Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

Homotropic cooperativity is widespread in biological regulation. The homo-oligomeric ring-shaped trp RNA binding attenuation protein (TRAP) from bacillus binds multiple tryptophan ligands (Trp) and becomes activated to bind a specific sequence in the 5’ leader region of the trp operon mRNA. Ligand-activated binding to this specific RNA sequence regulates downstream biosynthesis of Trp in a feedback loop. Characterized TRAP variants form 11- or 12-mer rings and bind Trp at the interface between adjacent subunits. Various studies have shown that a pair of loops that gate each Trp binding site is flexible in the absence of the ligand and become ordered upon ligand binding. Thermodynamic measurements of Trp binding have revealed a range of cooperative behavior for different TRAP variants, even if the averaged apparent affinities for Trp have been found to be similar. Proximity between the ligand binding sites, and the ligand-coupled disorder-to-order transition has implicated nearest-neighbor interactions in cooperativity. To establish a solid basis for describing nearest-neighbor cooperativity we engineered dodecameric (12-mer) TRAP variants constructed with two subunits connected by a flexible linker (dTRAP). We mutated one of the protomers such that only every other site was competent for Trp binding. Thermodynamic and structural studies using native mass spectrometry, NMR spectroscopy, and cryo-EM provided unprecedented detail into the thermodynamic and structural basis for the observed ligand binding cooperativity. Such insights can be useful for understanding allosteric control networks and for the development of new ones with defined ligand sensitivity and regulatory control. Significance Homo-oligomeric proteins are ubiquitous in biology, and their function is often regulated by activator ligands that bind cooperatively, via poorly understood mechanisms. TRAP is a bacterial protein responsible for sensing changes in cellular tryptophan concentration, and for downregulating its production when levels are elevated. By fusing two subunits via a flexible linker, we assembled protein rings in which every other of its twelve ligand binding sites is incapable of binding. We used calorimetry and native mass spectrometry to measure ligand binding and found that these nearest-neighbor interactions are essential for cooperative ligand binding. Cryo-EM of these engineered proteins provided the means to observe the structure-thermodynamic linkage essential for understanding ligand binding cooperativity. ### Competing Interest Statement The authors have declared no competing interest. * nMS : native mass spectrometry cryo-EM : cryogenic electron microscopy NMR : nuclear magnetic resonance Trp : tryptophan TRAP : rp RNA-binding attenuation protein Aha : Alkalihalobacillus halodurans dTRAP : a protein construct composed of two Aha TRAP chains connected by a flexible linker WT-WT/WT-Mut/Mut-WT/Mut-Mut dTRAP : dTRAP variants in which the first and second protomer are either the wild-type sequence (WT), or a Trp binding-defective mutant (Mut) NN : nearest-neighbor ITC : isothermal titration calorimetry.