Thermodynamic Characterization of ppGpp Binding to EF-G or IF2 and of Initiator tRNA Binding to Free IF2 in the Presence of GDP, GTP, or ppGpp

In addition to their natural substrates GDP and GTP, the bacterial translational GTPases initiation factor (IF) 2 and elongation factor G (EF-G) interact with the alarmone molecule guanosine tetraphosphate (ppGpp), which leads to GTPase inhibition. We have used isothermal titration calorimetry to determine the affinities of ppGpp for IF2 and EF-G at a temperature interval of 5–25 °C. We find that ppGpp has a higher affinity for IF2 than for EF-G (1.7–2.8 μM Kd versus 9.1–13.9 μM Kd at 10–25 °C), suggesting that during stringent response in vivo, IF2 is more responsive to ppGpp than to EF-G. We investigated the effects of ppGpp, GDP, and GTP on IF2 interactions with fMet-tRNAfMet demonstrating that IF2 binds to initiator tRNA with submicromolar Kd and that affinity is altered by the G nucleotides only slightly. This—in conjunction with earlier reports on IF2 interactions with fMet-tRNAfMet in the context of the 30S initiation complex, where ppGpp was suggested to strongly inhibit fMet-tRNAfMet binding and GTP was suggested to strongly promote fMet-tRNAfMet binding—sheds new light on the mechanisms of the G-nucleotide-regulated fMet-tRNAfMet selection.