title: Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements.
abstract: Protein-protein interactions are necessary for various cellular processes, and therefore, information related to protein-protein interactions and structural information of complexes is invaluable. To identify protein-protein interfaces using NMR, resonance assignments are generally necessary to analyze the data; however, they are time consuming to collect, especially for large proteins. In this paper, we present a rapid, effective, and unbiased approach for the identification of a protein-protein interface without resonance assignments. This approach requires only a single set of 2D titration experiments of a single protein sample, labeled with a unique combination of an (15)N-labeled amino acid and several amino acids (13)C-labeled on specific atoms. To rapidly obtain high resolution data, we applied a new pulse sequence for time-shared NMR measurements that allowed simultaneous detection of a ω(1)-TROSY-type backbone (1)H-(15)N and aromatic (1)H-(13)C shift correlations together with single quantum methyl (1)H-(13)C shift correlations. We developed a structure-based computational approach, that uses our experimental data to search the protein surfaces in an unbiased manner to identify the residues involved in the protein-protein interface. Finally, we demonstrated that the obtained information of the molecular interface could be directly leveraged to support protein-protein docking studies. Such rapid construction of a complex model provides valuable information and enables more efficient biochemical characterization of a protein-protein complex, for instance, as the first step in structure-guided drug development.
authors.affiliation: Japan Biological Informatics Consortium (JBIC), Koto-ku, Tokyo, Japan.
authors.forename: Yuya
authors.initials: Y
authors.lastname: Kodama
authors.forename: Michael L
authors.initials: ML
authors.lastname: Reese
authors.forename: Nobuhisa
authors.initials: N
authors.lastname: Shimba
authors.forename: Katsuki
authors.initials: K
authors.lastname: Ono
authors.forename: Eiji
authors.initials: E
authors.lastname: Kanamori
authors.forename: Volker
authors.initials: V
authors.lastname: Dötsch
authors.forename: Shuji
authors.initials: S
authors.lastname: Noguchi
authors.forename: Yoshifumi
authors.initials: Y
authors.lastname: Fukunishi
authors.forename: Ei-Ichiro
authors.initials: E
authors.lastname: Suzuki
authors.forename: Ichio
authors.initials: I
authors.lastname: Shimada
authors.forename: Hideo
authors.initials: H
authors.lastname: Takahashi
mesh_terms: D007553:Isotope Labeling; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins