Investigation of Specific Binding Proteins to Photoaffinity Linkers for Efficient Deconvolution of Target Protein.
Photoaffinity-based target identification has received recent attention as an efficient research tool for chemical biology and drug discovery. The major obstacle of photoaffinity-based target identification is the nonspecific interaction between target identification probes and nontarget proteins. Consequently, the rational design of photoaffinity linkers has been spotlighted for successful target identification. These nonspecific interactions have been considered as random events, and therefore no systematic investigation has been conducted regarding nonspecific interactions between proteins and photoaffinity linkers. Herein, we report the protein-labeling analysis of photoaffinity linkers containing three photoactivatable moieties: benzophenone, diazirine, and arylazide. Each photoaffinity linker binds to a different set of proteins in a structure-dependent manner, in contrast to the previous conception. The list of proteins labeled by each photoaffinity linker was successfully used to eliminate the nonspecific binding proteins from target candidates, thereby increasing the success rate of target identification.
Department of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University , Seoul 151-747, Korea.
Jongmin
J
Park
Department of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University , Seoul 151-747, Korea.
Minseob
M
Koh
Department of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University , Seoul 151-747, Korea.
Ja Young
JY
Koo
Department of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University , Seoul 151-747, Korea.
Sanghee
S
Lee
Department of Biophysics and Chemical Biology/N-Bio Institute, Seoul National University , Seoul 151-747, Korea.|Department of Chemistry, Seoul National University , Seoul 151-747, Korea.
Seung Bum
SB
Park
D001577:Benzophenones / Q000737:chemistry*; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism*; D016503:Drug Delivery Systems; D013058:Mass Spectrometry; D015394:Molecular Structure; D019920:Photoaffinity Labels / Q000737:chemistry* / Q000378:metabolism*
D001577:Benzophenones; D002352:Carrier Proteins; D019920:Photoaffinity Labels; C047723:benzophenone