Журнал компьютерных наук и системной биологии

Molecular Docking Studies of Type III Secretion System Effector Sopb Homolog in Vibrio vulnificus

Abstract

Rama Adiga, Iddya Karunasagar and Indrani Karunasagar

Pathogenic bacteria use the needle shaped Type III secretion system to inject effector proteins into the host cell. The SopB effector protein of Salmonella mediates invasion by evading the host immune response. Being a phosphoinositide phosphatase, it synthesizes phospholipids at the host cell membrane, after targeting host cell ubiquitin. Ubiquitination of SopB are known to control the biological activity of SopB at the plasma membrane. The identified SopB effector protein of Vibrio vulnificus which is a human pathogen found in the marine environment was homologous to SopB of Salmonella and E.coli. Structural superposition with available structure of SopB of Salmonella yielded a DNA linking domain similar to Salmonella SopB. Ubiquitination sites for SopB homolog in V.vulnificus was predicted by bioinformatics tools which was further supported by molecular docking studies. The ubiquitin binding sites were proposed to be structurally similar to the conserved ubiquitin binding motif of human polymerase complexed with ubiquitin (2KTF). The ubiquitin binding sites having Leu residue at 226, Leu 235 and Leu 234 were conserved whereas the hydrophobic Phe was replaced by Tyr at 223 in the sopB homolog of V.vulnificus. The conserved Glu 228 of SopB protein was predicted to be involved in imparting a electronegative potential in the ligand binding site. The ubiquitin molecule docked with SopB of V.vulnificus had Leu8 for binding interaction and recognition which was found to be similar to the ubiquitin-human polymerase complex. Thus the host immune response was predicted to be targeted by SopB effector in V.vulnificus by altering the ubiquitin pathway.