Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements

Yuya Kodama, Michael L. Reese, Nobuhisa Shimba, Katsuki Ono, Eiji Kanamori, Volker Dötsch, Shuji Noguchi, Yoshifumi Fukunishi, Ei ichiro Suzuki, Ichio Shimada, Hideo Takahashi

Research output: Contribution to journalArticle

3 Citations (Scopus)

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 15N-labeled amino acid and several amino acids 13C-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 ω1-TROSY-type backbone 1H-15N and aromatic 1H-13C shift correlations together with single quantum methyl 1H-13C 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.

Original languageEnglish (US)
Pages (from-to)434-442
Number of pages9
JournalJournal of Structural Biology
Volume174
Issue number3
DOIs
StatePublished - Jun 2011

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Proteins
Amino Acids
Membrane Proteins
Pharmaceutical Preparations

Keywords

  • Assignment free
  • NMR
  • Protein-protein docking
  • Protein-protein interaction
  • Time-sharing measurements
  • TROSY

ASJC Scopus subject areas

  • Structural Biology

Cite this

Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements. / Kodama, Yuya; Reese, Michael L.; Shimba, Nobuhisa; Ono, Katsuki; Kanamori, Eiji; Dötsch, Volker; Noguchi, Shuji; Fukunishi, Yoshifumi; Suzuki, Ei ichiro; Shimada, Ichio; Takahashi, Hideo.

In: Journal of Structural Biology, Vol. 174, No. 3, 06.2011, p. 434-442.

Research output: Contribution to journalArticle

Kodama, Yuya ; Reese, Michael L. ; Shimba, Nobuhisa ; Ono, Katsuki ; Kanamori, Eiji ; Dötsch, Volker ; Noguchi, Shuji ; Fukunishi, Yoshifumi ; Suzuki, Ei ichiro ; Shimada, Ichio ; Takahashi, Hideo. / Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements. In: Journal of Structural Biology. 2011 ; Vol. 174, No. 3. pp. 434-442.
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