Mechanism of activation of elongation factor Tu by ribosome: Catalytic histidine activates GTP by protonation

Aleksandrov, Alexey; Field, Martin J.

doi:10.1261/rna.040097.113

Cited by 21 publications

(44 citation statements)

References 41 publications

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“…Recent works (14,30) questioned some of the findings in our previous study of EF-Tu′. However, one of those works (14) had Fig.…”

Section: Exploring the Activation Of Ef-tumentioning

confidence: 84%

“…Although we repeatedly addressed the risk in the assumption that just running QM/MM calculations should give the correct result to major biological problems, we find it useful to discuss here as an example of a recent work on EF-Tu′ (14). As stated in section Exploring the Activation of EF-Tu, this work concluded that the barrier for the 1W mechanism in EF-Tu′ is around 50 kcal/mol, not recognizing that obtaining the 1W barrier in water is already far above the ability of what is in some respects a minimization-type mapping that does not attempt to produce any 2D surface of the type obtained in the careful study of ref.…”

Section: Discussionmentioning

confidence: 99%

“…That is, in addition to uncritical theoretical studies of phosphate hydrolysis by irrelevant gas phase and energy minimization studies (for discussion see ref. 11), even recent studies that involve some configurational sampling (12,13), or path search approaches (14) (see Exploring the Activation of EF-Tu and SI Text), have not provided yet reliable mechanistic picture. The difficulty to elucidate the mechanism reflected several problems including the most studies have not explored all of the possible options (including key earlier proposals).…”

Section: Quantifying the Relationship Between Competing Mechanisms Ofmentioning

confidence: 99%

See 2 more Smart Citations

Quantitative exploration of the molecular origin of the activation of GTPase

Plotnikov

Lameira

et al. 2013

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

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GTPases play a major role in cellular processes, and gaining quantitative understanding of their activation demands reliable free energy surfaces of the relevant mechanistic paths in solution, as well as the interpolation of this information to GTPases. Recently, we generated ab initio quantum mechanical/molecular mechanical free energy surfaces for the hydrolysis of phosphate monoesters in solution, establishing quantitatively that the barrier for the reactions with a proton transfer (PT) step from a single attacking water (1W) is higher than the one where the PT is assisted by a second water (2W). The implication of this finding on the activation of GTPases is quantified here, by using the ab initio solution surfaces to calibrate empirical valence bond surfaces and then exploring the origin of the activation effect. It is found that, although the 2W PT path is a new element, this step is not rate determining, and the catalytic effect is actually due to the electrostatic stabilization of the pre-PT transition state and the subsequent plateau. Thus, the electrostatic catalytic effect found in our previous studies of the Ras GTPase activating protein (RasGAP) and the elongation factor-Tu (EF-Tu) with a 1W mechanism is still valid for the 2W path. Furthermore, as found before, the corresponding activation appears to involve a major allosteric effect. Overall, we believe that our finding is general to both GTPases and ATPases. In addition to the biologically relevant finding, we also provide a critical discussion of the requirements from reliable surfaces for enzymatic reactions.D etailed understanding of many problems in biology boils down to the elucidation of the correct reaction mechanism in the protein and in solution and to the elucidation of the origin of the corresponding catalytic effect. However, this requires overcoming the challenge of obtaining accurate free energy surfaces in the condensed phase. Such a task can be accomplished, in principle, by the combined quantum mechanical/molecular mechanical (QM/ MM) method (1-5). However, the implementation of this method is still very challenging. At present, we are not at the stage reached in studies of gas phase reactions, where the results of ab initio calculations are sometimes considered almost as substitutes for experimental results. Nevertheless, recent advances in ab initio QM/MM [QM(ai)/MM] studies (2, 4-6) brought us closer to having quantitative results for solution reactions and in some respects to quantitative results for enzymes, especially if one evaluates reliable QM (ai)/MM free energy surfaces for the solution reaction and then use the resulting surfaces to calibrate empirical valence bond (EVB) surfaces for studying the relevant enzymatic reaction. Here we exploit these advances by exploring the hydrolysis of phosphate monoesters that is the key to the activation of GTPases. That is, we start by quantifying the energetics of the solution reaction and then use the solution free energy surface to calibrate EVB surface that allow us to reliably...

