Exploring the Reaction Surface of Cu(I) Transfer from Atx1 to Ccc2a Protein: A Theoretical Study

In this study, a detailed mechanism for the copper transfer between the yeast Atx1 and Ccc2a (P-type-ATPase) is proposed. To explore the potential energy surface (PES) of the reaction pathway, the density functional theory (DFT)-based B3LYP/6-31+G**_∪Lanl2DZ method was used for the active site model. The effect of protein environment on the reaction pathway was unraveled by Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM model) using B3LYP/6-31+G**_∪Lanl2DZ:UFF method. Results obtained from the calculations unveil the formation of kinetically stable 3-coordinated intermediate IM3(ONIOM). It also provides information on the irreversibility of Cu(I) transfer from Atx1 to Ccc2a domain. The proposed mechanism enables us to understand the rate-determining step and activation barrier of the transfer, which is 14.15 kcal/mol for active site model and 22.87 kcal/mol for ONIOM model. It is evident from NBO analysis that the interaction between K65-Atx1 and Cu(I)–S₃ unit is mediated by the water molecule, which is responsible for the stabilization of the 3-coordinate intermediate (IM3). These results provide a new insight into the Cu(I) transfer mechanism in chaperones.