Computational studies on seven helix transmembrane receptors

Seven transmembrane receptors (7TMRs) represent the largest family of integral membrane proteins across the three kingdoms of life. They are involved in the vast majority (~80%) of signal transduction pathways across the cell membrane. They respond both to the electromagnetic field and ligands. Very importantly, more than one third of all current drugs target human 7TMRs, called G-protein coupled receptors (GPCRs). In recognition of the importance of this protein family, the 2012 Nobel Prize for Chemistry has been recently awarded to Robert J. Lefkowitz and Brian K. Kobilka for “their studies of G-protein coupled receptors.” However, detailed structural data on cellular pathways of 7TMRs is still limited. Hence, computational methods play an important role for structural predictions of 7TMRs as well as their binding to ligands. This thesis is devoted to characterize structure-function relationships in 7TMRs using a variety of computational approaches. We focus not only on the 7TMRs but also on their downstream effectors. First, we have used classical molecular dynamics (MD) to investigate different forms of the Sensory Rhodopsin II in Halobacterium salinarium (HsSRII). This receptor functions as a light sensor mediating repellent responses to the blue-green light. The results allow us to suggest that: (i) the alteration of charge distribution and the rearrangement of water molecules in the active site along with the interhelical hydrogen bond interactions play a key role for conformational changes associated to light absorption; (ii) two extracellular loops, a cytoplasmic loop and the C-terminus may participate to the activation of HsSRII. Next, we have developed a hybrid molecular simulation method called MM/CG to study 7TMR/ligand interactions. The accuracy of the method has been established by comparison with recent atomistic MD simulations on the 7TMRs, HsSRII and human beta2 Adrenergic Receptor. The MM/CG simulations turn out to reproduce the key structural features of the active site, as found also in MD simulations carried out by us and another research group lead by Prof. Ursula Roethlisberger (EPFL). Due to its low computational cost, this method can be applied to the study of a large number of GPCR-ligand complexes. As the final step of the thesis, we have extended the study to 7TMR’s downstream effectors including Adenylyl Cyclase III (ACIII) and Cyclic Nucleotide-Gated (CNG) ion channel, two proteins involved in the olfactory signaling cascade. By using homology modeling approaches, we have built (i) the cytoplasmic domain structure of human ACIII - in complex with human Galpha-subunit of olfactory system, and (ii) the P helix, S6 and the C-linker of CNG channel in the closed and open states. Specially, in the work of CNG channel, in combination with experimental studies, we have proposed the initial conformational changes of the C-linker, S6 and P-helix upon cyclic nucleotide binding