FMO calculations for zinc metalloprotease:Fragmentation of amino-acid residues coordinated to zinc ion

Abstract

We investigated electronic states of a complex of zinc metalloprotease ubiquitin ligase 2 (UBR2) with its peptide ligand using ab initio fragment molecular orbital (FMO) calculations. UBR2 possesses three Zn ions and several residues of UBR2 are coordinated to each Zn ion to form an active site of UBR2. To provide a precise description of these coordination bonds, we included these residues in the same fragment as Zn ion in FMO calculations. The results revealed that all coordinated residues should be included in the same fragment as Zn ion for obtaining the converged results. This fact can be applicable equally to metalloproteases including other metal ions.