Computational Study on Compound I Redox-Active Species in Horseradish Peroxydase Enzyme: Conformational Fluctuations and Solvation Effects

Abstract

Molecular dynamics simulations for the compound I species in horseradish peroxidase were carried out over a nanoseconds time-scale. Results indicate that the supramolecular assembly composed of compound I in interaction with highly conserved distal residues (His42 and Arg38) exists in two well-defined conformations basically differing in the local position of the distal histidine (i.e., His42). Furthermore, we observe the presence of a biological channel in the distal side of the heme cavity, between Arg38 and Pro139 residues, that represents a direct link connecting the compound I (CpdI) species to bulk molecules. Our investigation supports the idea that when CpdI is formed, the biological machinery relaxes the local electrostatic forces, opening a structural channel through which an exchange of water molecules with the bulk solvent takes place without any significant kinetic barrier. Interestingly, we also show that the combined effect of enzyme and solvent, modulated by thermal fluctuations, affects the order and the energy difference between the lowest doublet and quartet magnetic states of the CpdI-His42-Arg38 complex. Consequently, when passing from the gas phase to the biological environment, the doublet spin state becomes slightly more stable than the higher spin multiplicity state. The distribution of the perturbed low-lying states energy variation, induced by surrounding fluctuations, yields results rather close to that obtained by other state of the art quantum-mechanics/molecular mechanics calculations, and still in line with previous polarizable continuum calculations.

How Does Replacement of the Axial Histidine Ligand in Cytochrome c Peroxidase by Nδ-Methyl Histidine Affect Its Properties and Functions? A Computational Study

“…In particular, C c P Cpd I has a protein radical (on Trp 191 ), while HRP and APX have a heme-based radical. Extensive computational studies using density functional theory, quantum mechanics/molecular mechanics and molecular dynamics studies have been performed on the various stages of the catalytic cycle of peroxidases and particularly on Cpd I [ 44 , 45 , 46 , 47 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 ]. These studies ( Scheme 1 ) confirmed Cpd I as a triradical species with three unpaired electrons, whereby two of those are on the metal (in the π* xz and π* yz orbitals), while the third radical is non-metal based [ 53 , 57 , 61 ].…”