Mechanism of Non-Selectivity in NAK Channel

Abstract

The amino acid sequence of the non-selectivity filter of the bacterial NaK channel (TVGDG) is similar to that of the K-selective KcsA channel (TVGYG), yet NaK conducts both Na+ and K+ equally well. To investigate the non-selectivity mechanism of NaK, we performed non-equilibrium molecular dynamics simulations using step-wise pulling protocols and Jarzynski's Equality. Two ions in the crystal structure of NaK were kept at site S3 (z ≈ 14.0 A) in the filter and in the small vestibule above S3, and one ion for pulling was placed at z = 0 A below the filter entrance. Two sets of simulations with either NaCl or KCl were compared to quantify how the filter dehydrates and conducts the different ions along the z-axis toward the extracellular surface. The simulations show that the entry of Na+ into the filter is favored by about 0.5-2 kcal/mol over K+ due to easier dehydration of Na+. This difference is attributed to the collapse of S3 by 11% in volume on Na+, resulting in a higher negative charge density of carbonyl oxygen atoms around Na+ than K+. When ions enter the filter and displace the ion at S3 (called Na3 or K3) into the small vestibule, the pulled K+ in S4 (below S3) is more dehydrated than the pulled Na+. K3 and the other K+ and water molecules in the filter become significantly more symmetric around the z-axis than Na+ and water molecules. This symmetric distribution of K+ ions and water favors the movement of K+ above S3, offsetting the slight ion selectivity at the filter entrance. We hypothesize that the non-selectivity filter of the NaK channel favors Na+ over K+ below S3, but becomes more selective for K+ than Na+ above S3, thus resulting into the non-selectivity as experimentally observed.