Cooperative binding of magnesium to transfer ribonucleic acid studied by a fluorescent probe

Lynch, Dennis C.; Schimmel, Paul

doi:10.1021/bi00706a012

Cited by 102 publications

(44 citation statements)

References 37 publications

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“…It cannot be expected that the models exactly follow the real Mg2' or spermidine-binding modes since, for example, minor partial, cooperative or non-obligatory effects are not taken into account. Several Mgz+ are known to be bound to the tRNA [6] but only a few of them are functionally of major importance. 1-4 ions in tRNA were required in the models of this work for various enzymes, the most complicated requirements were shown by Phe-tRNA synthetase and Ile-tRNA synthetase, and the simplest by Arg-tRNA synthetase and His-tRNA synthetase.…”

Section: Resultsmentioning

confidence: 99%

Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Airas

1996

European Journal of Biochemistry

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The magnesium dependences of the ATPJPP, exchange and tRNA aminoacylation of reactions were measured for six aminoacyl-tRNA synthetases (isoleucyl-, tyrosyl-and arginyl-tRNA synthetases from class I, and histidyl-, lysyl-and phenylalanyl-tRNA synthetases from class 11). The measured values were subjected to best-fit analyses using sum square error calculations between the data and the calculated curves in order to find the mode of participation of the Mg" and to optimize the sets of the kinetic constants.The following four dependences were observed: the class I1 synthetases require three Mgz+ for the activation reaction (including the one in MgATP), but the class I synthetases require only one Mgz+ (in MgATP) ; in class I1 synthetases both MgPP, and Mg,PP, participate in the pyrophosphorolysis of the aminoacyl adenylate. Arginyl-tRNA synthetase from class I also shows a better fit if also Mg,PP, reacts, but in the isoleucyl-and tyrosyl-tRNA synthetases only MgPP, but not Mg,PP, is used in the pyrophosphorolysis. Different synthetases have different requirements for the tRNA-bound Mg2+ and spermidine, independent of the enzyme class. 1-4 Mg" or spermidines are required in the best fit models. At the end of the reaction in all the synthetases analysed the dissociation of Mg" from the product aminoacyltRNA essentially enhances the subsequent dissociation of the aminoacyl-tRNA from the enzyme. The binding of ATP to the E . aminoacyl-tRNA complex also speeds up the dissociation of the aminoacyltRNA from most of these enzymes.

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Section: Resultsmentioning

confidence: 99%

Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Airas

1996

European Journal of Biochemistry

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“…Most formulations of the effects of Mg 2ϩ on RNA folding transitions have considered Mg 2ϩ as a ligand that binds stoichiometrically to sites in the folded forms of the RNA, e.g., I ϩ nMg 2ϩ º N⅐(Mg 2ϩ ) n (11)(12)(13). This approach oversimplifies the complex set of interactions taking place between RNA, Mg 2ϩ , monovalent cations, and anions (6).…”

Section: [1]mentioning

confidence: 99%

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Grilley

Soto²,

Draper³

2006

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

124

184

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Mg 2؉ ions are very effective at stabilizing tertiary structures in RNAs. In most cases, folding of an RNA is so strongly coupled to its interactions with Mg 2؉ that it is difficult to separate free energies of Mg 2؉ -RNA interactions from the intrinsic free energy of RNA folding. To devise quantitative models accounting for this phenomenon of Mg 2؉ -induced RNA folding, it is necessary to independently determine Mg 2؉ -RNA interaction free energies for folded and unfolded RNA forms. In this work, the energetics of Mg 2؉ -RNA interactions are derived from an assay that measures the effective concentration of Mg 2؉ in the presence of RNA. These measurements are used with other measures of RNA stability to develop an overall picture of the energetics of Mg 2؉ -induced RNA folding. Two different RNAs are discussed, a pseudoknot and an rRNA fragment. Both RNAs interact strongly with Mg 2؉ when partially unfolded, but the two folded RNAs differ dramatically in their inherent stability in the absence of Mg 2؉ and in the free energy of their interactions with Mg 2؉ . From these results, it appears that any comprehensive framework for understanding Mg 2؉ -induced stabilization of RNA will have to (i) take into account the interactions of ions with the partially unfolded RNAs and (ii) identify factors responsible for the widely different strengths with which folded tertiary structures interact with Mg 2؉ .cations ͉ ion interaction coefficients ͉ Wyman linkage relations M g 2ϩ ions strongly stabilize RNA tertiary structures under conditions that only weakly affect RNA secondary structure stability, a phenomenon first studied in the folding of transfer RNA (1, 2). Although the sensitivity of RNA folding to Mg 2ϩ has been amply documented for many RNAs, it is still unknown how this sensitivity is quantitatively related to the strengths of Mg 2ϩ -RNA interactions. Thus, for most RNAs, the magnitude of the intrinsic RNA instability is unknown, nor is it known how much more favorably Mg 2ϩ interacts with the native RNA structure than with structures from which folding takes place. Lacking this fundamental overview of Mg 2ϩ -RNA interaction free energies, it has not been possible to carry out extensive evaluations of theoretical models that seek to explain Mg 2ϩ -induced RNA folding in terms of the underlying physical interactions (3, 4).In this article, we parse the tertiary folding of two different RNAs into the intrinsic free energy of folding in the absence of Mg 2ϩ and the free energies of Mg 2ϩ interactions with folded and partially folded states. To obtain the relevant free energies, we devised a practical experimental method for measuring the effect of RNA on Mg 2ϩ ion activities and derived the equations necessary for extracting Mg 2ϩ -RNA interaction free energies from the experimental data. The two RNAs have vastly different stabilities in the absence of Mg 2ϩ and correspondingly large differences in the favorable interactions of the native RNA structures with Mg 2ϩ . Clearly, different RNAs use different strategies ...

