Fig. 1: Schematic overview and characterization of our coarse-grained (CG) models.
From: Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core
a Representative depiction of a CG simulation of spike trimers in membrane interacting with an adjacent membrane with ACE2 dimers. The insets depict the CG model components for the spike trimer (bottom), ACE2 dimer (upper left), and lipid membrane (upper right). Note that the protein CG sites are colored by monomer while glycans are represented by gray balls. b Probability distributions for RBD conformations projected onto the first time-lagged independent component (tIC1). The purple, gray, and orange distributions (N = 19383, 33810, and 21810, respectively) denote the three clusters identified by k-means clustering with labels indicating their representative conformational state. c Comparison of spike trimer conformational state populations (ranging from 0 to 3 open RBDs or shed RBDs, i.e., exposure of the S2 trimeric core) from CG simulations (N = 53076) and cryo-ET classification (N = 4220); the core exposed state is in the prefusion form in the CG simulations while it is in the postfusion form in the cryo-ET dataset. d Representative depiction of the average configuration of CG S1 (brown beads) within the identified k-means clusters. For reference, CG configurations of experimentally-resolved open and closed states of S1 are shown as magenta and cyan beads, respectively. Arrows indicate the positions of each respective RBDs. In all cases, the N-terminal domains of S1 are aligned.
