A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

Bhagavat, Raghu; Kim, Heung -Bok; Kim, Chang -Yub; Terwilliger, Thomas Charles; Mehta, Dolly; Srinivasan, Narayanaswamy; Chandra, Nagasuma

doi:10.1038/s41598-017-12471-8

Title: A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis

Journal Article · Mon Oct 02 00:00:00 EDT 2017 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-017-12471-8· OSTI ID:1411357

Bhagavat, Raghu ^[1];

^[2];

^[2]; Mehta, Dolly ^[1]; Srinivasan, Narayanaswamy ^[3]; Chandra, Nagasuma ^[1]

National Mathematics Initiative, Bangalore (India)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Molecular Biophysics Unit Indian Institute of Science, Bangalore (India)

Nucleoside tri-phosphates (NTP) form an important class of small molecule ligands that participate in, and are essential to a large number of biological processes. Here, we seek to identify the NTP binding proteome (NTPome) in M. tuberculosis (M.tb), a deadly pathogen. Identifying the NTPome is useful not only for gaining functional insights of the individual proteins but also for identifying useful drug targets. From an earlier study, we had structural models of M.tb at a proteome scale from which a set of 13,858 small molecule binding pockets were identified. We use a set of NTP binding sub-structural motifs derived from a previous study and scan the M.tb pocketome, and find that 1,768 proteins or 43% of the proteome can theoretically bind NTP ligands. Using an experimental proteomics approach involving dye-ligand affinity chromatography, we confirm NTP binding to 47 different proteins, of which 4 are hypothetical proteins. Our analysis also provides the precise list of binding site residues in each case, and the probable ligand binding pose. In conclusion, as the list includes a number of known and potential drug targets, the identification of NTP binding can directly facilitate structure-based drug design of these targets.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1411357

Report Number(s):: LA-UR-17-24509

Journal Information:: Scientific Reports, Vol. 7, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 5 works

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