Theoretical Investigation Of The Mechanism Of Chlorite Dismutase-catalyzed Reaction Of Non-natural Substrate

Heme-binding proteins and enzymes are a significant fraction of metalloproteins. They conduct the remarkable diversity of biochemical functions, working in oxidation/reduction, proton/electron transfer, monoxygenation, chlorination, small-molecule sensing, heme trafficking, etc. In this thesis, using unrestricted density functional theory(UDFT) with the B3 LYP functional, the decomposition of peracetic acid(PAA) catalyzed by heme-dependent chlorite dismutase(Cld) have been investigated. The energetics for the PAA reaction and the characterization of the transition states(TS) and intermediates involved are presented. The main results and conclusions are:(1) When pH=6, the Cld-catalyzed PPA reaction is revealed to proceed via a homolytic O-O bond cleavage to transiently form compound II(Cpd II) and acetate radical(OAc?), and a subsequent fast ET from Cpd II porphyrin to OAc? leading to compound I(Cpd I) and acetate anion. The second step of ET from Cpd II porphyrin to OAc? is rate-limiting with a overall energy barrier of 18.2 kcal/mol. The results highlight the importance of ET in heme chemistry and imply that the reaction mechanisms of heme enzymes may be masked by fast ET even if a key intermediate has been detected(like Cpd I in this case).(2) The reaction mechanism upon different hydrogen-bonding modes for the substrate were calculated. It has been found that the binding modes of the substrate do not change the reaction mechanism significantly.(3) When pH=8, the overall barrier is predicted to be 19.2 kcal/mol(1.4 kcal/mol higher than the case of pH = 6), showing that the protonated Arg183 gives a stronger stabilization to the leaving OAc?, thus promoting the decomposition of PAA.(4) The comparison with the Cld-catalyzed reaction of chlorite further indicates the Cld reaction mechanism is dependent on the electron affinity of leaving groups, indicating the sensitivity of heme to substrates, that is, a heme enzyme may employ different mechanisms for different substrates.