The Predominant Role of Coordination Number in Potassium Channel Selectivity

The chemical property of methyl groups that renders them indispensable to biomolecules is their hydrophobicity. Quantum mechanical studies undertaken here to understand the effect of point substitutions on potassium (K-) channels illustrate quantitatively how methyl-induced polarization also contributes to biomolecular function. K-channels regulate transmembrane salt concentration gradients by transporting K + ions selectively. One of the K + binding sites in the channel's selectivity filter, the S4 site, also binds Ba 2+ ions, which blocks K + transport. This inhibitory property of Ba 2+ ions has been vital in understanding K-channel mechanism. In most K-channels, the S4 site is composed of four threonine amino acids. The K channels that carry serine instead of threonine are significantly less susceptible to Ba 2+ block and have reduced stabilities. We find that these differences can be explained by the lower polarizability of serine compared with threonine, because serine carries one less branched methyl group than threonine. A T→S substitution in the S4 site reduces its polarizability, which, in turn, reduces ion binding by several kilocalories per mole. Although the loss in binding affinity is high for Ba 2+ , the loss in K + binding affinity is also significant thermodynamically, which reduces channel stability. These results highlight, in general, how biomolecular function can rely on the polarization induced by methyl groups, especially those that are proximal to charged moieties, including ions, titratable amino acids, sulfates, phosphates, and nucleotides. dispersion | ion channels | methylation | quantum chemistry | density-functional theory

Section: Resultsmentioning

confidence: 99%

Role of methyl-induced polarization in ion binding

Rossi

Tkatchenko

Rempe

et al. 2013

“…Debate lingers in the field about the underlying factors contributing to these selectivity differences. Although available structural studies of K þ channels seem to favor the classical snug-fit model to account for K þ over Na þ selectivity (11,12), computational studies on K þ channel selectivity, in some cases using an isolated K þ binding site in their calculations, usually invoke one or more of the following concepts: the coordination number of the ion, chemistry of carbonyl oxygen ligands, intrinsic dynamism of the selectivity filter, solvent exposure of the ion binding sites, or the free energy landscapes of ion entrance and translocation in a multiion configuration (13)(14)(15)(16)(17)(18)(19)(20)(21). To further understand the underlying principles of ion selectivity in tetrameric cation channels, we engineered a set of cation channel pores whose selectivity filters contain three (equivalent to sites 2-4 or sites 1-3 of a K þ channel) or four (equivalent to sites 1-4 of a K þ channel) ion binding sites and determined their structures to high resolution (1.55-1.75 Å).…”

mentioning

confidence: 99%

Tuning the ion selectivity of tetrameric cation channels by changing the number of ion binding sites

Derebe¹,

Sauer²,

Zeng

et al. 2010

106

180

Selective ion conduction across ion channel pores is central to cellular physiology. To understand the underlying principles of ion selectivity in tetrameric cation channels, we engineered a set of cation channel pores based on the nonselective NaK channel and determined their structures to high resolution. These structures showcase an ensemble of selectivity filters with a various number of contiguous ion binding sites ranging from 2 to 4, with each individual site maintaining a geometry and ligand environment virtually identical to that of equivalent sites in K þ channel selectivity filters. Combined with single channel electrophysiology, we show that only the channel with four ion binding sites is K þ selective, whereas those with two or three are nonselective and permeate Na þ and K þ equally well. These observations strongly suggest that the number of contiguous ion binding sites in a single file is the key determinant of the channel's selectivity properties and the presence of four sites in K þ channels is essential for highly selective and efficient permeation of K þ ions.nonselective cation channel | potassium channel T he structure determination of several K þ selective and, more recently, bacterial nonselective cation channels has, over the past decade, vastly increased our knowledge of ion selectivity mechanisms (1-8). In K þ channels, the TVGYG signature sequence has emerged as the fundamental element imparting high K þ over Na þ selectivity (9, 10), forming four contiguous and chemically equivalent K þ binding sites composed of backbone carbonyl oxygen atoms from filter residues together with the hydroxyl oxygen atoms from the conserved threonine. Conversely, the TVGDG filter sequence of the NaK channel from Bacillus cereus, although similar in length and amino acid composition to those of K þ channels, forms a nonselective filter preserving the two most intracellular sites of K þ channel filters along with a wide, water-filled vestibular region on the immediately extracellular side (7) (Fig. 1A). Debate lingers in the field about the underlying factors contributing to these selectivity differences. Although available structural studies of K þ channels seem to favor the classical snug-fit model to account for K þ over Na þ selectivity (11, 12), computational studies on K þ channel selectivity, in some cases using an isolated K þ binding site in their calculations, usually invoke one or more of the following concepts: the coordination number of the ion, chemistry of carbonyl oxygen ligands, intrinsic dynamism of the selectivity filter, solvent exposure of the ion binding sites, or the free energy landscapes of ion entrance and translocation in a multiion configuration (13-21). To further understand the underlying principles of ion selectivity in tetrameric cation channels, we engineered a set of cation channel pores whose selectivity filters contain three (equivalent to sites 2-4 or sites 1-3 of a K þ channel) or four (equivalent to sites 1-4 of a K þ channel) ion binding sites and determined their s...

“…The coordination cage of eight oxygen atoms has been examined intensely in recent years using reduced models (15,(18)(19)(20)(21), as well as KcsA itself (e.g., refs. [22][23][24].…”

mentioning

confidence: 99%

On the selective ion binding hypothesis for potassium channels

Kim

Allen

2011

130

The mechanism by which K þ channels select for K þ over Na þ ions has been debated for the better part of a century. The prevailing view is that K þ channels contain highly conserved sites that selectively bind K þ over Na þ ions through optimal coordination. We demonstrate that a series of alternating sites within the KcsA channel selectivity filter exists, which are thermodynamically selective for either K þ (cage made from two planes of oxygen atoms) or Na þ ions (a single plane of four oxygen atoms). By combining Bennett free energy perturbation calculations with umbrella sampling, we show that when K þ and Na þ are both permitted to move into their preferred positions, the thermodynamic preference for K þ over Na þ is significantly reduced throughout the entire selectivity filter. We offer a rationale for experimental measures of thermodynamic preference for K þ over Na þ from Ba 2þ blocking data, by demonstrating that the presence of Ba 2þ ions exaggerates K þ over Na þ thermodynamic stability due to the different binding locations of these ions. These studies reveal that K þ channel selectivity may not be associated with the thermodynamics of ions in crystallographic K þ binding sites, but requires consideration of the kinetic barriers associated with the different multi-ion permeation mechanisms.ion selectivity | potassium ion channel | BAR-US method