The Solution Structure of Yeast tRNA<sup>Phe</sup>as Studied by Nuclear Overhauser Effects in NMR

Hilbers, Cornelis W.; Heerschap, Arend; Haasnoot, C. A. G.; Walters, J. A. L. I.

doi:10.1080/07391102.1983.10507434

Cited by 38 publications

(32 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…17 and references and further discussion therein). Furthermore, interstem stacking is preserved within the T acceptor and D anticodon domains (12,26). Thus, the transition itself may involve the loss of one or more critically coordinated magnesium ions, believed to exist in the 8-12 turn and between the D and T loops.…”

Section: Discussionmentioning

confidence: 99%

Global flexibility of tertiary structure in RNA: Yeast tRNA ^Phe as a model system

Friederich

Vacano

Hagerman

1998

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The study of RNA structure using x-ray crystallography or NMR has yielded a wealth of detailed structural information; however, such approaches do not generally yield quantitative information regarding long-range f lexibility in solution. To address this issue, we describe a solution-based method that is capable of characterizing the global f lexibilities of nonhelix elements in RNA, provided that such elements are f lanked by helix (e.g., bulges, internal loops, or branches). The ''phased ratio'' method is based on the principle that, for RNA molecules possessing two variably phased bends, the relative birefringence decay times depend on the f lexibility of each bend, not simply the mean bend angles. The method is used to examine the overall f lexibility of the yeast tRNA Phe core (as unmodified transcript). In the presence of magnesium ions, the tRNA core is not significantly more f lexible than an equivalent length of RNA helix. In the absence of divalent ions, the tRNA core gains f lexibility under conditions where its secondary structure is likely to be largely preserved. The phased ratio approach should be broadly applicable to nonhelix elements in both RNA and DNA and to protein-nucleic acid interactions. Yeast tRNAPhe is a paradigm for the study of tertiary structure in RNA: its crystal structure is well-established (1-3), and under comparable ionic conditions, the crystal and solution structures possess nearly identical anticodon-acceptor (mean) interstem angles (1, 4, 5). However, relatively little is known regarding the global flexibility of the tRNA core. Harvey and coworkers (6) have considered the issue of hinge-type flexibility from the computational perspective, noting that largeamplitude bending motions between the acceptor and anticodon domains are not energetically prohibitive. However, a more recent normal-mode analysis of the bending motions for yeast tRNA Phe suggests that the actual range of hinge-type distortions is likely to be small in the absence of external forces (7), a result that is consistent with the small temperature factors for the crystal structure

show abstract

Section: Discussionmentioning

confidence: 99%

Global flexibility of tertiary structure in RNA: Yeast tRNA ^Phe as a model system

Friederich

Vacano

Hagerman

1998

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…The spectrum of yeast tRNAPh' has been solved independently by two different groups [243,2611 and can be considered the most reliable assignment as yet available. The results were confirmed by 2D-NOE spectroscopy, which was applicable even for a molecule of this size [262].…”

Section: Transfer Rnamentioning

confidence: 99%

“…Moreover, the imino protons involved in the tertiary interactions between the bases at the junction of the T-loop/D-loop and the junction of the extra arm/D-stem region could be accounted for in the spectra. Thus, as far as can be gleaned from the NMR experiments, the hydrogen-bonding scheme of the imino protons in solution and in the crystal structure is the same with the possible The influence of ionic conditions on the imino-proton hydrogen-bonding scheme has been examined quite extensively for yeast tRNAPhr [243,264]. Comparison of the spectra recorded with and without magnesium ions shows that, when exception (in yeast tZNAPh') of a hydrogen bond in the taken at the proper conditions, the imino-proton hydrogenanti-codon loop and the hydrogen bond between bond scheme is conserved, indicating that the solution strucm@26 and A44 bases that form a non-canonical base pair ture remains essentially the same as the crystal structure.…”

Section: Transfer Rnamentioning

confidence: 99%

Nucleic acids and nuclear magnetic resonance

Ven

Hilbers

1988

European Journal of Biochemistry

260

View full text Add to dashboard Cite

“…The assignments are summarised in Table 2. Recently, two-dimensional NOE spectra in H 2 0 have been used to assign imino proton resonances in tRNAs [35,40,411; this eliminates the irradiation of individual peaks and hence avoids ambiguities due to irradiation spillover to neighbouring peaks. These ambiguities in the one-dimensional NOE spectra can often be resolved by irradiating at intervals throughout the peaks in question.…”