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“…Recent works (14,30) questioned some of the findings in our previous study of EF-Tu′. However, one of those works (14) had Fig.…”

Section: Exploring the Activation Of Ef-tumentioning

confidence: 84%

Section: Discussionmentioning

confidence: 99%

Section: Quantifying the Relationship Between Competing Mechanisms Ofmentioning

confidence: 99%

See 1 more Smart Citation

Quantitative exploration of the molecular origin of the activation of GTPase

Plotnikov

Lameira

et al. 2013

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

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“…Mutations of H84 strongly affect the GTPase activity of the factor (5,7,(27)(28)(29). Several recent theoretical studies on the mechanism of GTP hydrolysis of EF-Tu (13,27,(29)(30)(31) have Significance Translational elongation factor Tu (EF-Tu) utilizes GTP hydrolysis to control the speed and fidelity of decoding. We explored the reaction coordinate for GTP hydrolysis by EF-Tu and the origins of the million-fold activation effect of the ribosome.…”

mentioning

confidence: 99%

Ribosome-induced tuning of GTP hydrolysis by a translational GTPase

Maracci

Peske

Dannies

et al. 2014

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

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GTP hydrolysis by elongation factor Tu (EF-Tu), a translational GTPase that delivers aminoacyl-tRNAs to the ribosome, plays a crucial role in decoding and translational fidelity. The basic reaction mechanism and the way the ribosome contributes to catalysis are a matter of debate. Here we use mutational analysis in combination with measurements of rate/pH profiles, kinetic solvent isotope effects, and ion dependence of GTP hydrolysis by EF-Tu off and on the ribosome to dissect the reaction mechanism. Our data suggest that-contrary to current models-the reaction in free EF-Tu follows a pathway that does not involve the critical residue H84 in the switch II region. Binding to the ribosome without a cognate codon in the A site has little effect on the GTPase mechanism. In contrast, upon cognate codon recognition, the ribosome induces a rearrangement of EF-Tu that renders GTP hydrolysis sensitive to mutations of Asp21 and His84 and insensitive to K + ions. We suggest that Asp21 and His84 provide a network of interactions that stabilize the positions of the γ-phosphate and the nucleophilic water, respectively, and thus play an indirect catalytic role in the GTPase mechanism on the ribosome.

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“…Several models have been proposed for the mechanism of GTP hydrolysis by EF-Tu and other GTPases based on structural, theoretical and biochemical studies. 20,[53][54][55][56][57][58][59][60][61][62] In general, the reaction proceeds through a nucleophilic attack of a water molecule on the c-phosphate of GTP. For the reaction to become efficient, the water molecule has to be activated.…”

Section: Multiple Pathways Of Gtp Hydrolysismentioning

confidence: 99%

Review: Translational GTPases

Maracci

Rodnina

2016

Biopolymers

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Translational GTPases (trGTPases) play key roles in facilitating protein synthesis on the ribosome. Despite the high degree of evolutionary conservation in the sequences of their GTP‐binding domains, the rates of GTP hydrolysis and nucleotide exchange vary broadly between different trGTPases. EF‐Tu, one of the best‐characterized model G proteins, evolved an exceptionally rapid and tightly regulated GTPase activity, which ensures rapid and accurate incorporation of amino acids into the nascent chain. Other trGTPases instead use the energy of GTP hydrolysis to promote movement or to ensure the forward commitment of translation reactions. Recent data suggest the GTPase mechanism of EF‐Tu and provide an insight in the catalysis of GTP hydrolysis by its unusual activator, the ribosome. Here we summarize these advances in understanding the functional cycle and the regulation of trGTPases, stimulated by the elucidation of their structures on the ribosome and the progress in dissecting the reaction mechanism of GTPases. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 463–475, 2016.

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Mechanism of activation of elongation factor Tu by ribosome: Catalytic histidine activates GTP by protonation

Cited by 21 publications

References 41 publications

Quantitative exploration of the molecular origin of the activation of GTPase

Quantitative exploration of the molecular origin of the activation of GTPase

Ribosome-induced tuning of GTP hydrolysis by a translational GTPase

Review: Translational GTPases

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