Molecular dynamics simulation of the follicle-stimulating hormone receptor. Understanding the conformational dynamics of receptor variants at positions N680 and D408 from in silico analysis

Abstract

Follicle-stimulating hormone receptor (FSHR) is a G-protein coupled receptor (GPCR) and a prototype of the glycoprotein hormone receptors subfamily of GPCRs. Structural data of the FSHR ectodomain in complex with follicle-stimulating hormone suggests a “pull and lift” activation mechanism that triggers a conformational change on the seven α-helix transmembrane domain (TMD). To analyze the conformational changes of the FSHR TMD resulting from sequence variants associated with reproductive impairment in humans, we set up a computational approach combining helix modeling and molecular simulation methods to generate conformational ensembles of the receptor at room (300 K) and physiological (310 K) temperatures. We examined the receptor dynamics in an explicit membrane environment of polyunsaturated phospholipids and solvent water molecules. The analysis of the conformational dynamics of the functional (N680 and S680) and dysfunctional (mutations at D408) variants of the FSHR allowed us to validate the FSHR-TMD model. Functional variants display a concerted motion of flexible intracellular regions at TMD helices 5 and 6. Disruption of side chain interactions and conformational dynamics were detected upon mutation at D408 when replaced with alanine, arginine, or tyrosine. Dynamical network analysis confirmed that TMD helices 2 and 5 may share communication pathways in the functional FSHR variants, whereas no connectivity was detected in the dysfunctional mutants, indicating that the global dynamics of the FSHR was sensitive to mutations at amino acid residue 408, a key position apparently linked to misfolding and variable cell surface plasma membrane expression of FSHRs with distinct mutations at this position.

Reshaping the dynamics of follicle-stimulant hormone receptor models in polyunsaturated lipid bilayers. Calculation of conformational free energy landscapes of α-helical domains from all-atom MD simulations

“…Initial box dimensions were 90 Å x 105 Å x 114 Å, respectively, for the x-, y- and z-axis. A total of 128979 atoms were included: 29231 water molecules, 248 SDPC lipid molecules, a sodium ion for charge neutrality, and the receptor FSHR-WT or mutant I423T, with 379 residues encompassing D317 to N695 [28].…”

“…In addition, we implemented a computational approach to determine the impact of point mutations in the interhelical region of the FSHR [28]. Interestingly, the conformational dynamics of the wild-type receptor (FSHR-WT), was sensitive to point mutations such as D408Y and D408A, according to an analysis of autocorrelation matrices of the helical domains [28]. Apparently, when replacing D408 by tyrosine or alanine, fluctuations in protein backbone atoms showed different patterns in correlated communities in a dynamical network analysis [28].…”

“…More recently, new findings in the naturally occurring I423T missense mutation located at the TM helix 2 of the FSHR (bearing the frequent polymorphic variant S680), demonstrated modestly-reduced expression at the cell surface plasma membrane and, more importantly, a significant impact of the replacement on cAMP/protein kinase A and β-arrestin-dependent ERK1/2 phosphorylation signaling [29]. According to our computational analysis, the helical integrity was well preserved in all phenotypes; nonetheless, deviations from the initial receptor coordinates were detected in some TM domains [28]. To examine in more detail the significance of conformational fluctuations in the helical domains of the FSHR-WT model, in this study we extended the simulation trajectories of the receptor to the ∼10 2 ns time scale.…”

Misfolded G Protein-Coupled Receptors and Endocrine Disease. Molecular Mechanisms and Therapeutic Prospects

“…We have recently employed computational modeling and molecular dynamics simulations (MDS) of the FSHR in an explicit membrane environment [pre-equilibrated lipid bilayer of 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC) molecules] as a tool to explore in more detail the impact of the substitution of aspartate with tyrosine, alanine, or arginine at position 408 [122]. The FSHR modelled allowed us to detect differences in the receptor dynamics at the transmembrane domains between the WT and mutant receptors, likely related to receptor function.…”

“…In these three-dimensional representations, it can be observed that the dynamics of the receptor disclosed differences in the amplitudes of interhelical domains (arrows) as a function of the mutation at position 408. See the text and Refs [115,122]. for data and details.…”