The environment of multinuclear copper metal linkages in protein structures

Abstract

 The extended environment, particularly of the second shell about multinuclear copper centers in protein tertiary structures, can be described in terms of polarity, hydrophobicity, secondary structures, solvent accessibility, H-bonding networks, and the presence of statistically significant residue clusters (e.g., histidine-acidic, histidine-cysteine-methionine). Six protein structures with a multinuclear copper core are examined: ascorbate oxidase [oxidized (1aoz – Protein Data Bank (PDB) code) and reduced form (1aso)], ceruloplasmin (hCP – PDB number unassigned), hemocyanin (oxidized 1oxy and deoxygenated forms 1lla), and nitrite reductase (2afn). Analysis of these descriptors for these copper-containing proteins reveals both known and also previously undescribed and possible functionally important features. The novel features are firstly that the trinuclear copper complex in ascorbate oxidase and in ceruloplasmin are similar in that each structure is coordinated in the same 3D orientation by four histidine pairs in the same primary sequence arrangement. By contrast, the second shell of (1aoz) is predominantly polar augmented with three water molecules, whereas the second shell of (hCP) is predominantly hydrophobic. Both structures possess a histidine-acidic cluster overlapping the trinuclear copper environment and extending to a nearby (about 13 Å away) blue copper (type I) center. While the acidic residues in this cluster are not copper ligands, in (hCP) they putatively bind iron ions as part of the enzyme ferroxidase activity. Ceruloplasmin also contains two other separated type I copper ions, and there is a distinctive cysteine-histidine-methionine residue cluster connecting these two separated copper environments. We also identified in ceruloplasmin a significant mixed-charge cluster on the protein surface distant from the several copper ions which may play a role in protein-protein interaction. The second shell of the oxidized dicopper hemocyanin is more hydrophilic than that of the reduced form, the latter being totally buried. The exclusive histidine-acidic and the methionine-cysteine-histidine clusters in nitrite reductase traverse the environment of the Cu (type I) and the nearby (12.7 Å) functionally linked Cu (type II). Analysis of repeats in ceruloplasmin reveals a triple repeat consonant with the three copper type I occurrences but not consistent with the ligation patterns of the trinuclear copper complex, suggesting the possibility of alternative coordination ligand choices and/or alternative structural conformational outcomes.