Dissecting Dynamic Allosteric Pathways Using Chemically Related Small-Molecule Activators

• Published in: Structure (London) 2016-07, Vol.24 (7), p.1155-1166
• Main Authors: Lisi, George P., Manley, Gregory A., Hendrickson, Heidi, Rivalta, Ivan, Batista, Victor S., Loria, J. Patrick
• Format: Article
• Language: English
• Subjects: Allosteric Regulation; Allosteric Site; Aminohydrolases - chemistry; Aminohydrolases - drug effects; Aminohydrolases - metabolism; Aminoimidazole Carboxamide - analogs & derivatives; Aminoimidazole Carboxamide - pharmacology; Chemical Sciences; Isoxazoles - pharmacology; Ligands; Molecular Docking Simulation; Ribonucleotides - pharmacology
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2016.04.010

The allosteric mechanism of the heterodimeric enzyme imidazole glycerol phosphate synthase was studied in detail with solution nuclear magnetic resonance spectroscopy and molecular dynamics simulations. We studied IGPS in complex with a series of allosteric activators corresponding to a large range of catalytic rate enhancements (26- to 4,900-fold), in which ligand binding is entropically driven. Conformational flexibility on the millisecond timescale plays a crucial role in intersubunit communication. Carr-Purcell-Meiboom-Gill relaxation dispersion experiments probing Ile, Leu, and Val methyl groups reveal that the apo- and glutamine-mimicked complexes are static on the millisecond timescale. Domain-wide motions are stimulated in the presence of the allosteric activators. These studies, in conjunction with ligand titrations, demonstrate that the allosteric network is widely dispersed and varies with the identity of the effector. Furthermore, we find that stronger allosteric ligands create more conformational flexibility on the millisecond timescale throughout HisF. This domain-wide loosening leads to maximum catalytic activity. •Allosteric ligand binding is correlated to structural dynamics in a model enzyme•A widely dispersed allosteric network has been identified•Catalytic rate enhancement varies with the degree of millisecond flexibility•Allosteric ligand binding is communicated over a 25-Å distance Lisi et al. use NMR and computational methods to probe the allosteric influence of small-molecule activators. Allosteric activator-induced changes in millisecond motions are responsible for enhancing the catalytic rate at a distant active site. Interestingly the most activating ligand results in the largest degree of motions.