Mesoscale simulations of membrane-tethered reactions to parameterize cell-scale models of signaling

Biochemical interactions at membranes are starting points for cell signaling. But reaction kinetics are difficult to measure on two-dimensional (2D) membranes and are usually measured in volumetric assays. Membrane tethering produces confinement and steric effects that will significantly impact binding rates; these cannot be determined by volumetric measurements. Additionally, because of the properties of 2D diffusion, bimolecular reactions may not conform to simple mass action kinetics. Here, we show how simulations using the SpringSaLaD software can be used to estimate a 2D rate constant based on a known 3D rate constant and coarse-grained molecular structures for the reactants; this approach accounts for confinement of the reaction to the near-membrane space as well as the steric environment and flexibility of the membrane-anchored binding sites. The approach is validated using theoretical solutions for dimerization in an idealized system containing a binding site at the end of a single stiff membrane anchor. With this ideal system, we also assess whether simple mass action rate constants can correctly describe the reaction rate, considering the diffusivity of the membrane anchors, the initial membrane densities of the reactants, and the desired level of completion of the reaction. We explore how factors such as molecular reach, steric effects, disordered domains, and diffusion affect the kinetics. We then apply our approach to epidermal growth factor receptor (EGFR)-mediated activation of the membrane-bound small GTPase Ras. The analysis reveals how binding of Ras to the allosteric site of SOS, a guanine nucleotide exchange factor that is recruited to EGFR, significantly accelerates Ras binding to the SOS catalytic site. A biochemical network model parametrized with the derived 2D rate constants demonstrates how recruitment of SOS via EGFR can significantly enhance Ras activation. Thus, we offer a novel method to more rigorously parameterize receptor-mediated steps in cell signaling.