Study of molecular recognition mechanism in protein GPI modification: a bioinformatics analysis of interaction between GPI-anchored proteins and modification enzyme

Abstract

The interaction for protein glycosylphosphatidylinositol (GPI) modification between the premature GPI-anchored proteins and the active sites in PIG-K, one of the GPI transamidase proteins, is discussed in this study by the homology modeling method and amino acid propensity analysis in the space around the ω-sites in premature GPI-anchored proteins. In particular, the direct interaction between ω-sites of GPI-anchored proteins and PIG-K was focused on, the root-mean-square deviation (RMSD) and three-dimensional amino acid propensity around the ω-sites were analyzed in the present study. As the results, PIG-K was considered to recognize the specific structure around the ω-sites of the GPI-anchored proteins, the positively-charged Lys (K) and Arg (R) residues around the ω-sites have the possibility to interact with the negatively-charged Asp (D) and Glu (E) residues around an active site of PIG-K, and Tyr (Y) and Ala (A) residues around the ω-sites are thought to be essential for molecular recognition by PIG-K. The findings in this study that structural recognition around the ω-site in the mature GPI-anchored proteins by PIG-K are useful for understanding the local mechanism of the GPI modification enzyme and can be applied for the development of cell-surface-engineering.

Keywords

• bioinformatics
• post-translational modification
• gpi-anchored protein
• pig-k
• mammalian protein