Early stages of clathrin aggregation at a membrane in coarse-grained simulations

Abstract

The self-assembly process of clathrin coated pits during endocytosis has been simulated by combining and extending coarse grained models of the clathrin triskelion, the adaptor protein AP2, and a flexible network membrane. The AP2's core, upon binding to membrane and cargo, releases a motif that can bind clathrin. In conditions where the core-membrane-cargo binding is weak, the binding of this motif to clathrin can result in a stable complex. We characterize the conditions and mechanisms resulting in the formation of clathrin lattices that curve the membrane, i.e., clathrin coated pits. The mechanical properties of the AP2 β linker appear crucial to the orientation of the curved clathrin lattice relative to the membrane, with wild-type short linkers giving rise to the inward curving buds enabling endocytosis while long linkers produce upside-down cages and outward curving bulges.

NERDSS: a non-equilibrium simulator for multibody self-assembly at the cellular scale

“…NERDSS has several advantageous features which make it a powerful and immediately useful tool for cell-scale simulations. First, NERDSS is transferrable between distinct systems thanks to its rate-based interaction framework, which avoids the time-consuming parameterization of energy functions often hard-coded for specific assembly systems 11 . Although protein geometries and orientations of bound complexes in NERDSS are system specific, we provide a GUI to facilitate user-design of proteins and their bound states.…”

“…The length and time-scales of such dynamics are difficult or impossible with the alternative and standard computational approach for self-assembly of coarse-grained molecular dynamics (MD)type models [9][10][11] . For those models, interactions emerge due to distance-dependent energy functions rather than rate-controlled events, so while they are more physically realistic, they lack systematic and transferable methods for involving enzymatic or ATP-driven reactions ubiquitous in cells.…”

“…Clathrin, a 600kDa trimeric protein, assembles into both flat and spherical lattices in vivo and in vitro, although in vivo this process only occurs on the plasma membrane, with the requirement of a host of accessory and adaptor proteins, as clathrin itself does not bind the membrane. Existing simulations of clathrin-cage assembly provide important physical insight into CME, but they use ad hoc energy-based models that require substantial expertise to develop 11,25,26 , or lack spatial resolution 27,28 . Here we implement an extensible multi-component model of clathrin lattice assembly to quantify distinct pathways and dynamics of assembly in solution and on the membrane, and directly reproduce fluorescence experiments 29 .…”

Gaussian curvature and the budding kinetics of enveloped viruses

“…We note that the 296 stalling described in the main text was observed for all subunit interaction geometries 297 that we have considered for the alphavirus model [1], as well as in another model for 298 proteins that adsorb onto the membrane [44], suggesting that the barrier is a generic 299 feature of assembly and budding on a membrane. We note that the stalling described in 300 the main text was not observed in some previous budding simulations because they only 301 considered early stages of budding [45][46][47]. While Refs.…”

“…44 modeled as rigid trimers of truncated cones, with each cone comprising a linear array of 45 six beads of increasing diameter. The cone angle was set so that in the absence of a 46 membrane, the GPs assembled into hollow, roughly icosahedral shells containing 80 47 trimers, though they form larger shells in the presence of a membrane [1]. The 48 membrane was represented by the implicit solvent model of Cooke and Deserno [13].…”