Probing the environment of Cu B in heme-copper oxidases

Abstract

Time-resolved step-scan FTIR (TRS 2-FTIR) and density functional theory have been applied to probe the structural dynamics of Cu B in heme-copper oxidases at room temperature. The TRS 2-FTIR data of cbb 3 from Pseudomonas stutzen indicate a small variation in the frequency of the transient CO bound to Cu B in the pH/pD 7-9 range. This observation in conjunction with density functional theory calculations, in which significant frequency shifts of the v(CO) are observed upon deprotonation and/or detachment of the Cu B ligands, demonstrates that the properties of the CU B ligands including the cross-linked tyrosine, in contrast to previous reports, remain unchanged in the pH 7-9 range. We attribute the small variations in the v(CO) of CUB to protein conformational changes in the vicinity of Cu B. Consequently, the split of the heme Fe-CO vibrations (a-, β-, and γ-forms) is not due to changes in the ligation and/or protonation states of the Cu B ligands or to the presence of one or more ionizable groups, as previously suggested, but the result of global protein conformational changes in the vicinity of Cu B which, in turn, affect the position of Cu B with respect to the heme Fe