Section: Remaining Assignmentsmentioning

confidence: 99%

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA₃^Gly

Hyde¹

1986

European Journal of Biochemistry

View full text Add to dashboard Cite

The imino region of the proton NMR spectrum of Escherichia coli tRNAQIY has been assigned mainly by sequential nuclear Overhauser effects between neighbouring base pairs and by comparison of assignments of other tRNAs. The effects of magnesium, spermine and temperature on the 'H and 31P NMR spectra of this tRNA were studied. Both ions affect resonances close to the G 15 . C48 tertiary base pair and in the ribosylthymine loop. The magnesium studies indicate the presence of an altered tRNA conformer at low magnesium concentrations in equilibrium with the high magnesium form. The temperature studies show that the A7 . U66 imino proton (from a secondary base pair) melts before some of the tertiary hydrogen bonds and that the anticodon stem does not melt sequentially from the ends. Correlation of the ion effects in the 'H and 31P NMR spectra has led to the tentative assignment of two 31P resonances not assigned in the comparable 31P NMR spectrum of yeast tRNAPhe. 31P NMR spectra of E. coli tRNAF'y lack resolved peaks corresponding to peaks C and F in the spectra of E. coli tRNAPhe and yeast tRNAPhe. In the latter tRNAs these peaks have been assigned to phosphate groups in the anticodon loop. Ion binding to E. coli tRNA?lY and E. coli tRNAPhe has different effects on their 'H NMR spectra which may reflect further differences in their charge distribution and conformation.The conformation of transfer ribonucleic acids in solution is of interest because of their role in protein synthesis. All tRNAs within a cell interact with the same initiation and elongation factors and ribosomes and hence must have elements of similar structure. Indeed most tRNAs can form cloverleaf secondary structures and have invariant or semiinvariant bases at tertiary folding sites. However, each group of isoaccepting tRNAs is charged with the appropriate aminoacid by a specific aminoacyl-tRNA synthetase. This specificity could derive either from direct interaction of the synthetase with base sequences unique to the isoaccepting tRNAs or from differences in the solution conformation of tRNAs. Differences in the conformation of tRNAs would result in differences in their charge distribution and hence in the binding of ions. I have therefore studied the binding of ions to tRNAs in solution in order to probe their conformational differences or similarities.The method of choice for such a study is nuclear magnetic resonance spectroscopy as NMR spectra are very sensitive to the chemical environment around each observed nucleus. In this study both low-field 'H NMR spectra and 31P NMR spectra have been used. The low-field 'H NMR spectra contain resonances from the hydrogen-bonded imino protons of the secondary and tertiary base pairs. In general, each base pair gives rise to a separate signal which can be monitored (reviewed in [I]). 31P NMR spectra give information complementary to the low-field 'H NMR spectra. Although phosphates in the helical stems and stacked regions of the tRNA resonate at similar frequencies and are not resolved,Correspondence to ...

show abstract

The Solution Structure of Yeast tRNA^Pheas Studied by Nuclear Overhauser Effects in NMR

Cited by 38 publications

References 46 publications

Global flexibility of tertiary structure in RNA: Yeast tRNA ^Phe as a model system

Global flexibility of tertiary structure in RNA: Yeast tRNA ^Phe as a model system

Nucleic acids and nuclear magnetic resonance

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA₃^Gly

Contact Info

Product

Resources

About

The Solution Structure of Yeast tRNAPheas Studied by Nuclear Overhauser Effects in NMR

Cited by 38 publications

References 46 publications

Global flexibility of tertiary structure in RNA: Yeast tRNA Phe as a model system

Global flexibility of tertiary structure in RNA: Yeast tRNA Phe as a model system

Nucleic acids and nuclear magnetic resonance

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA3Gly

Contact Info

Product

Resources

About

The Solution Structure of Yeast tRNA^Pheas Studied by Nuclear Overhauser Effects in NMR

Global flexibility of tertiary structure in RNA: Yeast tRNA ^Phe as a model system

Global flexibility of tertiary structure in RNA: Yeast tRNA ^Phe as a model system

Imino proton NMR assignments and ion‐binding studies on Escherichia coli tRNA₃^Gly