Protonation of the Copper(I) Form of the Blue Copper Proteins Plastocyanin and Amicyanin – A Molecular Dynamics Study

Abstract

The conformational space of the copper(I) forms of the cupredoxines amicyanin (ami) (Paracoccus versutus) and plastocyanin (pla) (Populus nigra) with a protonated histidine donor close to the C-terminus (“C-terminal histidine” ami: His96; pla: His87) was investigated with force field calculations that involve the experimentally determined structures of the protonated or unprotonated copper(I/II) forms: a setup of 36 conformers with a constrained torsional angle that involves the Cimidazole–Cmethylene (Cγ–Cβ) bond (chi2; 10° increments); strain energy minimization of all constrained conformers; a 10 ps molecular dynamics search around each conformer; constrained, followed by unconstrained optimization of each of the resulting low energy structures; cluster analysis of the resulting conformations. For both cupredoxines there are two major conformers which differ in their solvent accessibility. The plastocyanin and amicyanin structures are in excellent agreement with the experimentally observed crystallographic data; the two analyses lead to the proposal for a general mechanism for the protonation of reduced blue copper proteins. This is also in agreement with the results of a conformational analysis of a complex of the protonated copper(I) form of amicyanin with phosphate.