Fig. 3: Molecular dynamics simulations of SARS-CoV-2 3CLpro bound to human or mouse NEMO.

a Main contacts from MD simulations and predicted hot spots in WT 3CLpro bound to human NEMO_227–234. Contacts that persist for more than 70% of the simulation time are depicted. Hot spots predicted with either KFCa or KFCb are labeled in bold and those predicted with both methods are underlined. Persistent H-bonds are shown as dashed lines (Supplementary Table 2). A representative conformation of the short (aa. 227-234) and long constructs of NEMO in the binding site is shown as solid and transparent surfaces, respectively. b Sequence Logo generated with WebLogo⁷⁴ of NEMO (aa. 216-253) across 535 animal sequences, including those from placentals, bats, marsupials, birds, rodents, and primates. Clustal Omega⁷⁵ was used for the multiple sequence alignment and as an input for the WebLogo analysis. c Time evolution of the distance between the catalytic S⁻ in 3CLpro Cys145 and the carbonyl C of Gln231 in hNEMO_227–234 and mNEMO_227–234 computed from MD simulations.