Molecular simulation of Nrp1-Spike-protein trimer

The seven models of Nrp1:monomeric-S1 (res. 1–677) were considered for further analysis. Firstly, the modeled complex was superimposed with the full-length Spike protein trimer (res. 1–1146; chain C was used for superimposition). To relax and better accommodate the initial docked structures in the context of the full-length (1–1146) Spike protein trimer, we performed all-atom molecular dynamics simulation with one Nrp1 bound to the Spike protein trimer for each of the seven models for 20 ns. Standard simulation procedures were used with the NAMD version 2.12 package (²⁶). Specifically, all proteins were solvated by TIP3P water with 150 mM NaCl. Simulation parameters were set as 2 fs for time step, thermostat at 310 K, and barostat of 1 bar, using the CHARMM36m force field (²⁷). The system contained ∼530,000 atoms in a cubic periodic boundary, including water and ions. The root mean-square deviation of the Nrp1: Spike complex is plotted in Fig. S2, showingthat all the simulations are equilibrated (perhaps with exception of model 3). The pair interaction, solvation energy, and surface-accessible surface area between Nrp1 and Spike were calculated and listed in Fig. 2 b.