Estudo da flexibilidade da enzima InhA (EC 1.3.1.9) de Mycobacterium tuberculosis por simulações de dinâmica molecular

Abstract

The enzyme InhA of Mycobacterium tuberculosis, or 2-trans-enoyl-ACP (CoA) reductase (EC 1.3.1.9) is encoded by the inhA gene. This protein performs the fourth step of the pathway of synthesis of type II fatty acid (FAS II), which consists of monofunctional enzymes responsible for fatty acid precursor’s elongation producing long carbon chains of the meromycolate branch of mycolic acids. InhA converts 2-trans-enoyl-ACP to acyl-ACP by means of a hydride (H-) the transfer from NADH to the C3 position of the 2-trans-enoyl-ACP substrate, resulting in reduction of the double α-thioester bond (between C2 and C3) of the substrate´s lipid portion. This reaction can occur in a carbon chain ranging from 16-56 carbons. This substrate sizes’ range highlights the importance of the substrate binding cavity flexibility for InhA proper functioning. The topology of this enzyme is hair-like, characterized by a seven-strand β-sheet and eight α-helices, in a αβα sandwich architecture, forming the NADH coenzyme-binding site and the substrate-binding cavity. This cavity, in turn, is formed by three structural loops: loops A and B, and the substrate-binding loop. This structural composition is of fundamental importance for the functioning of InhA. It must be flexible enough to allow adaptation to substrates of varying sizes. Investigation of this flexibility is paramount for a better comprehension of which conformational features may be involved in the opening and closing events of its substrate-binding cavity. In this work, a computational method is used, through Molecular Dynamics simulations, to evaluate the flexibility of the substrate-binding cavity of the InhA enzyme and analyze the respective conformational changes.