Schematic representation of the proposed comprehensive ensemble model, which compounds the assumptions of both the MWC and the EAM models.

Each domain (blue and yellow) can be in R (Relaxed), T (Tensed) and I (Disordered) state. R and T are incompatible as assumed in the MWC model, and thus there are now seven possible combinations for protein states. Similar to the EAM model, the disordered I state of a domain does not have any interface interaction with the adjacent domain, and it does not bind to any ligand or substrate due to the lack of ordered structures. The expressions for the free energy (ΔGi) of each state (relative to RR as the reference state as that in the EAM model) were listed in the absence of ligand and substrate. ΔGR1 and ΔGR2 are the free energy of unfolding the R state of each domain, and Δgint,R and Δgint,T are the free energy of breaking the interface interactions in RR and TT, respectively, which were defined in a manner similar to the EAM model. ΔGRT1 and ΔGRT2 are the free-energy of the R-T transition for each domain. A is allosteric regulation ligand binding to one (blue) domain, and B is the substrate to the other (yellow) domain. A and B are different molecules, i.e., we consider the heterotropic allosteric effect. To enable both positive and negative allosteric effect for ordered proteins, we consider two binding modes for A: it can only bind to the R state of the blue domain (A-R binding mode) (as depicted here), or can only bind to the T state of the blue domain (A-T binding mode). B always binds only to the R state of the yellow domain.