Protein Surface Printer for Exploring Protein Domains

The
surface of proteins is vital in determining protein functions.
Herein, a program, Protein Surface Printer (PSP), is built that performs
multiple functions in quantifying protein surface domains. Two proteins,
PETase and cytochrome P450, are used to validate that the program
supports atomistic simulations with different combinations of programs
and force fields. A case study is conducted on the structural analysis
of the spike proteins of SARS-CoV-2 and SARS-CoV and the human cell
receptor ACE2. Although the surface domains of both spike proteins
are highly similar, their receptor-binding domains (RBDs) and the
O-linked glycan domains are structurally different. The O-linked glycan
domain of SARS-CoV-2 is highly positively charged, which may promote
binding to negatively charged human cells.