MOLECULAR MODELING & DYNAMICS OF ION CHANNEL PROTEINS IN MEMBRANES

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Through the use of the modeling tools provided by the Computer Graphics Laboratory, we have been able to generate a number of different models of the Influenza A M2 ion channel. We have inserted this channel into model membrane systems, and have performed molecular dynamics simulations extending into the nanosecond timescale. Preliminary results indicate that the protein remains in an alpha helical bundle, and that the closed state of the protein keeps water from passing through the channel. We plan further structural studies on this, and related proteins for which the resources at the CGL will continue to play an important role. This work is also the focus of a major component of a program project grant to study the molecular mechanisms leading to anesthesia. Our aim in this study is to elucidate the gating mechanism of M2 and to demonstrate the stability of a structural model of M2 in an explicit water-phospholipid bilayer system. We have performed several molecular dynamics simulations each consisting of a trajectory at least one nanosecond long. Each simulation corresponded to a different protonation state of the histidine residues in the gate. The unprotonated and single protonated forms involved in the proton shuttle mechanism were found to be stable over the full length of the trajectory. Furthermore, the orientation of water molecules inside the channel was conducive to effective proton transfer. In contrast, the form in which all four histidine residues are protonated, required in the water-wire mechanism, was unstable and disassociated on a timescale of 400-700 picoseconds. These results demonstrate the proton shuttle involving histidine residues of the protein is the most likely mechanism of proton transport in the M2 channel.