Side-Chain Ionization States in a Potassium Channel

Abstract

KcsA is a bacterial K+ channel that is gated by pH. Continuum dielectric calculations on the crystal structure of the channel protein embedded in a low dielectric slab suggest that side chains E71 and D80 of each subunit, which lie adjacent to the selectivity filter region of the channel, form a proton-sharing pair in which E71 is neutral (protonated) and D80 is negatively charged at pH 7. When K+ ions are introduced into the system at their crystallographic positions the pattern of proton sharing is altered. The largest perturbation is for a K+ ion at site S3, i.e., interacting with the carbonyls of T75 and V76. The presence of multiple K+ ions in the filter increases the probability of E71 being ionized and of D80 remaining neutral (i.e., protonated). The ionization states of the protein side chains influence the potential energy profile experienced by a K+ ion as it is translated along the pore axis. In particular, the ionization state of the E71-D80 proton-sharing pair modulates the shape of the potential profile in the vicinity of the selectivity filter. Such reciprocal effects of ion occupancy on side-chain ionization states, and of side-chain ionization states on ion potential energy profiles will complicate molecular dynamics simulations and related studies designed to calculate ion permeation energetics.

Through the Channel and around the Channel: Validating and Comparing Microscopic Approaches for the Evaluation of Free Energy Profiles for Ion Penetration through Ion Channels

“…In these cases we had to use the cycle of Fig. 3B,C and the relationship: (8) where ΔG PMF (Na (0) (z→z+δz)) is not negligible in these cases.…”

Intrinsic flexibility and gating mechanism of the potassium channel KcsA

“…The ionization states of their side chains could account for the observed pHsensitivity. The side chain of Glu-71 has been suggested to be protonated because it faces the presumably ionized side chain of Asp-80 (12,19). The latter also forms a salt bridge with Arg-89 near the N terminus of TM2 on the neighboring subunit.…”

“…Although there have been extensive simulation (4,6,(10)(11)(12)(13)(14)(15)(16) and modeling studies of KcsA (17), no attempt at simulating the large-scale conformational changes in the gating process of KcsA has been made. In this study, we applied normal mode analysis (NMA; ref.…”

Cooperative transport in a potassium ion channel

“…It has been suggested by both experimental and theoretical studies that Glu71, which is buried inside the protein, should be in a protonated ͑neutral͒ state. 10,[26][27][28] Other amino residues with ionizable side chains are located mostly at a solvent exposed area and were assigned to their ionized state. Other atomic charges of the selectivity filter have been proposed, 29 which indicates the need of electronically polarizable force fields.…”