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Targeted molecular dynamics of an open-state KcsA channel
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Image of FIG. 1.
FIG. 1.

Schematic of the KcsA channel immersed in a water/octane/water bilayer. The octane slab is comprised between the full lines. For clarity, only two of the four subunits in the pore region are shown. The selectivity filter , the cavity , the gate , the and helices, and the helices are labeled. The sequence of ions and water molecules is also drawn. Additional residues which appear in the resolution structure and not in resolution structure are shown in red cylinders.

Image of FIG. 2.
FIG. 2.

Skeleton of the crystallized closed-state protein modeled on the basis of the x-ray experiments (1K4C pdb file). Each group of carbons which are constrained during the targeted MD procedure is reported. These groups are detailed in Table I together with their associated constraint values. The red spots correspond to the known positions of the atoms in the open structure determined from EPR spectroscopy.

Image of FIG. 3.
FIG. 3.

Ramachandran plot of the open-state protein under constraint after targeted MD simulation. The two residues (Ala229 and Leu189) which are in generously allowed regions are shown while all the other residues are located in allowed regions.

Image of FIG. 4.
FIG. 4.

Root mean square displacements (in angstrom) of the protein backbone, the filter, the and the helices along the overall production phase of the dynamics . The evolution of values on groups 2 and 3 is indicated on the top axis while the corresponding simulation times are reported on the bottom axis.

Image of FIG. 5.
FIG. 5.

Separation distance between Leu110 and Leu213 and His124 and His227. While the Leu residues are located close to the narrow region of the presumed gate on the helices, the His residues are at the end of the helices in the intracellular side. The rapid increase of these distances and their different behavior with the constraint undoubtedly show that the pore opens like a zip starting from His residues.

Image of FIG. 6.
FIG. 6.

Separation distance between Leu110 and Leu213 and Leu316 and Leu419 showing the symmetric behavior of the pore opening.

Image of FIG. 7.
FIG. 7.

Superimposition of the open-state structure (red) obtained in conditions and the relaxed structure obtained in (black). In this latter structure, the constraint is only applied on the carbons known from the 1JQ1 structure.

Image of FIG. 8.
FIG. 8.

Separation distance between (a) Leu couples [Leu110, Leu213) and (Leu316, Leu419)] and (b) His couples [(His124, His227) and (His330, His433) showing the asymmetric behavior of the pore during relaxation of the open-state structure (i.e., releasing the constraint).

Image of FIG. 9.
FIG. 9.

Root mean square displacements associated to the file of ions and water molecules. After a few picoseconds of relaxation, large motions are observed whatever the ensemble or and whatever the removing procedure of the constraint.


Generic image for table
Table I.

Constraint values applied to the positions of the atoms belonging to selected groups during the opening of the channel (cf. Fig. 2).


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Targeted molecular dynamics of an open-state KcsA channel