Searching deeply into the conformational space of glycoprotein hormone receptors. Molecular dynamics of the human follitropin and lutropin receptors within a bilayer of (SDPC) poly-unsaturated lipids
AbstractGlycoprotein receptors are a subfamily of G-protein coupled receptors, including the follicle hormone (FSH) receptor (FSHR), thyroid-stimulating hormone receptor (TSH), and luteinizing/chorionic gonadotrophin hormone receptor (LHCGR). These receptors display common structural features such as a prominent extracellular domain, with a leucine-rich repeats (LRR) stabilized by {beta}-sheets, a long and flexible loop known as the hinge region (HR), and the transmembrane (TM) domain with seven -helices interconnected by intra- and extracellular loops. Binding of the ligand to the LRR resembles a hand coupling transversally to the - and {beta}-subunits of the hormone, with the thumb being the HR. The structure of the complex of FSHR-FSH suggests an activation mechanism in which Y335 at the HR binds into a pocket between the - and {beta}-chains of the hormone, leading to an adjustment of the extracellular loops. In this study, we performed molecular dynamics (MD) simulations to identify the conformational changes for the FSHR and LHCGR. We set up an FSHR structure as predicted by AlphaFold (AF-P23945); for the LHCGR structure we took the cryo-electron microscopy structure for the active state (PDB:7FII) as initial coordinates. Specifically, the flexibility of the HR domain and the correlated motions of the RLL and TMD were analyzed. From the conformational changes of the LRR, TMD, and HR we explored the conformational landscape by means of MD trajectories in all-atom approximation, including a membrane of polyunsaturated phospholipids. The distances and procedures here defined may be useful to propose reaction coordinates to describe diverse processes such as the active-to-inactive transition, to identify intermediaries suited for allosteric regulation, and biased binding to cellular transducers in a selective activation strategy. Author summaryIn the present study, we describe the results from a computational microscopy perspective (also known as molecular dynamics simulation) at the atomistic resolution for the two gonadotropin hormone receptors, the follicle-stimulant hormone receptor and the luteinizing/chorionic gonadotropin hormone receptor, which are essential for reproduction in humans. Several dysfunctional mutations in these receptors, leading to reproductive failure, have been detected in the clinical arena. To better understand the process whereby these two receptors perform their signaling tasks, triggering an intracellular response upon binding of their cognate agonist at the extracellular side, we assembled the receptor structures in a membrane bilayer of phospholipids with water molecules as solvent at both sides of the membrane. The systems included nearly 200 thousand atoms, each moving around at 300 kelvin and 1 bar given the interactions (attractive or repulsive forces) from each other. As the motion equations are solved in each time step (at femtoseconds time scale), the system evolves over time during hundreds of nanoseconds (millions of time steps) for three independent replicates. The receptor conformation, therefore, may display non-random motions due to the stability of specific structures in the complex molecular environment, including the hydrophobic membrane core, the bilayer interfaces, and the aqueous medium. From analysis of simulation trajectories and structural changes of the receptors, we could identify the main conformational changes exhibited by each receptor explored in a model cellular environment. We discussed the roll of the hinge domain at the extracellular domain in triggering the receptor conformational changes, as well as differences in the dynamics between these receptors in terms of the flexibility of the structures. Importantly, we proposed relative distances among the different receptor domains as parameters to characterize conformational intermediaries along a transition of states. Understanding of the signaling process in gonadotropin hormone receptors could be useful to explore new strategies for the modulation of the receptor functions, the bias of signaling pathways, or the selective binding of agonists.