Determinants of cation transport selectivity: Equilibrium binding and transport kinetics

Abstract

The crystal structures of channels and transporters reveal the chemical nature of ion-binding sites and, thereby, constrain mechanistic models for their transport processes. However, these structures, in and of themselves, do not reveal equilibrium selectivity or transport preferences, which can be discerned only from various functional assays. In this Review, I explore the relationship between cation transport protein structures, equilibrium binding measurements, and ion transport selectivity. The primary focus is on K+-selective channels and nonselective cation channels because they have been extensively studied both functionally and structurally, but the principles discussed are relevant to other transport proteins and molecules.

Structures of the Human HCN1 Hyperpolarization-Activated Channel

“…Multi K + ion occupancy will increase the probability that a Na + will exit from the same side it entered (because there is a K + ion blocking the other side) and thus permit kinetic selectivity. This behavior has been demonstrated through elegant experiments in the NaK channel (Derebe et al, 2011; Lockless, 2015; Shi et al, 2006), which also has only sites 3 and 4 in its selectivity filter (Figure 2D). The structure of the NaK filter is clearly different than the filter in HCN (Figure 2D and 2E), but the two channels have in common only two monovalent cation binding sites.…”

Cryo-EM and X-ray structures of TRPV4 reveal insight into ion permeation and gating mechanisms

“…That is, it cannot permeate. Multi-ion occupancy appears essential for selectivity, elegantly demonstrated in the NaK channel and its variants 48–51 . The exception we observed for Gd 3+ , which blocked the channel at millimolar concentration (Supplementary Fig.…”

Structure-Functional Basis of Ion Transport in Sodium–Calcium Exchanger (NCX) Proteins

“…A cascade of biological events at the cellular, organ, and systemic levels requires the direct or indirect contribution of distinct cations, such as H + , Na + , K + , Ca 2+ , and Mg 2+ , where protein structures can somehow manage the selective recognition of specific cations to couple the mechanical, catalytic, and transport activities possessed by a given protein [1,2,3]. Physiological concentrations of important cations in the extracellular, cytosolic, and subcellular (mitochondria, nuclei, and others) compartments are tightly controlled by membrane-intercalated proteins, channels, transporters and pumps, which can dynamically generate, retain, and modify ion homeostasis in time and space in accordance with the physiological demands of a given cell type [4,5,6].…”

“…However, identifying and quantifying the key conformational transitions governing the structure–functional specificity of ion-transporting proteins remains difficult, due to the limited capacities of current technologies for direct experimental measurement of the functionally relevant dynamic transitions. Although advanced computational approaches contributed significantly to a better understanding of the underlying mechanisms by providing a virtual route to complement the missing information, the rational integration of experimental data and theoretical calculations toward meaningful conclusions of fundamental significance remains challenging [1,2,3,7,8]. …”

“…Although the structure-dynamic determinants of ion transport mechanisms were relatively well studied in ion channels [1,2,3], recent breakthroughs in the structural biology of ion transporters and pumps provided novel insights and conceptual frameworks for the systematic investigation of ion selectivity and transport mechanisms in these proteins [12,13,14]. Nevertheless, we are only at the beginning in understanding the details and mechanistic relevance of the conformational dynamics associated with alternating access, where applying new biophysical approaches in combination with computational sciences is required for making further progress.…”