Study of interactions between Mycobacterium tuberculosis proteins: SigK and anti-SigK

• Published in: Journal of molecular modeling Vol. 17; no. 5; pp. 1109 - 1119
• Main Authors: Malkhed, Vasavi, Gudlur, Bargavi, Kondagari, Bhargavi, Dulapalli, Ramasree, Vuruputuri, Uma
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.05.2011
• Subjects: Amino Acid Sequence; Antigens, Bacterial - genetics; Antigens, Bacterial - metabolism; Antitubercular Agents - chemistry; Antitubercular Agents - therapeutic use; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding Sites; Characterization and Evaluation of Materials; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; Gene Expression Regulation, Bacterial; Membrane Proteins - genetics; Membrane Proteins - metabolism; Models, Molecular; Molecular Dynamics Simulation; Molecular Medicine; Molecular Sequence Data; Mycobacterium bovis; Mycobacterium tuberculosis - chemistry; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - metabolism; Original Paper; Protein Binding; Protein Structure, Tertiary; Repressor Proteins - chemistry; Repressor Proteins - genetics; Repressor Proteins - metabolism; Rhodobacter sphaeroides; Sequence Homology, Amino Acid; Sigma Factor - chemistry; Sigma Factor - genetics; Sigma Factor - metabolism; Theoretical and Computational Chemistry; Transcription Factors - chemistry; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic; Tuberculosis - drug therapy; Tuberculosis - microbiology; Docking; RNA polymerase sigma factor sigma K; Molecular dynamics (MD) simulation; ECF subfamily; Anti-sigma K factor rskA; Homology modeling
• ISSN: 1610-2940; 0948-5023
• DOI: 10.1007/s00894-010-0792-7

The development of novel antituberculosis therapeutic molecules is a global health concern. Complex gene expression in Mycobacterium tuberculosis is mediated mainly by various sigma factors. The SigK protein binds to RNA polymerase, facilitating the expression of genes encoding the antigenic proteins mpt70 and mpt83. The anti-SigK protein is a negative regulator of SigK and inhibits the initiation of transcription. This study focuses on the interactions between SigK and the N-terminal domain of anti-SigK. The 3D structures of SigK (187 residues) and the N-terminal domain of anti-SigK (92 residues) are elucidated, using the crystal structures of the A and B chains of sigma E and anti-sigma ChrR of Rhodobacter spheroides (PDB code: 2Q1Z) as templates, respectively. Molecular dynamic simulations were performed for the SigK and anti-SigK proteins to refine their structures. The predicted active sites of SigK and anti-SigK and the results of protein–protein docking studies revealed the residues that are important for binding. The models generated and the binding site residues identified in this work throw new light on the interactions between the sigma K and anti-sigma K proteins, which should further aid the modulation of antigenic protein production in Mycobacterium tuberculosis .