NMR Line Shapes in Molecular Mechanisms with Ligand Binding and Multiple Conformers

Abstract

ABSTRACTInteractions of ligands with biological macromolecules are sensitively detected through changes of chemical shifts and line shapes of the NMR signals. This paper reports a mathematical analysis and simulations of NMR line shapes expected in titrations when ligand binding is coupled to multiple isomerization transitions. Such molecular mechanisms may correspond to ligand binding by intrinsically disordered proteins or by autoinhibited enzymes. Based on the simulation results, we anticipate several specific effects that may be observed in practice. First, the presence of non-binding conformers of the receptor molecule leads to a remarkable broadening in the binding transition even if the exchange between binding and non-binding conformers is very slow. Second, the ligand-binding mechanisms involving induced fit are expected to demonstrate deceptively decelerated exchange regimes even when the underlying kinetics are very fast. Conversely, the observation of fast-exchange shifting resonances with modest line-broadening (“marching peaks”) in practical NMR titrations may involve conformational selection transitions but less likely to be observed for the induced fit. Finally, in auto-inhibited molecules that open to form multiple binding-competent conformers, the fast dynamics of opening/closing transition are capable of masking the true kinetics of interconversion among transiently open forms of the receptor.