Molecular Dynamics and Network-based investigation of human bitter taste receptors activation: the case of TAS2R46.

The sense of taste is pivotal to evaluating food and discriminating nutrients from toxic substances. The five basic tastes commonly recognized are sweet, umami, bitter, sour, and salty. Among these, bitter taste perception is related to the protection of the organism against the ingestion of spoiled or poisonous food compounds and is based on a multiscale signal transduction process. The first stage of this process is established through taste receptors, specific proteins that, because of conformational changes due to the interaction with specific agonists, permit the triggering of these signalling transduction pathways. Bitter taste receptors are members of a sub-family (Class T) of G protein-coupled receptors (GPCRs), called the “Taste 2 receptor family” (TAS2R). In this context, the mechanisms underlying TAS2Rs activation are still poorly understood because of the lack of experimental structures for TAS2Rs. However, the experimental structure of TAS2R46 has been recently reported in both active and inactive states, paving the way for a deeper understanding of bitter taste perception. Among the investigating techniques, computational molecular modeling, such as Molecular Dynamics (MD), allows to highlight the key molecular features of their activation process. In addition, network analysis of molecular systems, such as the Protein structure network (PSN), allows to gain insights into mechanisms underlying signal transfering within biomolecular structures, uncovering changes in structural communication upon the activation process. This work aims to explore the key features of the activation process of TAS2R46 and underline the main differences between the active and inactive states. More in detail, computational tools allowed us to perform extensive all-atom molecular dynamics (MD) simulations of systems related to the two experimental structures, both with and without the presence of a bitter tastant, namely strychnine. Conformational analyses (such as extracellular loop movements, the volume of the binding pocket, and specific distances between the main residues of the receptor), the PSN method, and the calculation of correlation matrices allowed to shed light on specific differences between the apo-state and the bound-state and changes in the transmission of information from the extracellular to the intracellular region between the two states. In detail, the PSN analysis identifies the involvement of different receptor areas in the G-protein binding site in the intracellular region between the two states: the presence of the ligand inside the binding pocket changes the intracellular area of the receptor involved in the interaction with the G Protein. Accordingly, correlation matrices give major correlation values when these receptor regions are involved in the transfer of information along the protein. Then, regarding conformational changes, the main difference between the two states is related to the volume of the binding pocket, which turns out to assume higher values in the inactive state. Overall, our results suggested that computational tools can provide new insights into TAS2Rs molecular mechanisms, representing an important starting point to deeply understand the precise mechanism of their activation process.