Bridging the gap between ribosome structure and biochemistry by mechanistic computations

Åqvist, Johan; Lind, Christoffer; Sund, Johan; Wallin, Göran

doi:10.1016/j.sbi.2012.07.008

Cited by 24 publications

(20 citation statements)

References 80 publications

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“…In the suggested scenario, the nonbridging oxygen at A2662 positions His84 in its catalytic conformation, thus enabling it to act as a general base by subtracting a proton from the hydrolytic water that attacks the γ-phosphate of GTP (12). This model stimulated an intense scientific discussion in the field (22,23), because it is not fully compatible with certain biochemical, genetic (24), structural (25), and molecular dynamics simulation (26) data.…”

mentioning

confidence: 99%

Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

Koch

Flür

Kreutz

et al. 2015

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

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Elongation factor-catalyzed GTP hydrolysis is a key reaction during the ribosomal elongation cycle. Recent crystal structures of G proteins, such as elongation factor G (EF-G) bound to the ribosome, as well as many biochemical studies, provide evidence that the direct interaction of translational GTPases (trGTPases) with the sarcin-ricin loop (SRL) of ribosomal RNA (rRNA) is pivotal for hydrolysis. However, the precise mechanism remains elusive and is intensively debated. Based on the close proximity of the phosphate oxygen of A2662 of the SRL to the supposedly catalytic histidine of EF-G (His87), we probed this interaction by an atomic mutagenesis approach. We individually replaced either of the two nonbridging phosphate oxygens at A2662 with a methyl group by the introduction of a methylphosphonate instead of the natural phosphate in fully functional, reconstituted bacterial ribosomes. Our major finding was that only one of the two resulting diastereomers, the SP methylphosphonate, was compatible with efficient GTPase activation on EF-G. The same trend was observed for a second trGTPase, namely EF4 (LepA). In addition, we provide evidence that the negative charge of the A2662 phosphate group must be retained for uncompromised activity in GTP hydrolysis. In summary, our data strongly corroborate that the nonbridging proSP phosphate oxygen at the A2662 of the SRL is critically involved in the activation of GTP hydrolysis. A mechanistic scenario is supported in which positioning of the catalytically active, protonated His87 through electrostatic interactions with the A2662 phosphate group and H-bond networks are key features of ribosome-triggered activation of trGTPases.

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mentioning

confidence: 99%

Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

Koch

Flür

Kreutz

et al. 2015

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

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“…Neither of these hypotheses can be completely verified or disproved without an in vitro vertebrate mitochondrial translation assay, but no such system is available at present. However, computational modelling and molecular dynamics (MD) simulations have been remarkably successful in predicting key features of several steps involved in the translation process 18 , including termination by class-1 RFs 19,20 , and may offer a useful strategy for exploring the mitochondrial termination problem.…”

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confidence: 99%

Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons

2013

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A key feature of mitochondrial translation is the reduced number of transfer RNAs and reassignment of codons. For human mitochondria, a major unresolved problem is how the set of stop codons are decoded by the release factors mtRF1a and mtRF1. Here we present threedimensional structural models of human mtRF1a and mtRF1 based on their homology to bacterial RF1 in the codon recognition domain, and the strong conservation between mitochondrial and bacterial ribosomal RNA in the decoding region. Sequence changes in the less homologous mtRF1 appear to be correlated with specific features of the mitochondrial rRNA. Extensive computer simulations of the complexes with the ribosomal decoding site show that both mitochondrial factors have similar specificities and that neither reads the putative vertebrate stop codons AGA and AGG. Instead, we present a structural model for a mechanism by which the ICT1 protein causes termination by sensing the presence of these codons in the A-site of stalled ribosomes.

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“…A hydrogen-bonding network is formed involving the substrates and water molecule in the structure of transition states. This hydrogen bond network plays a main factor in decreasing the activation energy [26]. The two hydrogen bonds enhance the hydrogen bond network.…”

Section: The Two-step Reaction Mechanism Involved In One Water Moleculementioning

confidence: 99%

“…Zaher et al have found that the catalysis is at least 100-fold slower with the dA76-substituted peptidyl-tRNA substrate and that the peptidyl transferase center undergoes a slow inactivation when the peptidyl-tRNA lacks the 2 0 -OH group of A76 [14]. However, these results cannot rule out the role of the 2 0 -OH A76 in peptidyl transferase reaction [26]. Secondly, the function of the group 2 0 -OH of A2451 is identified as orienting the ribose of A76 in the proton shuttle process by hydrogen bond to 2 0 -OH of A76 directly [12,[27][28][29][30][31][32].…”

Section: Introductionmentioning

confidence: 99%

A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism

2015

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Bridging the gap between ribosome structure and biochemistry by mechanistic computations

Cited by 24 publications

References 80 publications

Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons

A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism

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