ArticleBiophysical journal2010
A combined molecular dynamics and rapid kinetics approach to identify conserved three-dimensional communication networks in elongation factor Tu.
Article in Biophysical journal, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 16 citations in OpenAlex.
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion.Nucleic acids research · 2018Article
- Trade-off and flexibility in the dynamic regulation of the cullin-RING ubiquitin ligase repertoire.PLoS computational biology · 2017Article
- Tetracycline does not directly inhibit the function of bacterial elongation factor Tu.PloS one · 2017Article
- The C-terminal Helix of Pseudomonas aeruginosa Elongation Factor Ts Tunes EF-Tu Dynamics to Modulate Nucleotide Exchange.The Journal of biological chemistry · 2016Article
- A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu.Scientific reports · 2015Article
- An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation.Nucleic acids research · 2014Article
- Elongation factor Ts directly facilitates the formation and disassembly of the Escherichia coli elongation factor Tu·GTP·aminoacyl-tRNA ternary complex.The Journal of biological chemistry · 2013Article
- Computational studies of molecular machines: the ribosome.Current opinion in structural biology · 2012Review
- Characterization of the emergent properties of a synthetic quasi-cellular system.BMC bioinformatics · 2012Article
- A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.PLoS computational biology · 2012Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Elongation factor (EF) Tu delivers aminoacyl-tRNAs to the actively translating bacterial ribosome in a GTP-hydrolysis-dependent process. Rapid recycling of EF-Tu, catalyzed by EF-Ts, is required for efficient protein synthesis in vivo. Here we report a combined theoretical and experimental approach aimed at identifying three-dimensional communication networks in EF-Tu. As an example, we focus on the mechanistic role of second-shell residue Asp(109). We constructed full-length structural models of EF-Tu from Escherichia coli in the GDP-/GTP-bound state and performed several 10-ns-long molecular-dynamics simulations. During these simulations, the side chain of Asp(109) formed a previously undetected transient hydrogen bond to His(22), an invariant residue in the phosphate-binding loop (P-loop). To experimentally validate our molecular-dynamics results and further analyze the role of this hydrogen bond, we determined all rate constants for the multistep reaction between EF-Tu (wild-type and two mutants), EF-Ts, GDP, and GTP using the stopped-flow technique. This mutational analysis revealed that the side chain of Asp(109) is important for acceleration of GDP, but not for GTP dissociation by EF-Ts. The possibility that the Asp(109) side chain has a role in transition-state stabilization and coupling of P-loop movements with rearrangements at the base side of the nucleotide is discussed.
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