Research On Conformational Changes During Nak Channel Opening

The report of the crystal structure of KcsA in 1998 contributes to the breakthrough in revealing the atomic scale mechanisms of selectivity of potassium channels, after that, more and more attention was drawn to their gating properties. However, due to a lack of single channel crystal structures in both closed and open conformations, many dynamic properties concerning channel gating remain unclear. It provides a good opportunity to study potassium channel gating owing to the determination of the NaK channel structure of closed and open states in 2006 and 2009, respectively. In this thesis, by performing a targeted MD simulation stretching the closed structure of the NaK channel towards its open structure, I have two important findings.Firstly, we proposed a new GIG hinge model and use this model to explain the decoupling mechanism of twist and bending motions. Previous models either support bend opening, twist opening or regular bend/twist opening, whereas I find in the NaK channel gating that twist and bending motions starts in different sites of the inner helix, twist motions concentrate in the GIG motif; bending motions starts in V91 beneath the hinge. On the other hand, twist and bending motions changes differently along the inner helix, twist starts quickly in the GIG motif and changes to its maximum degree, but remains unchanged beneath the hinge; while bending increases linearly along the length of the inner helix until the C-terminal. This decoupling mechanism between bending and twist motions greatly contributes to our understanding of gating mechanisms of ion channels.Secondly, we analyzed the changes of the water permeating orifice and its blocking mechanisms during conformational changes of the NaK channel. The change of the diameter of the orifice is due to twisting motion in the inner helix and is constricted at residue V91. This mechanism differs from that of gate opening, which is contributed by both bending and twist motions in the inner helix. This finding specifies the differences and correlations between two"gates"of water permeation and explains their relations with conformational changes in the inner helix. About the blockage of the the orifice, the side chain benzene ring of F92 in the inner helix and F28 in the outer helix forms very stable interactions, which cause the blockage of the outer mouth of the orifice, this interaction is also very important for channel stabilization during its open state; Lacking the constriction from inter-subunit Hydropobic Patch, the benzene ring in the side chain of F92 swings irrugularly and causes random blockage of the inner mouth of the orifice.