Fig. 6: Allosteric tylosin promotes the binding of orthosteric substrate.

Molecular dynamics simulations of monomeric binding (purple) and non-binding (blue) allosteric tylosin and octameric binding (red) and non-binding (yellow) allosteric tylosin. a The conformation of AKRtyl-NADP(H) (white in cartoon) is mainly clustered into four categories based on loop 232–237 (red in cartoon) during simulations. At the monomer level, the conformations are mainly partly out-folded or half out-folded, after allosteric binding, the ensemble becomes more open with totally out-folded state emerging and no inner-folded conformation. At the octamer level, the conformations are mainly partly outer-folded, and the allosterically bound ensemble has additional accessible half out-folded conformations. b Calculation of the solvent-accessible surface area (SASA) of the substrate binding site during simulations. (Monomer-Allosteric Tylosin, n = 1500; Monomer+Allosteric Tylosin n = 758; Octamer-Allosteric Tylosin, n = 1500; Octamer +Allosteric Tylosin n = 1500). On violin plots, the upper and lower lines define the range of values while the box defines values between 0.25 and 0.75 quartiles; the white dot points the median. The substrate binding pocket was larger with a higher SASA both after allosteric tylosin binding at both monomer and octamer level.