The protonation state of phosphotyrosine in protein interaction interface has an important impact on protein interactions, and thus should be determined correctly before computational study. Using the NMR structure of the SH2 domain of SHC1 bound with a phosphorylated CD247 chain of T cell receptor as an example, the protonation state of phosphotyrosine was studied by thermodynamic integration with AMBER/parm99 force field and GBobc implicit water model for the first time. The result showed that the computation was accurate, and the protonation state determined by this computation was in accordance with the experimental result. This study suggests that this method not only make a sound foundation for the future computational structural studies with phosphotyrosines involved, but also have potential application to the protonation state determinations of other amino acids with titratable groups.

Key words: receptor tyrosine kinase, phosphotyrosin, protonation, generalized Born model, thermodynamic integration