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“…Several Mg2+ or polyamine ions are known to be bound to tRNA [13, [25][26][27]. The ions affect the conformation and charge of the tRNA and thereby the binding of tRNA to the enzyme [24,28] Kd (E .…”

Section: Effect Of Mgzmentioning

confidence: 99%

Analysis of the isoleucyl‐tRNA synthetase reaction by total rate equations

Airas¹

1992

European Journal of Biochemistry

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Derivation of a steady-state rate equation for the aminoacyl-tRNA synthetases is described, and its suitability for the analysis of various details of the reaction is tested. The equation is applied to the magnesium and spermidine dependences of the isoleucyl-tRNA synthetase reaction. Earlier work The transfer reaction is rather slow, and, at least under some conditions, it participates in rate limitation. (d) A Mg2+-induced reduction in the aminoacylation rate seems to be directed to the dissociation of the aminoacyl-tRNA from the enzyme. This dissociation rate is enhanced if a Mg2+ is first dissociated from the enzyme or tRNA. An increase in the Mg2+ concentration shifts the rate limitation from the transfer reaction towards dissociation of the product.The aminoacyl-tRNA synthetase reaction contains three substrates and three products, and in a simple case the total reaction has 15 intermediates (Scheme 1). If activators such as Mg2 + and polyamines are added, the number of different intermediates rises to hundreds. Consequently, the steadystate rate equation for such a reaction is complex. A total rate equation, however, could provide a means to test the compatibility of separately measured kinetic parameters, and, in addition, it could be used to test some dependences of the enzyme system. Within the aminoacyl-tRNA synthetases, the aim is to calculate the discrimination of the incorrect amino acids.Much kinetic work has been performed on the isoleucyltRNA synthetase from Escherichia coli [l -41. Therefore, it is a good model for studies using a total rate equation, too, especially to test how well the scattered parameters function with each other. In previous work [S, 61, a rate equation for isoleucyl-tRNA synthetase has been derived, the roles of Mg2+ and spermidine in the reaction analysed. The Mg2+ and polyamine dependences were used as means to test the correctness of the mechanism and to estimate various kinetic constants. A somewhat different approach for checking the compatibility of the measured parameters has been used by Okamoto and Savageau [7,8].The present paper describes kinetic measurements made by changing the tRNA concentrations. The steady-state rate equation was improved and the constants were estimated to fit the results. The analysis led to adjustments ofthe constants, especially at the transfer reaction and thereafter. The relationship between the rates of aminoacylation of tRNA and the ATP/PPi exchange (uacyl/uexch) proved to be an efficient way to test parameters at the aminoacyl adenylation step. MATERIALS AND METHODSThe isoleucyl-tRNA synthetase from E. coli B (specific activity 1.2 ymol inin-' mg protein-') and the assay mcthods

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Cooperative binding of magnesium to transfer ribonucleic acid studied by a fluorescent probe

Cited by 102 publications

References 37 publications

Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Analysis of the isoleucyl‐tRNA synthetase reaction by total rate equations

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Cooperative binding of magnesium to transfer ribonucleic acid studied by a fluorescent probe

Cited by 102 publications

References 37 publications

Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Differences in the Magnesium Dependences of the Class I and Class II Aminoacyl‐tRNA Synthetases from Escherichia coli

Mg 2+ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures

Analysis of the isoleucyl‐tRNA synthetase reaction by total rate equations

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Product

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Mg ²⁺ –RNA interaction free energies and their relationship to the folding of RNA tertiary structures