On the Role of Tyrosine as Catalytic Base in Nitrile Hydratase

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

A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site.

Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications

Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for zinc complexes

A set of 44 Zinc-ligand bond-lengths and of 60 ligand-metal-ligand bond angles from 10 diverse transition-metal complexes, representative of the coordination spheres of typical biological Zn systems, were used to evaluate the performance of a total of 18 commonly available density functionals in geometry determination. Five different basis sets were considered for each density functional, namely two all-electron basis sets (a double-zeta and triple-zeta formulation) and three basis sets including popular types of effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden. The results show that there are presently several better alternatives to the popular B3LYP density functional for the determination of Zn-ligand bond-lengths and angles. BB1K, MPWB1K, MPW1K, B97-2 and TPSS are suggested as the strongest alternatives for this effect presently available in most computational chemistry software packages. In addition, the results show that the use of effective-core potentials (in particular Stuttgart-Dresden) has a very limited impact, in terms of accuracy, in the determination of metal-ligand bond-lengths and angles in Zinc-complexes, and is a good and safe alternative to the use of an all-electron basis set such as 6-31G(d) or 6-311G(d,p).