The electrostatic molecular potential of tRNA<sup>Phe</sup>. IV. The potentials and steric accessibilities of sites associated with the bases

Lavery, Richard; Pullman, Alberte; Pullman, Bernard; Oliveira, Marçal de

doi:10.1093/nar/8.21.5095

Cited by 35 publications

(19 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Fig. 5 shows a comparison between the potentials calculated for all the phosphates of the backbone of the tRNAPhe molecule and the ApK values measured in this work for positions 8,34,47 and 76 (3' end) in the chains of representative tRNAs, each in four buffers (1,5,6,10) chosen so as to indicate the limits of the observed ApK. The scales of the calculated potentials and the measured ApK values are arbitrary.…”

Section: Discussionmentioning

confidence: 99%

Electrostatic potential of macromolecules measured by pK_a shift of a fluorophore

Friedrich

Woolley

Steinhäuser

1988

European Journal of Biochemistry

View full text Add to dashboard Cite

The procedures developed earlier (Friedrich and Woolley, preceding paper in this journal) for probing electrostatic potential with the fluorescein label were applied to transfer RNA. By using tRNA species that contain chemically reactive bases we were able to label these bases with fluorescein derivatives and thus to 'map' the electrostatic potential around the molecule. Both the electrostatic potential and the fluorescence emission anisotropy data that were obtained at the same time could be understood in terms of the well-known, paradigmatic crystal structure of tRNAPhe. However, within the distribution of the various tRNA species, tRNA,M"' appeared to occupy an extreme position, which suggests a relation between the conformation in solution and the initiation function of this molecule. Comparison with theoretical predictions by others of the electrostatic potential map of tRNA showed agreement in respect of trends, but the values of the potentials measured were orders of magnitude lower than predicted. This we attribute primarily to solvation.We have demonstrated in the preceding paper [l] that the pK, of the fluorescein label can be used as a probe of electrostatic potential; the theoretical basis of this leads to the simple relationship y = -58.2 ApK,, where y is the potential at the position occupied by the fluorophore and ApK, is the shift in pK, of the bound fluorescein compared with a chemically identical fluorescein derivative not bound to a macromolecule. The method was applied to the 16s RNA molecule, with the fluorescein label bound at its 3' end.Here we investigate the electrostatics of the tRNA molecule. This molecule allows a much more detailed investigation, as the various tRNA species contain many chemically modified bases, at known positions, that can react specifically with various derivatives of fluorescein. Since these bases are found at different locations on the molecule, comparisons can be made and an overall picture can be built up. An advantage of tRNA is that it is less easily denatured than the larger RNA molecules and solution structures may readily be compared. Further, the electrostatics of this molecule have been investigated theoretically [2 -71 so that experimental results can be interpreted in more depth.Of the more than 200 tRNA sequences determined to date, no exception to the clover-leaf structure [8,9] has been found. The X-ray structure of tRNAPhe from yeast and that of tRNA,M"' from Escherichia coli are not greatly different [lo, 111 and it is highly probable that the yeast tRNAPhe crystal Correspondence to' P. Woolley, Kemisk Institut, Aarhus Universitet, DK-8000 k h u s , DenmarkAbbreviations. FITC, fluorescein isothiocyanate; FTSC, fluorescein thiosemicarbazide; IAFl, iodacetamidofluorescein; X, 3-(3-amino-3-carboxypropyl)-uridine; Q, (4,5-cis-dihydroxy-l-cyclopenten-3-yl aminomethyl)-7-deazoguanidine; s4U, 4-thiouridine; mams2U, 5-methylaminomethyl-2-thiouridine.

show abstract

Section: Discussionmentioning

confidence: 99%

Electrostatic potential of macromolecules measured by pK_a shift of a fluorophore

