Determination of the Catalytic Pathway of a Manganese Arginase Enzyme Through Density Functional Investigation

Abstract

The catalytic mechanism of dimanganese-containing arginase enzyme has been investigated by DFT calculations. Two exchange-correlation functionals, B3 LYP and MPWB1 K, have been used to construct the potential energy profiles for the hydrolysis of an arginine substrate performed by an arginase active site model system. Two reaction mechanisms have been investigated, one involving a water molecule (mechanism 1) and the other involving a hydroxide ion (mechanism 2) as nucleophilic agent. Results obtained in the gas phase and in the protein environment have indicated that mechanism 1 involving a water molecule entails structural features as well as an activation energy for the rate-determining step that are inconsistent with experimental data available for the arginase enzyme. On the other hand, when a hydroxide ion is present at the Mn2 site, a lower activation energy and a structural arrangement closer to the experimental indication are obtained.

The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases

“…This tendency has been previously noted in other enzymes for the hydrogen-transfer process and depends on the functional used for computations, namely B3LYP. As discussed in the previous manuscript, this anomalous trend was fixed adopting other functionals [150]. As discussed in the previous manuscript, this anomalous trend was fixed adopting other functionals [150].…”

“…As discussed in the previous manuscript, this anomalous trend was fixed adopting other functionals [150]. As discussed in the previous manuscript, this anomalous trend was fixed adopting other functionals [150].…”

Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation

“…The effect of the rest of the enzyme and solvent environment can be modelled, as noted previously, with explicit water molecules or through a dielectric constant using an implicit solvation model, such as IEF‐PCM, C‐PCM, the C‐PCM closely related COSMO, etc. According to previous studies on active sites in proteins, an empirical dielectric constant of 4 gives good agreement with experimental results, and accounts for the average effect of both the protein and buried water molecules . In spite of the limitations of the cluster model, this approach has already proven to be quite a powerful and useful tool in the study of enzymatic reactions.…”

“…In spite of the limitations of the cluster model, this approach has already proven to be quite a powerful and useful tool in the study of enzymatic reactions. A number of important problems have been solved already and it is not difficult to predict that many more questions will be answered in the future . When model systems contain more than 250 atoms, in general, high‐level quantum chemical calculations cannot be used on the whole system because of the high computational cost and hardware limitations.…”

Manganese Transport, Trafficking and Function in Invertebrates

“…2,[35][36][37][38][39][40][41][42][43][44][45] Manganese-dependent enzymes that participate in these processes typically utilize manganese in Lewis acid-base reactions or as a reduction/oxidation center to facilitate catalysis. These types of reaction are exemplified by arginase (Lewis acid) and Mn superoxide dismutase (reduction/oxidation), 2,3,46,47 and the role of manganese in these reactions is shown in Figure 1 …”