Probing allosteric regulations with coevolution-driven molecular simulations

Protein-mediated allosteric regulations are essential in biology, but their quantitative characterization continues to posit formidable challenges for both experiments and computations. Here, we combine coevolutionary information, multiscale molecular simulations, and free-energy methods to interrogate and quantify the allosteric regulation of functional changes in protein complexes. We apply this approach to investigate the regulation of adenylyl cyclase (AC) by stimulatory and inhibitory G proteins—a prototypical allosteric system that has long escaped from in-depth molecular characterization. We reveal a surprisingly simple ON/OFF regulation of AC functional dynamics through multiple pathways of information transfer. The binding of G proteins reshapes the free-energy landscape of AC following the classical population-shift paradigm. The model agrees with structural and biochemical data and reveals previously unknown experimentally consistent intermediates. Our approach showcases a general strategy to explore uncharted functional space in complex biomolecular regulations.