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.