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Poster Presentations
Day 3, June 24（Tue.）
Room P (Maesato East, Foyer, Ocean Wing)
- 3P-AM-25
Assessment of the solvent-accessible surfaces of proteins observed by LC-MS
(1Sch. of Sci., Kitasato Univ., 2Cent. Disease Proteomics, Sch. of Sci., Kitasato Univ.)
Eiji Kojitani1, Arisa Suto1, Taichi Takasawa1, Yoshio Kodera1,2, oTakashi Matsui1,2
Structural proteomics techniques are useful for identifying the surface of a target protein bound with binding partners. The protein surface is normally labeled using a hydroxy radical, deuterium, or various chemicals. The binding partners capped the surface on the target protein, thus the difference of the label strength with and without the partner is determined, consequently, the strength difference was mapped onto the three-dimensional structure deposited in the Protein Data Bank to identify the binding surface and/or the binding surface accompanied with the conformational change. However, unfortunately, the surface-accessible sites identified by structural proteomics techniques are often inconsistent with those calculated based on PDB coordinates. It speculated that the techniques may determine the efficient sites of the labeling rather than the solvent accessibility.
In this study, the solvent-accessible surface of human serum albumin was analyzed using covalent protein labeling and subsequently compared to the surfaces derived from the 27 highest-resolution structures deposited in PDB. The results indicated that the inconsistencies in the solvent-accessible surface calculated from PDB are due to the lack of PDB data representing the structures in the solution.