Nanomechanical Differences between Inactive and Active States of Rhodopsin from Molecular-Scale Simulation

Abstract

Several membrane proteins, including G protein-coupled receptors (GPCRs), present a challenge in studying their structural and dynamical properties under physiological conditions. Moreover, to better understand the activity of proteins requires examination of single molecule behaviors rather than ensemble averaged behaviors. In this work we report the Force-distance curve-based AFM (FD-AFM) which was utilized to directly probe and localize the conformational states of a GPCR within an artificial membrane at nanoscale resolution. We have further validated the experimental results by molecular scale coarse-grained (CG) simulations of rhodopsin biomolecules. In the past, our CG model has been applied successfully for the study of the mechanical properties of large biological assemblies such as β-amyloid and α-synuclein fibrils. Both FD-AFM experimental results and the computational force profiles revealed that the active state of the receptor has a higher Young's modulus compared to the inactive state of the receptor. We show how the deformation of the hydrogen bond network triggers this difference and by the statistical analysis of the native contacts we highlight the underlying mechanism. Hence, the inactive and active states of rhodopsin could be differentiated based on the stiffness of the receptor. Our work paves the route towards the molecular characterization of protein states based on the Young's modulus, which is clear indication of the mechanochemical interplay of proteins within the cell membrane.