Figure 16.
(A) Schematic of the proposed solvation free energy cycle in Mpro. The M1/downpro → 2·M1/down transition rate is governed by counterbalancing (denoted by a seesaw metaphor) between the favorable expulsion of H-bond depleted and slowly exchanging water from channel 1. A portion of this energy is stored in the form of trapped water within channel 2 (which persists in both substrate- and inhibitor-bound structures). Venting of this water subsequent to product dissociation resets domain 3 back to the M1/downpro state (a specific case of the general paradigm proposed in Figure 3). However, the seesaw is tipped toward M2/down via substrate binding (green rectangle), followed by possibly rapid dimerization (orange rectangle), resulting in the expulsion of additional H-bond depleted solvation from the AS and dimer interface. Product release promotes opening of channel 2, and venting of the trapped water (see below), which in turn, drives the 2·M2/downpro → M1/down state transition (including restoration and resolvation of channel 1). Product turnover and dissociation act as a “check valve” (denoted by the single-headed arrows), preventing backflow through the cycle. (B) Dynamic cycle, annotated with the crystal structures in which the aforementioned states have been captured.