A microscopic view of ion conduction through the K+ channel

Abstract

Recent results from x-ray crystallography and molecular dynamics free-energy simulations have revealed the existence of a number of specific cation-binding sites disposed along the narrow pore of the K ؉ channel from Streptomyces lividans (KcsA), suggesting that K ؉ ions might literally ''hop'' in single file from one binding site to the next as permeation proceeds. In support of this view, it was found that the ion configurations correspond to energy wells of similar depth and that ion translocation is opposed only by small energy barriers. Although such features of the multiion potential energy surface are certainly essential for achieving a high throughput rate, diffusional and dissipative dynamical factors must also be taken into consideration to understand how rapid conduction of K ؉ is possible. To elucidate the mechanism of ion conduction, we established a framework theory enabling the direct simulation of nonequilibrium fluxes by extending the results of molecular dynamics over macroscopically long times. In good accord with experimental measurements, the simulated maximum conductance of the channel at saturating concentration is on the order of 550 and 360 pS for outward and inward ions flux, respectively, with a unidirectional flux-ratio exponent of 3. Analysis of the ionconduction process reveals a lack of equivalence between the cation-binding sites in the selectivity filter. molecular dynamics ͉ Brownian dynamics ͉ potential of mean force ͉ membrane potential ͉ Poisson-Boltzmann equation P otassium channels are transmembrane proteins that have the ability to conduct K ϩ ions at nearly the diffusion limit while remaining very selective (1). The availability of high-resolution crystallographic structures (2-4), together with the development of sophisticated computer models (5-10), is providing us with a unique opportunity to refine our understanding of these systems at an unprecedented level. Although the complexity of these channels does present a formidable challenge to biomolecular modeling, it is particularly encouraging to note that many of the recent results from molecular dynamics (MD) simulations based on realistic all-atom models have been consistent with the information emerging from higher-resolution structural data (for a recent review, see ref. 11). In particular, the free-energy profile, or potential of mean force (PMF), associated with the position of three K ϩ along the axis of the pore was calculated with umbrella sampling simulations of the K ϩ channel from Streptomyces lividans (KcsA) embedded in a phospholipid membrane with explicit solvent (5). This MD calculation reproduced the four cation-binding sites (S 1 -S 4 ) located in the narrow selectivity filter that were already known from x-ray diffraction data at 3.2-Å resolution (3) and also anticipated the existence of two additional sites (S ext and S 0 ) located on the extracellular side of the channel, which were observed independently in diffraction data at 2.0-Å resolution (2). This result increased the confidence in the abili...

Initial steps of inactivation at the K + channel selectivity filter

“…We observe that this configuration is permissive for rotation of a filter-lining carbonyl group (of Val-60) (Figs. 7 and 8), which in turn, can raise an energy barrier to prevent K + permeation (28)(29)(30). Our electrophysiological and computational results are consistent with a working hypothesis, in which Ca 2+ (but not Mg 2+ ), by preventing refilling of the pore with K + , can stabilize ion configurations in the selectivity filter that favor transitions to a nonconducting, inactivated state (Fig.…”

“…The adjacent energy well, appearing as a shoulder to the right of the S5 energy well, is located at the S4 site within the selectivity filter (approximately z = −5.5 Å). The relatively small (1-2 kcal/mol) energy barrier for K + movement from S5 to S4 under these conditions is consistent with a permeation mechanism in which a K + ion moves from the cavity region to S4, where it may subsequently drive outward movement of K + ions at S3 and S1, similar to the knockon permeation mechanism suggested for the K + channel KcsA (28,29). In contrast, with K + ions in the S2/S4 positions ( Fig.…”

Electrodiffusion: A continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution

“…Numerical PNPE solvers have been developed for both simple onedimensional phenomenological models [10][11][12] and complex 3D models for protein ion channel permeation, [13][14][15][16] and comparisons with 3D Brownian dynamics simulations have been performed. [17][18][19][20] Typically, a finite difference method ͑with exception of Ref. 15 that used a spectral element method͒ has been used to approximate the solution in the membrane channel with either atomic-level resolution or using simplified descriptions.…”

Cooperative transport in a potassium ion channel

“…Ion mobilities and ion fluxes have been measured by Brownian dynamics simulations, [7][8][9][10] and the potential profiles and free energy surface of ions inside the pore have been calculated employing molecular dynamics [11][12][13][14] and Monte Carlo simulations. 15 Comparing many classical transport theories in soft and solid state matter based on microscopic-mechanistic concepts with our present understanding of ion transport in potassium channels, the situation is not satisfactory, at least from a theoretical point of view.…”