Computational Delineation of the Bioenergetics of Protein-Mediated Orchestration of Membrane Vesiculation in Clathrin-Dependent Endocytosis

Abstract

Internalization of extracellular cargo by eukaryotic cells via the clathrin-dependent endocytosis (CDE) is an important regulatory process prominent in several cellular functions. Subsequent to receptor activation, a sequence of molecular events in CDE is responsible for the recruitment of various accessory proteins such as AP-2, epsin, AP180, eps15, dynamin, amphiphysin, endophilin, and clathrin to the plasma membrane to orchestrate membrane vesiculation. While the involvement of these proteins have been established and their roles in membrane deformation, cargo recognition, and vesicle scission have been identified, current conceptual understanding falls short of a mechanistic description of the cooperativity and the bioenergetics of the underlying vesicle nucleation event which we address here using theoretical models based on an elastic continuum representation for the membrane and atomistic to coarse-grained representations for the proteins. We employ the surface evolution approach to describe membrane geometries by minimizing the Helfrich Hamiltonian in a curvilinear coordinate system and address how the energetics of vesicle formation in a membrane is impacted by the presence of a growing clathrin coat. We consider two limiting scenarios: (1) the clathrin assembly model in which the clathrin coat induces membrane curvature by forming a curvilinear scaffold; (2) the accessory curvature-inducing protein assembly model, in which the clathrin lattice merely serves as a template to spatially pattern curvature inducing proteins such as epsin which collectively induce membrane curvature. Analyzing the energy required for vesicle formation from a planar bilayer, we demonstrate the role of the CDE protein assembly in driving membrane vesiculation. Furthermore, using a time-dependent Ginzburg-Landau formalism along with the thermodynamic method of free energy perturbation, we calculate the free energy the nucleated vesicle and quantify the finite-temperature corrections to the energy landscape of vesicle nucleation in CDE.