Energetics of activation of GTP hydrolysis on the ribosome

Wallin, Göran; Kamerlin, Shina Caroline Lynn; Åqvist, Johan

doi:10.1038/ncomms2741

Cited by 55 publications

(127 citation statements)

References 38 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: 56%

“…30 (the original phosphate as a base mechanism), and the corresponding results are summarized in Table S6. The calculations (see SI Text) avoid the instability involved in evaluating the PT step that leads to the formation of an OH − ion (which is strongly interacting with the protonated His84), and went directly to the TS through the plateau.…”

Section: Exploring the Activation Of Ef-tumentioning

confidence: 99%

“…Here, in contrast to the implication of ref. 30, it seems that the TS stabilization is different in EF-Tu and EF-Tu′ due to the change in interaction with the active site groups (Fig. 6B).…”

Section: Exploring the Activation Of Ef-tumentioning

confidence: 99%

“…Now, although it is very reasonable to challenge some of our finding by simple and in some cases reliable calculations of PT energies (as well as by logical arguments), some of the points brought to support the arguments of ref. 30 are unjustified. Thus, we will provide the main details of the clarifications in the SI Text and allow the reader to focus on the actual open issues here.…”

Section: Exploring the Activation Of Ef-tumentioning

confidence: 99%

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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: 56%

Section: Exploring the Activation Of Ef-tumentioning

confidence: 99%

Section: Exploring the Activation Of Ef-tumentioning

confidence: 99%

Section: Exploring the Activation Of Ef-tumentioning

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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“…These nucleotides form part of the longest universally conserved rRNA sequence known, the SRL loop. G2661 and A2662 are essential to the function of the SRL loop and were recently implicated in EF-Tu-and EF-G-mediated GTP hydrolysis 26,27 . During translation elongation, the SRL loop is also required for anchoring of EF-G to the ribosome during translocation 28 .…”

Section: Discussionmentioning

confidence: 99%

VapC20 of Mycobacterium tuberculosis cleaves the Sarcin–Ricin loop of 23S rRNA

et al. 2013

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The highly persistent and often lethal human pathogen, Mycobacterium tuberculosis contains at least 88 toxin-antitoxin genes. More than half of these encode VapC PIN domain endoribonucleases that inhibit cell growth by unknown mechanisms. Here we show that VapC20 of M. tuberculosis inhibits translation by cleavage of the Sarcin-Ricin loop (SRL) of 23S ribosomal RNA at the same position where Sarcin and other eukaryotic ribotoxins cleave. Toxin-inhibited cells can be rescued by the expression of the antitoxin, thereby raising the possibility that vapC20 contributes to the extreme persistence exhibited by M. tuberculosis. VapC20 cleavage is inhibited by mutations in the SRL that flank the cleavage site but not by changes elsewhere in the loop. Disruption of the SRL stem abolishes cleavage; however, further mutations that restore the SRL stem structure restore cleavage, revealing that the structure rather than the exact sequence of the SRL is important for this activity.

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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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Energetics of activation of GTP hydrolysis on the ribosome

Cited by 55 publications

References 38 publications

Quantitative exploration of the molecular origin of the activation of GTPase

Quantitative exploration of the molecular origin of the activation of GTPase

VapC20 of Mycobacterium tuberculosis cleaves the Sarcin–Ricin loop of 23S rRNA

Review: Translational GTPases

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