A flexible, allosteric loop regulates protein activity and rewires electrostatics

Allostery is a key driver of protein function and behavior in biological systems. Historically, allosteric regulation has been attributed to conformational and dynamic changes, mostly derived from well-structured regions of proteins. While the regulatory contributions of specific unstructured elements, such as catalytic loops near the active site, have been widely characterized, the role of distal, flexible loops remains poorly understood. Here, we investigate the allosteric protein chorismate mutase (CM), a homodimeric enzyme critical for the biosynthesis of aromatic amino acids. Although CM is differentially regulated by tryptophan and tyrosine via a shared pocket over 25 Å from the active site, their near-identical NMR spectra suggest that alternative mechanisms may explain TrpCM and TyrCM's distinct functional landscapes. We demonstrate that a mutation within a structurally invisible and highly flexible loop, loop 11-12, located far from the active site, drastically alters CM's activity landscape. Using paramagnetic labeling of the loop, we show that loop 11-12 undergoes transient excursions toward the active site, but only in the presence of the activator Trp, which binds over 20 Å away. Furthermore, employing a novel NMR approach, we show that loop 11-12 modulates CM's electrostatics, potentially influencing charge distribution to provide another control of enzymatic activity. Our findings support a sophisticated allosteric process in which a flexible, distal loop is functionally coupled to both the effector binding region and the active site. This mechanism provides new insights into the diverse ways proteins achieve allosteric regulation and may contribute to understanding flexible regions in other allosteric systems.