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

Abstract

Biochemical interactions at membranes are the starting points for cell signaling networks. But bimolecular reaction kinetics are difficult to experimentally measure on 2-dimensional membranes and are usually measured in volumetric in vitro assays. Membrane tethering produces confinement and steric effects that will significantly impact binding rates in ways that are not readily estimated from volumetric measurements. Also, there are situations when 2D reactions do not conform to simple mass action kinetics. Here we show how highly coarse-grained molecular simulations using the SpringSaLaD software can be used to estimate membrane-tethered rate constants from experimentally determined volumetric kinetics. The approach is validated using an analytical solution for dimerization of binding sites anchored via stiff linkers. This approach can provide 2-dimensional bimolecular rate constants to parameterize cell-scale models of receptor-mediated signaling. We explore how factors such as molecular reach, steric effects, disordered domains, local concentration and diffusion affect the kinetics of binding. We also develop a general scheme to assess whether simple mass action rate constants can be applied for a given scenario, taking into account the diffusivity of the membrane anchors and tethered binding sites, the initial membrane densities of the reactants and the desired level of completion for the fitted rate constant. 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 (GEF) that is recruited to EGFR, significantly accelerates Ras binding to the SOS catalytic site. A small biochemical network model parametrized with the derived 2D rate constants shows how recruitment of SOS via EGFR can significantly enhance Ras activation. SIGNIFICANCE STATEMENT: In cell signaling, the activation of a surface receptor leads to a cascade of intracellular biochemical events. Many protein interactions occur near the inner plasma membrane surface. However, accurate rate parameters for these steps in models of signaling are rarely available because membrane-tethered reaction kinetics are difficult to experimentally measure. Here, we use a highly coarse-grained molecular simulator to model the kinetics of reactions between binding sites that are tethered to a membrane. We can fit these simulation outputs with 2-dimensional rate laws to obtain rate constants that can be used to build complex models of cell signaling. The derived rate constants can also be analyzed to understand the key biophysical features controlling the kinetics of bimolecular membrane reactions.