Paper Citing NAMD - Abstract
Domene, Carmen; Klein, Michael L.; Branduardi, Davide; Gervasio, Francesco L.; Parrinello, Michele
Conformational changes and gating at the selectivity filter of potassium channels
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:9474-9480, JUL 23 2008
The translocation of ions and water across cell membranes is a prerequisite for many of life's processes. K(+) channels are a diverse family of integral membrane proteins through which K(+) can pass selectively. There is an ongoing debate about the nature of conformational changes associated with the opening and closing and conductive and nonconductive states of potassium (K(+)) channels. These changes depend on the membrane potential, the K(+) concentration gradient, and large scale motions of transmembrane helices and associated residues. Experiments also suggest that local structural changes in the selectivity filter may act as the dominant gate referred to as C-type inactivation. Herein we present an extensive computational study on KirBac, which supports the existence of a physical gate or constriction in the selectivity filter (SF) of K(+) channels. Our computations identify a new selectivity filter structure, which is likely associated with C-type inactivation. Specifically, the four peptide chains that comprise the filter adopt an unusual structure in which their dihedrals alternate between left- and right-handed Ramachandran angles, which also justifies the need for conservation of glycine in the K(+) selectivity filter, since it is the only residue able to play this bifunctional role.
