Dynamics and Stability of the Metal Binding Domains of the Menkes ATPase and Their Interaction with Metallochaperone HAH1

Abstract

Human copper-ATPases ATP7A and ATP7B are essential for intracellular copper homeostasis. The main roles of the Menkes protein, ATP7A, are the delivery of copper to the secretory pathway and the export of excess copper from the enterocytes. The N-terminal domain of membrane protein ATP7A consists of six repetitive sequences of 60-70 amino acids (Mnk1-Mnk6) that fold into individual metal binding domains (MBDs) and bind a single copper ion in the reduced Cu(I) form via two cysteine residues. The structure of each individual MBD is known from nuclear magnetic resonance experiments. Here, we were interested in the stability and dynamics of each isolated MBD in their apo and holo forms and their interactions with the soluble metallochaperone HAH1 that delivers copper to ATP7A. Using molecular dynamics simulations of the MBDs under different conditions, we show that some MBDs (Mnk1 and Mnk5) present large root-mean-square deviations from initial structures or large root-mean-square fluctuations, and great care has to be taken in setting up the simulations. We propose that the first MBD, Mnk1, probably important in the transfer of copper between the metallochaperone and ATPase, could be stabilized by interactions with other MBDs, including a domain located in the loop between Mnk1 and Mnk2. An important result of this work is the apparent direct correlation between the difference in the fluctuations of the metal binding site loop in its apo and holo forms and the measured affinity of the MBD for copper. This difference decreases from Mnk1 to Mnk6, Mnk4, and Mnk2 in this order. The study of the exposure to the solvent of the metal and the residues of the metal binding loop of the MBDs also shows different behavior for each MBD. In particular, copper in serine-rich domain Mnk3 and largely fluctuating domain Mnk5 appears to be more solvent-exposed than in the other MBDs. In the second part of this work, we investigated the importance of electrostatics in the MBD-chaperone interactions using different docking programs. Mnk1 and Mnk4 present a large electrostatic dipole moment and large stabilizing interaction energies with HAH1. Finally, we propose a model structure of ATP7A from Mnk6 (E561) to P1413 based on the crystal structure of LpCopA and docking simulations.