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Probing mechanisms of resistance to the tuberculosis drug isoniazid: Conformational changes caused by inhibition of InhA, the enoyl reductase from Mycobacterium tuberculosis

¹ Graduate Program in Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794-3400, USA
² The Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, USA
³ Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA

(RECEIVED January 3, 2007; FINAL REVISION April 25, 2007; ACCEPTED May 1, 2007)

The front-line tuberculosis drug isoniazid (INH) inhibits InhA, the NADH-dependent fatty acid biosynthesis (FAS-II) enoyl reductase from Mycobacterium tuberculosis (MTB), via formation of a covalent adduct with NAD⁺ (the INH-NAD adduct). Resistance to INH can be correlated with many mutations in MTB, some of which are localized in the InhA cofactor binding site. While the InhA mutations cause a substantial decrease in the affinity of InhA for NADH, surprisingly the same mutations result in only a small impact on binding of the INH-NAD adduct. Based on the knowledge that InhA interacts in vivo with other components of the FAS-II pathway, we have initiated experiments to determine whether enzyme inhibition results in structural changes that could affect protein–protein interactions involving InhA and how these ligand-induced conformational changes are modulated in the InhA mutants. Significantly, while NADH binding to wild-type InhA is hyperbolic, the InhA mutants bind the cofactor with positive cooperativity, suggesting that the mutations permit access to a second conformational state of the protein. While cross-linking studies indicate that enzyme inhibition causes dissociation of the InhA tetramer into dimers, analytical ultracentrifugation and size exclusion chromatography reveal that ligand binding causes a conformational change in the protein that prevents cross-linking across one of the dimer–dimer interfaces in the InhA tetramer. Interestingly, a similar ligand-induced conformational change is also observed for the InhA mutants, indicating that the mutations modulate communication between the subunits without affecting the two conformational states of the protein that are present.

Keywords: enoyl reductase; InhA; fatty acid synthesis; isoniazid; Mycobacterium tuberculosis

Abbreviations: MTB, Mycobacterium tuberculosis; FAS-II, fatty acid synthase type two; INH, isoniazid; INH-NAD, isoniazid-NAD adduct; SE, sedimentation equilibrium; SV, sedimentation velocity.

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.062749007.

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