The first branching point in porphyrin biosynthesis: A systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen‐III decarboxylase

Abstract

In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol(-1) at 298.15 K. The rate-limiting step was found to be the initial proton transfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various active site residues as well as several other functional groups.

A Multi-Scale Computational Study on the Mechanism of Streptococcus pneumoniae Nicotinamidase (SpNic)

“…This annealing process was stopped after a further 50 ps interval held at 300 K. The final structure from the trajectory was then optimized using the AMBER99 force field. We have successfully used this MD protocol in studies on other enzymes [28,29].…”

“…The α-carbon of each residue in the MM-layer was held fixed at its final AMBER99 optimized position (see above). This computational approach has been successfully applied in studies on related enzymatic systems [28].…”

A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums

“…This structure was then optimized with the CHARMM22 force field and used to obtain a suitable enzyme complex for further investigation (see below). We have successfully applied this MD protocol in the study of other enzymatic systems [55]. …”

“…To ensure the integrity of the active site model during calculations, the α-carbons of each residue as well as that of the capping methyl in NAD + were held fixed at their final CHARMM22 optimized positions (see above). This computational approach has been widely used previously, and successfully applied in studies on related enzymatic systems [55]. …”

The Importance of the MM Environment and the Selection of the QM Method in QM/MM Calculations

“…Uroporphyrinogen decarboxylase (UROD) is yet another example of catalytic rate enhancement. This enzyme performs the quadruple decarboxylation of its substrate URO-III in mere seconds (Bushnell, Erdtman, Llano, Eriksson, & Gauld, 2011). In the absence of this enzyme, the half-life for this same reaction (under standard conditions in solution) is 2.3 billion years (Lewis & Wolfenden, 2008).…”