Friedrich

Woolley

Steinhäuser

1988

European Journal of Biochemistry

View full text Add to dashboard Cite

show abstract

“…Also, a single probe radius of 1.2 A, corresponding to the hydrogen of a water molecuIe, is used and an attempt is made to include effects of the electrostatic surface of the molecule. 5 We believe our method of examining the "accessible surface" a t various probe radii to be more realistic in predicting reactivity of the bulky reagents used to study nucleic acid structure experimentally. The only modification reaction specifically discussed by IAavery et al5 was the kethoxal modificaticn of guanine,18 and the results are in agreement with those presented here, even though the methods differ.…”

Section: Methodsmentioning

confidence: 99%

Correlation between chemical modification and surface accessibility in yeast phenylalanine transfer RNA

Holbrook

Kim

1983

Biopolymers

View full text Add to dashboard Cite

SynopsisChemical reactivities of the functional groups of yeast phenylalanine transfer RNA are compared with surface accessibilities of the groups calculated with various probe radii representing effective radii of the chemical reagents used. We observe 97% agreement with the hypothesis that the chemically modified bases are those with the greatest surface accessibility. This overall strong correlation supports the conclusion that base exposure is an important determinant of chemical modification in this polynucleotide.

show abstract

“…In a previous publication of this series [4] we have presented the electrostatic potentials and the associated atomic steric accessibilities of sites on the bases of tRNAPhe susceptible to electrophilic attack. For reasons of space we cannot reproduce these tables here and must refer the reader to our earlier publication in the discussion that follows.…”

Section: Resultsmentioning

confidence: 99%

“…For reasons of space we cannot reproduce these tables here and must refer the reader to our earlier publication in the discussion that follows. [The following corrections should be introduced in the data on the potential of [4] The potentials referred to above were calculated for tRNAPhe in the presence of the four crystallographic Mg2+ ions without their waters of hydration. Before introducing these water molecules, let us first complete these results by presenting the potentials and accessibilities for the hypermodified Y base (Y37 in yeast tRNAPhe), which were not given earlier.…”

Section: Resultsmentioning

confidence: 99%

The electrostatic molecular potential of tRNAPhe. V. The influence of counterion binding on the potential and the steric accessibility

Lavery

Corbin

Pullman

1981

Int. J. Quantum Chem.

Self Cite

View full text Add to dashboard Cite

An investigation is carried out of the influence of counterions bound to yeast tRNAPhc on the electrostatic potential and steric accessibility of this macromolecule. Two types of cations are considered, the Mg2+ ions located in the crystal of tRNAPhe, with their waters of hydration, and Na+ ions, which are positioned by theoretical estimation. Possible effects of the counterions on the chemical reactivity of tRNAPhe are pointed out.

show abstract

The electrostatic molecular potential of tRNA^Phe. IV. The potentials and steric accessibilities of sites associated with the bases

Cited by 35 publications

References 17 publications

Electrostatic potential of macromolecules measured by pK_a shift of a fluorophore

Electrostatic potential of macromolecules measured by pK_a shift of a fluorophore

Correlation between chemical modification and surface accessibility in yeast phenylalanine transfer RNA

The electrostatic molecular potential of tRNAPhe. V. The influence of counterion binding on the potential and the steric accessibility

Contact Info

Product

Resources

About

The electrostatic molecular potential of tRNAPhe. IV. The potentials and steric accessibilities of sites associated with the bases

Cited by 35 publications

References 17 publications

Electrostatic potential of macromolecules measured by pKa shift of a fluorophore

Electrostatic potential of macromolecules measured by pKa shift of a fluorophore

Correlation between chemical modification and surface accessibility in yeast phenylalanine transfer RNA

The electrostatic molecular potential of tRNAPhe. V. The influence of counterion binding on the potential and the steric accessibility

Contact Info

Product

Resources

About

The electrostatic molecular potential of tRNA^Phe. IV. The potentials and steric accessibilities of sites associated with the bases

Electrostatic potential of macromolecules measured by pK_a shift of a fluorophore

Electrostatic potential of macromolecules measured by pK_a shift of a fluorophore