead cleavage patterns at U1
73 ngly with the L1 stalk compared to elongator tRNA(Phe), as seen in previous single-molecule experimen
76 slation, we synthesized the unmodified yeast tRNA(Phe)ASL and ASLs with various derivatives of U(39)a
77 tely inhibit the Pb2(+)-ribozyme activity of tRNAPhe at 25 degrees C, pH 7.0 and 15 mM MgCl2, Zn2 HIV
79 nylalanine-specific transfer RNA from yeast (tRNAPhe) because the unfolding rates and the correspondi
80 oss-link is in the central D region of yeast tRNAPhe between C11 and C25 and the third cross-link bri
85 ld of the anticodon loop of Escherichia coli tRNA(Phe), but these elements do not result in this sign
86 alteration enhances the k(cat)/K(M) for ppp-tRNA(Phe) by nearly 100-fold relative to that of wild-ty
88 ynthesized for every approximately 7,300 Phe-tRNA(Phe), compatible with an error rate in translation
91 near-UV light, various derivatives of yeast tRNA(Phe) containing 2-azidoadenosine at the 3' terminus
92 lent adduct with 5-fluorouracil (FUra)-tRNA (tRNA(Phe) containing FUra in place of Ura) to form a put
94 S) catalyzed aminoacylation of cognate yeast tRNA(Phe) corroborated the peptide's binding to the anti
95 has a U-turn structure similar to the yeast tRNA(Phe) crystal structure, unlike previously proposed
97 MuLV; however, infectivity was restored when tRNA(Phe)D(-) was directly transfected into the cytoplas
98 In contrast, tRNA(Phe) without the D loop (tRNA(Phe)D(-)) was retained within the nucleus and did n
102 tive E. coli, bovine liver, yeast, and wheat tRNA(Phe) do not, nor do a variety of base- or sugar-mod
104 tion of Tyr-tRNAPhe (5%), but not deacylated tRNAPhe during amino acid starvation, limiting Gcn2p kin
109 perature of the cloverleaf, unmodified yeast tRNAPhe exists in a Mg2+-dependent equilibrium between s
112 onding to the anticodon stem-loop of E. coli tRNA(Phe) formed a stem-loop minihelix (minihelix(Phe))
113 ed anticodon stem-loop from Escherichia coli tRNA(Phe) forms a trinucleotide loop in solution, but Mg
114 ed anticodon stem-loop from Escherichia coli tRNA(Phe) forms a trinucleotide loop in solution, but Mg
115 metal-binding sites of the anticodon loop of tRNA(Phe) from E. coli and of a tetraloop containing a G
116 e report the crystal structure of unmodified tRNA(Phe) from Escherichia coli at a resolution of 3 A.
117 the PRF occurred through +1 slippage of the tRNA(phe) from UUU to UUC within a conserved msi172-enco
119 he genes tRNA(Thr)(UGU), tRNA(Leu)(UAA), and tRNA(Phe) (GAA) therefore attributes the seemingly neutr
125 in the catalytic efficiency (kcat/KM) of Tyr-tRNA(Phe) hydrolysis, suggesting a role for the B2 domai
126 ) stabilizes the tertiary structure of yeast tRNA(Phe) in part by accumulating in regions of high neg
128 g of frameshift efficiency could explain why tRNA(Phe) in some eukaryotes is not fully modified but,
131 of PKR by a natively folded T7 transcript of tRNA(Phe)in vivo supporting the importance of tRNA modif
132 in complexes carrying an aminoacyl tRNA, Phe-tRNA(Phe), in the A site, indicating that the SD interac
133 ce of a peptidyl tRNA analogue, N-acetyl-Phe-tRNA(Phe), in the A site, which mimicked the post-peptid
135 hift frequencies are highest if the slippery tRNAPhe is capable of stable base pairing in the shifted
136 ce of Mg2+, the extent of destabilization of tRNAPhe is greater but appears to be confined to interna
137 em in which yeast (Saccharomyces cerevisiae) tRNAPhe is provided in trans to complement the replicati
138 agnesium ions: the interstem angle for yeast tRNAPhe is reduced by nearly 50 % upon addition of 2 mM
140 equilibrium folding of the unmodified yeast tRNA(Phe) is studied as a function of Na(+), Mg(2+), and
141 entary RNA duplexes and the unmodified yeast tRNA(Phe) is studied as a function of urea and Mg(2+) co
142 it, it is extremely specific as only one Tyr-tRNA(Phe) is synthesized for every approximately 7,300 P
143 , and m7G46 to C48 in the variable loop (for tRNAPhe), is identified in the free tRNA, conforming wit
144 d ASL(Phe)-Gm(34),m(5)C(40) and native yeast tRNA(Phe) (K(d) congruent with 2.3 and 3.8 microM, respe
145 ted that the B2 domain is distant from bound tRNA(Phe), leaving the role of this module in question.
