Hammes, Gordon G.; Chang, Yu-Chu; Oas, Terrence G.

Proceedings of the National Academy of Sciences of the United States of America (2009), 106(33), 13737-13741 CODEN: PNASA6; ISSN: 0027-8424. English.

The mechanism of ligand binding coupled to conformational changes in macromols. has recently attracted considerable interest. The 2 limiting cases are the "induced fit" mechanism (binding first) or "conformational selection" (conformational change first). Described here are the criteria by which the sequence of events can be determined quant. The relative importance of the 2 pathways is determined not by comparing rate consts. (a common misconception) but instead by comparing the flux through each pathway. The simple rules for calculating flux in multistep mechanisms are described and then applied to 2 examples from the literature, neither of which has previously been analyzed using the concept of flux. The first example is the mechanism of conformational change in the binding of NADPH to dihydrofolate reductase (DHFR). The second example is the mechanism of flavodoxin folding coupled to binding of its cofactor, FMN. In both cases, the mechanism switches from being dominated by the conformational selection pathway at low ligand concentration to induced fit at high ligand concentration Over a wide range of conditions, a significant fraction of the flux occurs through both pathways. Such a mixed mechanism likely will be discovered for many cases of coupled conformational change and ligand binding when kinetic data are analyzed by using a flux-based approach.