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The crystal structure of the NADH:quinone oxidoreductase PA1024 has been solved in complex with NAD + to 2.2 Å resolution. The nicotinamide C4 is 3.6 Å from the FMN N5 atom, with a suitable orientation for facile hydride transfer. NAD + binds in a folded conformation at the interface of the TIM-barrel domain and the extended domain of the enzyme. Comparison of the enzyme-NAD + structure with that of the ligand-free enzyme revealed a different conformation of a short loop (75-86) that is part of the NAD + -binding pocket. P78, P82, and P84, provide internal rigidity to the loop, whereas Q80 serves as an active site latch that secures the NAD + within the binding pocket. An interrupted helix consisting of two α-helices connected by a small threeresidue loop binds the pyrophosphate moiety of NAD + . The adenine moiety of NAD + appears to π-π stack with Y261. Steric constraints between the adenosine ribose of NAD + , P78, and Q80, control the strict specificity of the enzyme for NADH. Charged residues do not play a role in the specificity of PA1024 for the NADH substrate.

Changes in the concentration of different ions modulate several cellular processes, such as Ca(2+) and Zn(2+) in inflammation. Upon activation of immune system effector cells, the intracellular Ca(2+) concentration rises propagating the activation signal, leading to degranulation and generation of reactive oxygen species, which increases the Zn(2+) intracellular concentration as a consequence of the cellular antioxidant machinery. In this context, S100A12 is of special interest because it is a pro-inflammatory protein expressed in neutrophils whose structure and function are modulated by both Ca(2+) and Zn(2+). The current hypothesis about its mechanism of action was built based on biochemical and crystallographic data. However, there are missing connections between molecular structure and the way in which many events are concatenated at the triggering and along the inflammatory process. In this work we use molecular dynamics simulations to describe how variations in Zn(2+) and Ca(2+) concentrations modulate the structural dynamics of the calcium-free S100A12 dimer and monomer, which was not considered a part of the mechanism of action before. Our results suggest that (i) Zn(2+) have a determinant role in the dimerization step, as well as in the unbinding of the Na(+) complexed to the N-terminal EF-hand; (ii) the N-terminal EF-hand domain is the first to bind Ca(2+), and not the C-terminal, as usually accepted; and that (iii) Ca(2+) modulates the structural dynamics of H-III.

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Proteins are inherently dynamic, and proper enzyme function relies on conformational flexibility. In this study, we demonstrated how an active site residue changes an enzyme’s reactivity by modulating fluctuations between conformational states. Replacement of tyrosine 249 (Y249) with phenylalanine in the active site of the flavin-dependent d-arginine dehydrogenase yielded an enzyme with both an active yellow FAD (Y249F-y) and an inactive chemically modified green FAD, identified as 6-OH-FAD (Y249F-g) through various spectroscopic techniques. Structural investigation of Y249F-g and Y249F-y variants by comparison to the wild-type enzyme showed no differences in the overall protein structure and fold. A closer observation of the active site of the Y249F-y enzyme revealed an alternative conformation for some active site residues and the flavin cofactor. Molecular dynamics simulations probed the alternate conformations observed in the Y249F-y enzyme structure and showed that the enzyme variant with FAD samples a metastable conformational state, not available to the wild-type enzyme. Hybrid quantum/molecular mechanical calculations identified differences in flavin electronics between the wild type and the alternate conformation of the Y249F-y enzyme. The computational studies further indicated that the alternate conformation in the Y249F-y enzyme is responsible for the higher spin density at the C6 atom of flavin, which is consistent with the formation of 6-OH-FAD in the variant enzyme. The observations in this study are consistent with an alternate conformational space that results in fine-tuning the microenvironment around a versatile cofactor playing a critical role in enzyme function.