Evaluating how rimantadines control the proton gating of the influenza A M2-proton port via allosteric binding outside of the M2-channel: MD simulations

Abstract

In order to understand how rimantadine (RMT) inhibits the proton conductance in the influenza A M2 channel via the recently proposed “allosteric mechanism”, molecular dynamics simulations were applied to the M2-tetrameric protein with four RMTs bound outside the channel at the three protonation states: the 0H-closed, 1H-intermediate and 3H-open situations. In the 0H-closed state, a narrow channel with the RMT-Asp44-Trp41 H-bond network was formed, therefore the water penetration through the channel was completely blocked. The Trp41-Asp44 interaction was absent in the 1H-intermediate state, whilst the binding of RMT to Asp44 remained, which resulted in a weakened helix-helix packing, therefore the channel was partially prevented. In the 3H-open state it was found that the electrostatic repulsion from the three charged His37 residues allowed the Trp41 gate to open, permitting water to penetrate through the channel. This agreed well with the potential of the means force which is in the following order: 0H > 1H > 3H.

Keywords::

• H1N1 strain
• protonation state
• potential of means force
• proton transport

Acknowledgements

P.I. thanks the Post-Doctoral programme from the Commission on Higher Education. S.H. thanks the Centre of Excellence for Petroleum, Petrochemicals, and Advanced Materials, Chulalongkorn University. Research facilities, software packages and computing time were provided by the Computer Centre for Advanced Research and the Computational Chemistry Unit Cell, Faculty of Science, Chulalongkorn University. Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR-01081).

Declaration of interest

This work was supported by The Thailand Research Fund.