10.1021/acs.jproteome.6b00624.s001 Lingfei Zeng Lingfei Zeng Woong-Hee Shin Woong-Hee Shin Xiaolei Zhu Xiaolei Zhu Sung Hoon Park Sung Hoon Park Chiwook Park Chiwook Park W. Andy Tao W. Andy Tao Daisuke Kihara Daisuke Kihara Discovery of Nicotinamide Adenine Dinucleotide Binding Proteins in the Escherichia coli Proteome Using a Combined Energetic- and Structural-Bioinformatics-Based Approach American Chemical Society 2016 NAD binders software Patch-Surfer 2.0. filter-assisted sample preparation Nicotinamide Adenine Dinucleotide Binding Proteins nicotinamide adenine dinucleotide Escherichia coli Proteome Escherichia coli proteome FASP pulse proteolysis NAD-binding proteins 12 proteins 2016-11-18 00:00:00 Journal contribution https://acs.figshare.com/articles/journal_contribution/Discovery_of_Nicotinamide_Adenine_Dinucleotide_Binding_Proteins_in_the_Escherichia_coli_Proteome_Using_a_Combined_Energetic-_and_Structural-Bioinformatics-Based_Approach/4286204 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.