title: In silico and experimental validation of protein-protein interactions between PknI and Rv2159c from Mycobacterium tuberculosis.
abstract: Protein-protein interactions control the diverse and essential molecular processes inside the cell. To maintain the cellular physiology, protein kinases not only signal their substrates through reversible phosphorylation, but they also physically interact with them. PknI, a serine/threonine protein kinase of Mycobacterium tuberculosis is known to be important for cellular homoeostasis. In this study, we have identified the interacting proteins for PknI. We screened for proteins interacting with PknI using an in vitro assay, Far-western blot. This protein kinase specifically interacts with two peroxidase proteins of M. tuberculosis, Rv2159c and Rv0148. The PknI-Rv2159c interaction pair was further studied for the critical amino acid residues in Rv2159c that are responsible for the interaction. Rv2159c, a hypothetical protein is predicted to be an antioxidant with peroxidase activity. We performed homology modelling of Rv2159c protein and molecular docking using multiple docking servers such as Z-Dock and ClusPro. Further, the most favorable conformation of PknI-Rv2159c interaction was obtained using molecular dynamics simulation. The critical amino acid residues of the Rv2159c involved in interaction with PknI were identified. Mutation and docking analysis showed that the Ala1-Gly2-Trp3 residues in Rv2159c structure are responsible for the interaction. The free binding energy between the wild type and mutant complexes using MM-GBSA has provided insight about the stability of PknI-Rv2159c interaction. We propose that, PknI physically interacts with Rv2159c both in vitro and in silico studies.
authors.affiliation: Department of Immunology, National Institute for Research in Tuberculosis, #1, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600 031, India.
authors.forename: Arunkumar
authors.initials: A
authors.lastname: Venkatesan
authors.affiliation: Department of Bioinformatics, National Institute for Research in Tuberculosis, #1, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600 031, India.
authors.forename: Sameer
authors.initials: S
authors.lastname: Hassan
authors.affiliation: Department of Immunology, National Institute for Research in Tuberculosis, #1, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600 031, India.
authors.forename: Kannan
authors.initials: K
authors.lastname: Palaniyandi
authors.affiliation: Department of Immunology, National Institute for Research in Tuberculosis, #1, Mayor Sathiyamoorthy Road, Chetpet, Chennai 600 031, India. Electronic address: sujatha.sujatha36@gmail.com.
authors.forename: Sujatha
authors.initials: S
authors.lastname: Narayanan
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D057927:Hydrophobic and Hydrophilic Interactions; D062105:Molecular Docking Simulation; D009169:Mycobacterium tuberculosis / Q000201:enzymology; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D011493:Protein Kinase C / Q000737:chemistry*; D017433:Protein Structure, Secondary; D037521:Virulence Factors / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; C578340:Rv2190c protein, Mycobacterium tuberculosis; D037521:Virulence Factors; C061570:protein kinase N; D011493:Protein Kinase C
keywords: Binding free energy; Homology modeling; Molecular dynamics; PknI; Protein docking; Protein–protein interaction