UC Davis

Hydrogenases are a family of enzymes that catalyze the reversible redox reaction of molecule hydrogen (H2). There are several kinds of hydrogenases, including [Fe] hydrogenases, [NiFe] hydrogenases, and [FeFe] hydrogenases, found in a variety of organisms. Hydrogenases have attracted much attention from chemists, physicists, and biologists due to their special roles in energy metabolism, as they can produce the cleanest carbon-neutral fuel, H2. Among these hydrogenases, [FeFe] hydrogenases are characterized by their special di-iron ([FeFe]) cluster called the “H-cluster”. The maturation process of the [FeFe] hydrogenases is the biosynthesis of the H-cluster by the enzymes HydE, HydF, and HydG, and the delivery of the H-cluster into HydA. In this thesis, we describe hybrid quantum mechanics (QM)/ molecular mechanics (MM) simulations of the maturation process, including the catalytic processes in HydG and HydE. The results were published in Biochemistry journal as an article titled ”Quantum chemical study of a radical relay mechanism for the HydG-catalyzed synthesis of a Fe(II)(CO)2(CN)cysteine precursor to the H-cluster of [FeFe] hydrogenase”. We proposed a radical-relay mechanism for how HydG catalyzes the decomposition of the tyrosine substrate into COO•− and HCN. These species are converted into CO and CN at the [5Fe-5S] auxiliary cluster in HydG, which bind to the fifth “dangler” Fe and result in the [Fe(II)(CO)2(CN)cysteine] “synthon” product. HydE, as the downstream protein of HydG, modifies this Fe(II) complex into a 5-coordinate Fe(I) cluster via a radical mechanism. Using QM/MM simulations we proposed a feasible radical mechanism for this conversion, as well as a dimerization pathway from the 5-coordinated Fe(I) cluster to a diamagnetic di-iron cluster that is proposed to be the product of HydE.In addition, studies have been done to understand the behavior of a circadian clock protein, KaiB. KaiB is a key component of the KaiABC circadian clock system in cyanobacteria. KaiB changes its folding to bind to KaiA and KaiC respectively to adjust the expression of different kinase proteins. The folding change in KaiB, also named fold-switching, is classified as metamorphic behavior because it involves changes between the secondary structures and three-dimensional structures in contrast to conventional protein conformational changes. Classical, all-atom molecular dynamics simulations exceeding (>100 μs) in length were carried out to study the fold-switching process of the KaiB in explicit solvent. We also developed a new feature, named diversity index (DI), that can distinguish the metamorphic protein sequences from other monomorphic sequences (i.e. one native fold sequences), and this work was published in Biophysical Journal in 2021 titled ”Sequence-based Prediction of Metamorphic Behavior in Proteins”.