A computational study of ion binding and protonation states in the KcsA potassium channel

We report results from microscopic molecular dynamics and free energy pertu rbation simulations of the KcsA potassium channel based on its experimental atomic structure. Conformational properties of selected amino acid residue s as well as equilibrium positions of K+ ions inside the selectivity filter and the internal water cavity are examined. Positions three and four (coun ting from the extracellular site) in the experimental structure correspond to distinctly separate binding sites for K+ ions inside the selectivity fil ter. The protonation states of Glu71 and Asp80, which are close to each oth er and to the selectivity filter, as well as K+ binding energies are determ ined using free energy perturbation calculations. The Glu71 residue which i s buried inside a protein cavity is found to be most stable in the neutral form while the solvent exposed Asp80 is ionized. The channel altogether exo thermically binds up to three ions, where two of them are located inside th e selectivity filter and one in the internal water cavity. Ion permeation m echanisms are discussed in relation to these results. (C) 2000 Elsevier Sci ence B.V. All rights reserved.