The binding of Class II sRNA MgrR to two different sites on matchmaker protein Hfq enables efficient competition for Hfq and annealing to regulated mRNAs

The scheme of the reactions used to model the progress of MgrR annealing to eptB133 and ygdQ145. The numbers correspond to the following reactions: (1) M + E = ME; (2) M + H = MH; (3) H + E = HE; (4) MH + E = MEH; (5) HE + M = MEH; (6) MEH + M = MEHM; (7) ME + MH = MEHM; (8) MEH + E = MEHE; (9) ME + HE = MEHE, where M is MgrR, E is mRNA (either eptB133 or ygdQ145 in respective reactions), ME is binary complex of MgrR with respective mRNA, MH is binary complex of MgrR with Hfq, HE is binary complex of respective mRNA with Hfq, MEH is a ternary complex of Hfq with MgrR and respective mRNA, MEHE is a complex of Hfq with MgrR and two molecules of respective mRNA, MEHM is a complex of Hfq with respective mRNA and two molecules of MgrR. Colored arrows (blue, green, red) mark reactions included in three closed thermodynamic loops that were constrained during the data fitting to the model.