Discovery of Nicotinamide Adenine Dinucleotide Binding Proteins in the Escherichia coli Proteome Using a Combined Energetic- and Structural-Bioinformatics-Based Approach.
Protein-ligand interaction plays a critical role in regulating the biochemical functions of proteins. Discovering protein targets for ligands is vital to new drug development. Here, we present a strategy that combines experimental and computational approaches to identify ligand-binding proteins in a proteomic scale. For the experimental part, we coupled pulse proteolysis with filter-assisted sample preparation (FASP) and quantitative mass spectrometry. Under denaturing conditions, ligand binding affected protein stability, which resulted in altered protein abundance after pulse proteolysis. For the computational part, we used the software Patch-Surfer2.0. We applied the integrated approach to identify nicotinamide adenine dinucleotide (NAD)-binding proteins in the Escherichia coli proteome, which has over 4200 proteins. Pulse proteolysis and Patch-Surfer2.0 identified 78 and 36 potential NAD-binding proteins, respectively, including 12 proteins that were consistently detected by the two approaches. Interestingly, the 12 proteins included 8 that are not previously known as NAD binders. Further validation of these eight proteins showed that their binding affinities to NAD computed by AutoDock Vina are higher than their cognate ligands and also that their protein ratios in the pulse proteolysis are consistent with known NAD-binding proteins. These results strongly suggest that these eight proteins are indeed newly identified NAD binders.
Lingfei
L
Zeng
Woong-Hee
WH
Shin
School of Life Science, Anhui University , Hefei, Anhui 230601, China.
Xiaolei
X
Zhu
Research Institute of Food and Biotechnology, SPC Group , Seoul 06737, South Korea.
Sung Hoon
SH
Park
Chiwook
C
Park
W Andy
0000-0002-5535-5517
WA
Tao
Daisuke
0000-0003-4091-6614
D
Kihara
D045424:Complex Mixtures / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D008024:Ligands; D062105:Molecular Docking Simulation; D009243:NAD / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D055550:Protein Stability; D059748:Proteolysis; D020543:Proteome / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012984:Software; D013820:Thermolysin / Q000737:chemistry
D045424:Complex Mixtures; D029968:Escherichia coli Proteins; D008024:Ligands; D020543:Proteome; D009243:NAD; D013820:Thermolysin
Patch-Surfer2.0; binding pocket comparison; binding pocket screening; protein−ligand interaction; pulse proteolysis; quantitative mass spectrometry; structural bioinformatics; tandem mass tags labeling