A molecular dynamics investigation of the resting, hydrogen peroxide-bound and compound II forms of cytochrome C peroxidase and Artromyces ramosus peroxidase

Abstract

Molecular Dynamics (MD) simulations have been used to study structural and dynamic properties of the resting, hydrogen peroxide adduct and compound II forms of cytochrome C peroxidase (CCP) and Artromyces ramosus peroxidase (ARP). MD simulations of CCP show that: (i) hydrogen peroxide might form an outer sphere complex within the active site of the enzyme before the coordination to the iron centre takes place; (ii) Trp51 and His52 residues play a crucial role in the recognition and binding of hydrogen peroxide, while Arg48 is not directly involved; (iii) distal histidine (His52) allows an easy proton 1,2 shift within the H2O2 molecule, while Arg48 is not expected to play a role as crucial as His52 in promoting the heterolytic O–O bond breaking; (iv) the large mobility (about 2Å) of the side chain of Arg48 in the compound II form allows the formation of a hydrogen bond (H-bond) with the ferryl oxygen, which contributes to the stabilisation of such an intermediate. The active site of the ARP enzyme is characterised by structural and dynamic features slightly different from the CCP active site. In particular, (i) the outer sphere complex with hydrogen peroxide occurring in CCP is not observed in ARP because of the substitution of Trp51 of CCP with the more hydrophobic residue Phe55 of ARP; (ii) His56 and the carbonyl group of Arg52 are determinant in controlling the hydrogen peroxide binding and its orientation in the active site. In ARP, both H2O2 and His56 have orientation different than in CCP, but still suited for an easy 1,2 proton shift. (iii) Arg52 in ARP is on average more distant from the heme-iron than in CCP, but its relative orientation is suited to promote an easy cleavage of H2O2. (iv) In compound II form of ARP, the Arg52 side chain is too far from the oxy-ferryl group to form a hydrogen bond and therefore ARP looses a stabilising factor, which is present in the corresponding form of CCP.