A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation

J Gen Physiol. 2013 Oct;142(4):451-63. doi: 10.1085/jgp.201311049. Epub 2013 Sep 16.

Abstract

Electrophysiological studies have established that the permeation of Ba(2+) ions through the KcsA K(+)-channel is impeded by the presence of K(+) ions in the external solution, while no effect is observed for external Na(+) ions. This Ba(2+) "lock-in" effect suggests that at least one of the external binding sites of the KcsA channel is thermodynamically selective for K(+). We used molecular dynamics simulations to interpret these lock-in experiments in the context of the crystallographic structure of KcsA. Assuming that the Ba(2+) is bound in site S(2) in the dominant blocked state, we examine the conditions that could impede its translocation and cause the observed "lock-in" effect. Although the binding of a K(+) ion to site S(1) when site S(2) is occupied by Ba(2+) is prohibitively high in energy (>10 kcal/mol), binding to site S0 appears to be more plausible (ΔG > 4 kcal/mol). The 2D potential of mean force (PMF) for the simultaneous translocation of Ba(2+) from site S(2) to site S(1) and of a K(+) ion on the extracellular side shows a barrier that is consistent with the concept of external lock-in. The barrier opposing the movement of Ba(2+) is very high when a cation is in site S(0), and considerably smaller when the site is unoccupied. Furthermore, free energy perturbation calculations show that site S(0) is selective for K(+) by 1.8 kcal/mol when S(2) is occupied by Ba(2+). However, the same site S(0) is nonselective when site S(2) is occupied by K(+), which shows that the presence of Ba(2+) affects the selectivity of the pore. A theoretical framework within classical rate theory is presented to incorporate the concentration dependence of the external ions on the lock-in effect.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / antagonists & inhibitors
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Barium / pharmacology*
  • Binding Sites
  • Ion Channel Gating
  • Molecular Dynamics Simulation*
  • Molecular Sequence Data
  • Potassium / metabolism
  • Potassium Channel Blockers / pharmacology*
  • Potassium Channels / chemistry*
  • Potassium Channels / metabolism
  • Streptomyces / chemistry

Substances

  • Bacterial Proteins
  • Potassium Channel Blockers
  • Potassium Channels
  • prokaryotic potassium channel
  • Barium
  • Potassium