Rotational dynamics of transfer ribonucleic acid: effect of ionic strength and concentration

Jc, Thomas; Schurr, J. Michael; Dr, Hare

doi:10.1021/bi00318a005

Cited by 16 publications

(18 citation statements)

References 40 publications

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“…is more intriguing. This, and other work (Thomas et al, 1984), indicates that, prior to the removal of magnesium, tRNA?' behaves quite similarly to tRNAPhc and, in particular, these two tRNAs have essentially identical rotational relaxation times (-24-26 ns in water at 20 "C).…”

Section: Discussionsupporting

confidence: 54%

“…Our observation of two fluorescence decay components even without Mg2+ differs from the results of Tao et al (1970), who detected only one decay component in the absence of Mg2+. We have previously noted (Thomas et al, 1984) that, since the latter authors had lower time resolution than the present experiments and did not deconvolute their raw data, it would have been difficult to detect a small-amplitude (-7%), fast decay time (-34s) component. Thus, there is general agreement between the present and previous work on tRNAPhe.…”

Section: Discussionmentioning

confidence: 73%

“…There is also the suggestion that both lifetimes decrease somewhat with increasing Mg2+ concentration. We have previously suggested (Thomas et al, 1984) that these two components may be associated with a larger population that contains intercalated ethidium (the major, 25-11s component) and a much smaller population with ethidium bound to a more open part of the tRNA molecule, perhaps in the Plo cavity, giving rise to the short-lifetime component.…”

Section: T H O M a S Etmentioning

confidence: 98%

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Effect of magnesium(2+) on the solution conformation of two different transfer ribonucleic acids

Jc¹,

Schurr²,

Br³

et al. 1984

Biochemistry

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We have investigated the effect of Mg2+ on the solution conformation of two different tRNAs by studying the decay of the fluorescence polarization anisotropy of intercalated ethidium on a nanosecond time scale. In the presence of endogenous Mg2+, yeast tRNAPhe and Escherichia coli tRNAVal1 exhibit similar behavior; i.e., the fluorescence from the intercalated ethidium decays biexponentially with lifetimes of approximately 25 and approximately 5 ns, and the fluorescence polarization anisotropy decays with a lifetime of approximately 25 ns. However, once Mg2+ is removed from the two tRNAs, their behavior is no longer similar. In the case of yeast tRNAPhe, it appears that titrating with Mg2+ restores the tRNA to the condition that it was in prior to the Mg2+ removal. This is not so for E. coli tRNAVal1, in which case titrating with Mg2+ results in a two-component anisotropy decay with lifetimes of approximately 25 and approximately 6 ns. Rudimentary calculations indicate that the 6-ns component does not result simply from a change in conformation of the tRNA. However, torsional motions in the tRNA facilitated by a torsion "joint" with a rigidity approximately 1/40 that of intact linear phi 29 DNA would yield a decay component on this time scale with about the right amplitude. We are thus left with the possibility that (after initially removing magnesium) titrating tRNAVal1 with Mg2+ leads to increased internal flexibility and a significant amplitude of a deformational relaxation mode. At any rate, there is no question that after removal of Mg2+ tRNAPhe and tRNAVal1 display quite different solution conformation behavior. These findings are in qualitative agreement with recent 500-MHz 1H NMR results from solutions of these two tRNAs.

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Section: Discussionsupporting

confidence: 54%

Section: Discussionmentioning

confidence: 73%

Section: T H O M a S Etmentioning

confidence: 98%

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Effect of magnesium(2+) on the solution conformation of two different transfer ribonucleic acids

Jc¹,

Schurr²,

Br³

et al. 1984

Biochemistry

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“…This is because the translational diffusion coefficient of the charged particles is increased by repulsive Coulomb interactions causing them to diffuse faster (33-36). The rotational diffusion coefficient is not significantly affected at the low ionic strengths and particle concentrations in the range used in this study (37,38). The effect on translational diffusion coefficient is most noticeable at high protein concentration and low ionic strength.…”

Section: Discussionmentioning

confidence: 67%

Dissecting Amelogenin Protein Nanospheres

Bromley

Kiss

Lokappa

et al. 2011

Journal of Biological Chemistry

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Amelogenin self-assembles to form an extracellular protein matrix, which serves as a template for the continuously growing enamel apatite crystals. is involved in protein-protein interaction. The truncated rP148 formed similar but smaller oligomers, suggesting that the C terminus is not critical for amelogenin oligomerization. We propose a model for nanosphere formation via oligomers, and we predict that nanospheres will break up to form oligomers in mildly acidic environments via histidine protonation. We further suggest that oligomeric structures might be functional components during maturation of enamel apatite.

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“…(4.56)] under all conditions studied. (187,188) The normalized amplitudes and lifetimes for (extrapolated to zero concentration) are and The results for are similar. (188) This requirement for two (or more) exponentials is unequivocal evidence for at least two ethidium binding sites.…”

Section: Ethidium Fluorescencementioning

confidence: 60%