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Elongation Factor Tu’s Nucleotide Binding Is Governed by a Thermodynamic Landscape Unique among Bacterial Translation Factors
- Source :
- Journal of the American Chemical Society
- Publication Year :
- 2019
- Publisher :
- American Chemical Society (ACS), 2019.
-
Abstract
- Molecular switches such as GTPases are powerful devices turning "on" or "off" biomolecular processes at the core of critical biological pathways. To develop molecular switches de novo, an intimate understanding of how they function is required. Here we investigate the thermodynamic parameters that define the nucleotide-dependent switch mechanism of elongation factor (EF) Tu as a prototypical molecular switch. EF-Tu alternates between GTP- and GDP-bound conformations during its functional cycle, representing the "on" and "off" states, respectively. We report for the first time that the activation barriers for nucleotide association are the same for both nucleotides, suggesting a guanosine nucleoside or ribose-first mechanism for nucleotide association. Additionally, molecular dynamics (MD) simulations indicate that enthalpic stabilization of GDP binding compared to GTP binding originates in the backbone hydrogen bonding network of EF-Tu. In contrast, binding of GTP to EF-Tu is entropically driven by the liberation of bound water during the GDP- to GTP-bound transition. GDP binding to the apo conformation of EF-Tu is both enthalpically and entropically favored, a feature unique among translational GTPases. This indicates that the apo conformation does not resemble the GDP-bound state. Finally, we show that antibiotics and single amino acid substitutions can be used to target specific structural elements in EF-Tu to redesign the thermodynamic landscape. These findings demonstrate how, through evolution, EF-Tu has fine-tuned the structural and dynamic features that define nucleotide binding, providing insight into how altering these properties could be exploited for protein engineering.
- Subjects :
- Molecular switch
chemistry.chemical_classification
Binding Sites
Guanosine
Chemistry
General Chemistry
GTPase
Molecular Dynamics Simulation
Peptide Elongation Factor Tu
010402 general chemistry
01 natural sciences
Biochemistry
Catalysis
GTP Phosphohydrolases
0104 chemical sciences
Biological pathway
Colloid and Surface Chemistry
Prokaryotic translation
Escherichia coli
Biophysics
Thermodynamics
Nucleotide
EF-Tu
Subjects
Details
- ISSN :
- 15205126 and 00027863
- Volume :
- 141
- Database :
- OpenAIRE
- Journal :
- Journal of the American Chemical Society
- Accession number :
- edsair.doi.dedup.....1845c9f44c25194a6e0e521f6e4e0b86
- Full Text :
- https://doi.org/10.1021/jacs.9b01522