146 ve strain, increased levels of aminoacylated tRNA(Phe) led to continued synthesis of the PheL leader
148 ion enthalpy for tertiary unfolding of yeast tRNAPhe measured previously by temperature-jump relaxati
149 ption was the G34A anticodon mutation of hmt-tRNA(Phe) (mitochondrial DNA mutation G611A), which is a
150 , the tRNA construct comprises an unmodified tRNA(Phe) molecule in which the anticodon and acceptor s
151 unctions of individual, specifically labeled tRNAPhe molecules exhibit nonexponential character as a
152 ity about 17-fold lower than that for intact tRNAPhe, mostly due to a decrease in apparent substrate
155 sport and the selection of the primer, yeast tRNA(Phe) mutants were designed such that the native tRN
157 restored by extension of the 3' end of these tRNA(Phe) mutants with sequences complementary to the HI
160 taining the peptidyl-tRNA analogues N-Ac-Phe-tRNAPhe, N-Ac-Met-tRNAMet or f-Met-tRNAfMet with puromyc
161 ks were determined in the presence of deacyl-tRNA(Phe) or N-acetyl-Phe-tRNA(Phe) using poly(U) or an
163 he hypermodified wybutosine-37 in the native tRNA(Phe) placed the peptide across the anticodon loop a
164 cleic acids including: calf thymus (CT) DNA, tRNA(Phe), polymeric RNAs and DNAs, and viral RNAs inclu
165 the nonexponential decay indicates that the tRNAPhe-probe adduct fluctuates between two states, one
166 a primer binding site complementary to yeast tRNA(Phe) (psHIV-Phe) was not infectious unless yeast tR
167 er binding site (PBS) complementary to yeast tRNA(Phe) (psHIV-Phe), which relies on exogenous yeast t
168 enosine of the peptidyl-tRNA analogue, AcPhe-tRNA(Phe), remains in close contact with U2506 regardles
169 bacterial RNase P holoenzyme in complex with tRNAPhe revealed the structural basis for substrate reco
170 cleotide changes in the T(Psi)C stem-loop of tRNA(Phe) revealed an unexpected, essential role of this
171 riphosphate (EF-Tu.GDPNP) bound to yeast Phe-tRNA(Phe) reveals that EF-Tu interacts with the tRNA bod
172 te RNA comprising the anticodon stem loop of tRNA(Phe) reveals that enzyme binding induces a dramatic
173 contrast, substitution of the 3'-OH group of tRNA(Phe) severely impaired editing and revealed an esse
176 binding and catalysis are determined using a tRNAPhe substrate that is significantly cleaved at more
177 e reaction (k2) have been determined using a tRNA(Phe) substrate containing a 2'-deoxy residue at the
179 nalysis of mutations in the acceptor stem of tRNA(Phe) suggested that an intact acceptor stem RNA str
180 within the editing site had no effect on Phe-tRNA(Phe) synthesis, but abolished hydrolysis of Tyr-tRN
181 The structure of an analogue of the yeast tRNAPhe T Psi C stem-loop has been determined by NMR spe
182 the association of variously modified yeast tRNA(Phe) T-half molecules (nucleosides 40-72) with the
184 ough deletion analysis of unmodified E. coli tRNA(Phe) that the minimum substrate for s4U modificatio
185 ing the poorest results in this recent work: tRNA(Phe), the adenine and cyclic-di-GMP riboswitches, a
186 al substrates, including synthetic wild-type tRNAPhe, the anticodon stem-loop (ACSLPhe) of tRNAPhe, a
187 ive in polymerization with mitochondrial Phe-tRNA(Phe), this variant has low activity in the formatio
188 plex formation by analyzing hybridization of tRNAphe to a complete set of complementary oligonucleoti
189 be impaired in the enzymatic binding of Phe-tRNAPhe to the A site, although the interaction of N-ace
190 re-determined the crystal structure of yeast tRNA(Phe) to 2.0 A resolution using 15 year old crystals
193 onse by switching to the incorporation of mt-tRNA(Phe) to generate translationally competent machiner
194 , we use a variety of known mutations in hmt-tRNA(Phe) to investigate the mechanisms that lead to mal
196 nthetic anticodon stem-loop analogs (ASL) of tRNA(Phe) to systematically identify ribose 2'-hydroxyl
197 placed by 4-thiouridines in transfer RNAPhe (tRNAPhe) transcribed in a T7 RNA polymerase system.
201 termolecular cross-link, 16S rRNA (C1400) to tRNA(Phe)(U33), was made with either poly(U) or the mRNA
202 o that for the normal substrate (full-length tRNA(Phe) unmodified at A37), although the K(m) for mini
204 presence of deacyl-tRNA(Phe) or N-acetyl-Phe-tRNA(Phe) using poly(U) or an mRNA analogue containing a
206 Asp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52
207 eotide in which the loop sequence of E. coli tRNA(Phe) was preserved, but the 5 base pair helix stem
209 RNA(Val) compared with the porcine use of mt-tRNA(Phe) We have explored this observation further.
210 ine derivative m-Tyr after its attachment to tRNA(Phe) We now show in Saccharomyces cerevisiae that P
211 ing to the anticodon arm of Escherichia coli tRNA(Phe), we have investigated the structural and dynam
213 intracellular E. coli tRNA3Lys than of yeast tRNAPhe were needed to achieve equal levels of infectiou
214 of editing, cellular levels of aminoacylated tRNA(Phe) were elevated during amino acid stress, wherea
215 graphically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage
216 site can readily accommodate a model of Tyr-tRNA(Phe) where deacylation occurs from either the 2'- o
217 helix analogue of the anticodon stem-loop of tRNA(Phe) where the base corresponding to A37 was replac
218 to bind only in the presence of poly(U) and tRNA(Phe), whereas quinolines bind in a similar manner t
219 mentation were lower than that for wild-type tRNA(Phe), which did undergo transport and aminoacylatio
220 te secondary structure constraints for yeast tRNA(Phe), which is accurately predicted in the absence
221 mplexes were assembled with participation of tRNA(Phe), which targeted triplet UUC of the derivative
222 firmed by converting E.coli tRNAAlaand yeast tRNAPhe, whose acceptor stem sequences differ significan
230 proportional effect was true also for deacyl-tRNA(Phe) with poly(U), but the decrease in the C967 x C
231 omyces cerevisiae that PheRS misacylation of tRNA(Phe) with the more abundant Phe oxidation product o
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