Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane

• DOI: 10.1021/acs.jpcb.0c04553
• Publication Date: 2020-06-19T19:09:46Z
• Authors: Hyeonuk Woo; Sang-Jun Park; Yeol Kyo Choi; Taeyong Park; Maham Tanveer; Yiwei Cao; Nathan R. Kern; Jumin Lee; Min Sun Yeom; Tristan I. Croll; Chaok Seok; Wonpil Im
• Keywords: Viral membrane; Loop modeling; Viral protein

This technical study describes all-atom modeling and simulation of a fully glycosylated full-length SARS-CoV-2 spike (S) protein in viral membrane. First, starting from PDB: 6VSB 6VXX, S structures were modeled using template-based modeling, de-novo structure prediction, loop techniques GALAXY suite. Then, the recently determined most occupied glycoforms, 22 N-glycans 1 O-glycan each monomer Glycan Reader & Modeler CHARMM-GUI. These model assessed further refined against low-resolution data their respective experimental maps ISOLDE. We then used CHARMM-GUI Membrane Builder to place proteins membrane performed molecular dynamics simulations. All are available COVID-19 Archive (http://www.charmm-gui.org/docs/archive/covid19) so that researchers can use these models carry out innovative novel research for prevention treatment COVID-19.