Amino acid selective cross-saturation method for identification of proximal residue pairs in a protein-protein complex

Journal of the American Chemical Society
Shunsuke IgarashiIchio Shimada

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 ub...Continue Reading

References

Feb 1, 1996·Journal of Molecular Graphics·R KoradiK Wüthrich
Sep 1, 1996·Journal of Biomolecular NMR·D S Waugh
Jul 16, 1999·The EMBO Journal·S C JohnstonC P Hill
Mar 4, 2000·Nature Structural Biology·H TakahashiI Shimada
Jun 8, 2002·Journal of Molecular Biology·Tamiji NakanishiIchio Shimada
Nov 26, 2002·Nature Structural Biology·Noritaka NishidaIchio Shimada
Nov 20, 2003·Journal of the American Chemical Society·Michael L Reese, Volker Dötsch
Nov 25, 2003·Nature Structural Biology·Helen BermanHaruki Nakamura
Jan 20, 2004·European Journal of Biochemistry·Christian KlammtFrank Bernhard
Jan 31, 2004·Journal of Biomolecular NMR·Jianxia ShiDavid E Wemmer
Feb 26, 2004·Journal of the American Chemical Society·Philip J HajdukBruce A Beutel
Aug 25, 2005·Journal of the American Chemical Society·Mariko YokogawaIchio Shimada
Feb 21, 2006·Current Opinion in Structural Biology·Alexandre M J J Bonvin
Mar 21, 2006·Current Opinion in Structural Biology·Jeffrey J Gray
Jul 11, 2006·Magnetic Resonance in Chemistry : MRC·David StauntonIain D Campbell
Mar 29, 2007·Journal of Biomolecular NMR·Koh TakeuchiGerhard Wagner
Aug 19, 2007·The EMBO Journal·Osamu IchikawaIchio Shimada
Jun 14, 1999·Angewandte Chemie·Moriz Mayer, Bernd Meyer

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Citations

May 2, 2014·Quarterly Reviews of Biophysics·Takumi UedaIchio Shimada
Dec 23, 2015·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Fabien FerrageDavid Cowburn
Sep 19, 2015·Scientific Reports·Shin-ichiro OzawaMasanori Osawa
Jan 13, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Toshihiko SugikiChojiro Kojima

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