title: Amino acid selective cross-saturation method for identification of proximal residue pairs in a protein-protein complex.
abstract: We describe an NMR-based approach, the amino acid selective cross-saturation (ASCS) method, to identify the pairs of the interface residues of protein-protein complexes. ASCS uses a "cross-saturation (CS)-donor" protein, in which only one amino acid is selectively (1)H-labeled in a (2)H-background, and a "CS-acceptor" protein with uniform (2)H, (15)N labeling. Irradiation of the (1)H-labeled amino acid, which exists only in the donor, decreases the intensity of the (1)H- (15)N HSQC signals of the acceptor residues proximal to the (1)H-labeled CS-source residue(s) through the CS phenomenon. Given the three-dimensional structure of each protein in the complex, but not the complex structure, the combinatorial analysis of multiple ASCS results specify the CS-source residue(s), based on the spatial complementarity between the CS-source residues on the CS donor and the cross-saturated amide protons on the acceptor. NMR investigations of the labeling selectivity and efficiency in an E. coli host, which are critical for ASCS, revealed that Ala, Arg, His, Ile, Leu, Lys, Met, Phe, Pro, Trp, and Tyr are selectively labeled with a high (1)H/(2)H ratio. The observation of the ASCS was then confirmed using the known structure of the yeast ubiquitin (Ub) and yeast ubiquitin hydrolase 1 (YUH1). Conversely, reasonable candidates for the CS-source residues were suggested by the analysis of the ASCS results, with reference to the individual structures of YUH1 and Ub. The pairwise distance information between the CS-source residues and the cross-saturated amide groups obtained by ASCS will be useful for modeling protein-protein complexes.
authors.affiliation: Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Igarashi
authors.forename: Masanori
authors.initials: M
authors.lastname: Osawa
authors.forename: Koh
authors.initials: K
authors.lastname: Takeuchi
authors.forename: Shin-ichiro
authors.initials: S
authors.lastname: Ozawa
authors.forename: Ichio
authors.initials: I
authors.lastname: Shimada
mesh_terms: D000596:Amino Acids / Q000032:analysis* / Q000737:chemistry; D010450:Endopeptidases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D011522:Protons; D025801:Ubiquitin / Q000737:chemistry* / Q000378:metabolism
chemical_list: D000596:Amino Acids; D011522:Protons; D025801:Ubiquitin; D010450:Endopeptidases; C059237:ubiquitin-Nalpha-protein hydrolase