The C-terminal cavity of the Na,K-ATPase analyzed by docking and electrophysiology

Abstract

The Na,K-ATPase is essential to all animals, since it maintains the electrochemical gradients that energize the plasma membrane. Naturally occurring inhibitors of the pump from plants have been used pharmaceutically in cardiac treatment for centuries. The inhibitors block the pump by binding on its extracellular side and thereby locking it. To explore the possibilities for designing an alternative way of targeting the pump function, we have examined the structural requirements for binding to a pocket that accommodates the two C-terminal residues, YY, in the crystal structures of the pump. To cover the sample space of two residues, we first performed docking studies with the 400 possible dipeptides. For validation of the in silico predictions, pumps with 13 dipeptide sequences replacing the C-terminal YY were expressed in Xenopus laevis oocytes and examined with electrophysiology. Our data show a significant correlation between the docking scores from two different methods and the experimentally determined sodium affinities, which strengthens the previous hypothesis that sodium binding is coupled to docking of the C-terminus. From the dipeptides that dock the best and better than wild-type YY, it may therefore be possible to develop specific drugs targeting a previously unexplored binding pocket in the sodium pump.

Keywords::

• Na,K-ATPase
• drug target
• regulation
• electrophysiology
• docking
• C-terminus

Acknowledgements

This study was funded by the European Drug Initiative on Channels and Transporters (EDICT) program. PUMPKIN is a Center of Excellence funded by the Danish National Research Foundation. PN was supported by the ERC Advanced program BIOMEMOS. HP was supported by grants from the Carlsberg Foundation, the Lundbeck Foundation and L'Oréal/UNESCO. RA was supported by ERC grant 209825. We are grateful to A. Skov Kristensen and M. H. Poulsen (University of Copenhagen) for supplying oocytes and to M. V. Clausen for discussions on electrogenic transport.

Declaration of interest: The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.