A biophysical model of molecular clusters: interplay of multivalency, membrane localization, steric hindrance, molecular flexibility and intracellular crowding

Dynamic molecular clusters are assembled through weak multivalent interactions and are platforms for a variety of critical cellular functions, most importantly receptor-mediated signaling mechanisms. However, the molecular and cellular biophysical rules that control cluster kinetics, size and composition are not well understood. Modeling can offer insights, but molecular dynamics calculations would be excessively expensive because of the size of these systems and the > ms time scales for their formation; cellular reaction diffusion simulations, on the other hand, do not have the requisite molecular detail, failing to account for steric effects or molecular flexibility. To address this problem, we developed mesoscale kinetic Langevin dynamics models using the SpringSaLaD software. We used coarse grain models of a ternary molecular system based on the membrane-bound receptor nephrin, the adaptor protein Nck and the actin nucleation promoting factor NWASP. Kinetics of cluster formation and their steady state size distributions were analyzed as a function of molecular and cellular features using a reference system consisting of 36 molecules. The distribution at steady state favored stoichiometries that optimized binding interaction, but still was quite broad. A balance of enthalpy and entropy limited the number of molecules per cluster, with complete annealing into a single 36-mer complex being exceedingly rare. Domains close to binding sites sterically inhibited clustering much less than terminal domains because the latter effectively restrict access to the interior of nascent clusters. Increased flexibility of the interacting molecules diminished clustering by shielding binding sites within compact conformations. Membrane association of nephrin increased the cluster size distribution in a surface density-dependent manner. These properties provide insights into how molecular clusters can function to localize and amplify cell signaling.