Protein Surface Printer for Exploring Protein Domains

Abstract

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. Statistically, the outer surface of ACE2 displays less correlation with the RBD of SARS-CoV-2 than that of SARS-CoV. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells. Our program paves the way for an accurate understanding of protein binding for aggregation and ligand recognition.