Multiphasic interactions between nucleotides and target proteins

TL;DR

This study reveals that nucleotide-protein interactions in bacteria are better described by multiphasic profiles with distinct phases and jumps, challenging the traditional curvilinear models.

Contribution

It introduces the multiphasic analysis approach to characterize nucleotide-protein binding profiles, providing a more accurate representation than traditional curvilinear models.

Findings

Multiphasic profiles fit binding data significantly better than curvilinear models.

Transitions in binding profiles include non-contiguous jumps.

Nucleotide-protein interactions exhibit complex multiphasic behavior.

Abstract

The nucleotides guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp) bind to target proteins to promote bacterial survival (Corrigan et al. 2016). Thus, the binding of the nucleotides to RsgA, a GTPase, inhibits the hydrolysis of GTP. The dose response, taken to be curvilinear with respect to the logarithm of the inhibitor concentration, is instead much better (P<0.001 when the 6 experiments are combined) represented as multiphasic, with high to exceedingly high absolute r values for the straight lines, and with transitions in the form of non-contiguities (jumps). Profiles for the binding of radiolabeled nucleotides to HprT and Gmk, GTP synthesis enzymes, were, similarly, taken to be curvilinear with respect to the logarithm of the protein concentration. However, the profiles are again much better represented as multiphasic than as curvilinear (the P values range from 0.047 to <0.001 for each of the 8 experiments for binding of ppGpp and pppGpp to HprT). The binding of GTP to HprT and the binding of the three nucleotides to Gmk are also poorly represented by curvilinear profiles, but well represented by multiphasic profiles (straight and, in part, parallel lines).