Using Computer Simulations to Understand Enzyme Mechanism: Application to Mycobacterium tuberculosis CYP121 Unusual Reaction

DUMAS, VICTORIA GISEL; DEFELIPE, LUCAS ALFREDO; TURJANSKI, ADRIAN GUSTAVO; MARTI, MARCELO ADRIÁN

Santiago de Chile

Congreso; 2nd ISCB Latin America 2012 Conference on Bioinformatics; 2012

Understanding enzyme mechanism at molecular level is invaluable information in the field of protein inhibitor design, protein de novo engineering and general biochemistry. Computer simulation methods, mainly Quantum Mechanics (QM) and Classical Molecular Dynamics (MD) based methods, provide an extraordinary tool to study enzyme reaction mechanism, since they allow to actually simulate and see the reaction happen in the computer. Our group has over 10 years experience in the study of enzyme reactions, particularly for tough cases like metallo‐proteins that involve complex biochemical reactions. In the present talk we will present our recent finding on the unusual reaction performed by Mycobacterium tuberculosis (Mt) Cytochrome‐p450 protein 121 (CYP121) (see Fig Cytochromes of the p450 type are a large and ubiquitous family of heme proteins which usually catalyze oxidation (in most cases hydroxylation) of organic compounds. In mammals they are responsible for the metabolism of majority of pharmacological compounds, and they are also studied as potential antimicrobial targets or as potential enzymes for biotechnological purposes. Among the 20 cytochromes p450 encoded by Mt genome, CYP121 was encountered as essential for the viability of the bacilli, making it a potential target for antitubercular drugs design. Interestingly, the mechanism by which CYP121 carries out its activity remains unknown. There is evidence that indicates that this protein is responsible for catalyzing the formation of a C‐C bond between the two aromatic cycles of cyclopeptide cyclo(l‐Tyr‐l‐Tyr) (cYY) resulting in a new chemical entity, a reaction which is quite unusual for CYPs. In this work, we have used a combination of classical molecular dynamics (MD) and hybrid quantum‐classical (QM/MM) methodologies in order to elucidate the reaction mechanism carried out by this interesting and important protein.