Ion pumps

Na+ Binding and Transport: Insights from Light-Driven Na+-Pumping Rhodopsin

Na+ plays a vital role in numerous physiological processes across humans and animals, necessitating a comprehensive understanding of Na+ transmembrane transport. Among the various Na+ pumps and channels, light-driven Na+-pumping rhodopsin (NaR) has emerged as a noteworthy model in this field. This review offers a concise overview of the structural and functional studies conducted on NaR, encompassing ground/intermediate-state structures and photocycle kinetics. The primary focus lies in addressing key inquiries: (1) unraveling the translocation pathway of Na+; (2) examining the role of structural changes within the photocycle, particularly in the O state, in facilitating Na+ transport; and (3) investigating the timing of Na+ uptake/release. By delving into these unresolved issues and existing debates, this review aims to shed light on the future direction of Na+ pump research.

ProBLM web server: protein and membrane placement and orientation package

The 3D structures of membrane proteins are typically determined without the presence of a lipid bilayer. For the purpose of studying the role of membranes on the wild type characteristics of the corresponding protein, determining the position and orientation of transmembrane proteins within a membrane environment is highly desirable. Here we report a geometry-based approach to automatically insert a membrane protein with a known 3D structure into pregenerated lipid bilayer membranes with various dimensions and lipid compositions or into a pseudomembrane. The pseudomembrane is built using the Protein Nano-Object Integrator which generates a parallelepiped of user-specified dimensions made up of pseudoatoms. The pseudomembrane allows for modeling the desolvation effects while avoiding plausible errors associated with wrongly assigned protein-lipid contacts. The method is implemented into a web server, the ProBLM server, which is freely available to the biophysical community. The web server allows the user to upload a protein coordinate file and any missing residues or heavy atoms are regenerated. ProBLM then creates a combined protein-membrane complex from the given membrane protein and bilayer lipid membrane or pseudomembrane. The user is given an option to manually refine the model by manipulating the position and orientation of the protein with respect to the membrane.

Bioelectric state and cell cycle control of Mammalian neural stem cells

The concerted action of ion channels and pumps establishing a resting membrane potential has been most thoroughly studied in the context of excitable cells, most notably neurons, but emerging evidences indicate that they are also involved in controlling proliferation and differentiation of nonexcitable somatic stem cells. The importance of understanding stem cell contribution to tissue formation during embryonic development, adult homeostasis, and regeneration in disease has prompted many groups to study and manipulate the membrane potential of stem cells in a variety of systems. In this paper we aimed at summarizing the current knowledge on the role of ion channels and pumps in the context of mammalian corticogenesis with particular emphasis on their contribution to the switch of neural stem cells from proliferation to differentiation and generation of more committed progenitors and neurons, whose lineage during brain development has been recently elucidated.

Tissue-specific versus isoform-specific differences in cation activation kinetics of the Na,K-ATPase

The experiments described in this report reconcile some of the apparent differences in isoform-specific kinetics of the Na,K-ATPase reported in earlier studies. Thus, tissue-specific differences in Na+ and K+ activation kinetics of Na,K-ATPase activity of the same species (rat) were observed when the same isoform was assayed in different tissues or cells. In the case of alpha1, alpha1-transfected HeLa cell, rat kidney, and axolemma membranes were compared. For alpha3, the ouabain-insensitive alpha3*-transfected HeLa cell (cf. Jewell, E. A., and Lingrel, J. B. (1991) J. Biol. Chem. 266, 16925-16930), pineal gland, and axolemma (mainly alpha3) membranes were compared. The order of apparent affinities for Na+ of alpha1 pumps was axolemma approximately rat alpha1-transfected HeLa > kidney, and for K+, kidney approximately alpha1-transfected HeLa > axolemma. For alpha3, the order of apparent affinities for Na+ was pineal gland approximately axolemma > alpha3*-transfected HeLa, and for K+, alpha3*-transfected HeLa > axolemma approximately pineal gland. In addition, the differences in apparent affinities for Na+ of either kidney alpha1 or HeLa alpha3* as compared to the same isoform in other tissues were even greater when the K+ concentration was increased. A kinetic analysis of the apparent affinities for Na+ as a function of K+ concentration indicates that isoform-specific as well as tissue-specific differences are related to the apparent affinities for both Na+ and K+, the latter acting as a competitive inhibitor at cytoplasmic Na+ activation sites. Although the nature of the tissue-specific modulation of K+/Na+ antagonism remains unknown, an analysis of the nature of the beta isoform associated with alpha1 or alpha3 using isoform-specific immunoprecipitation indicates that the presence of distinct beta subunits does not account for differences of alpha1 of kidney, axolemma, and HeLa, and of alpha3 of axolemma and HeLa; in both instances beta1 is the predominant beta isoform present or associated with either alpha1 or alpha3. However, a kinetic difference in K+/Na+ antagonism due to distinct betas may apply to alpha3 of axolemma (alpha3beta1) and pineal gland ( alpha3beta2).

Coupling mechanisms in ATP-driven pumps

Because the kinetic reaction schemes for primary and secondary active transport can be identical, the same fundamental relationship holds among rate and equilibrium constants: the ratio of coupled to uncoupled flux is no greater than the ratio of substrate dissociation constants in an initial complex and a conformationally altered state. Further, the role played by each substrate in coupling depends in the same way on its order of addition to the carrier. It follows that the structural principles governing the design and operation of the carrier proteins are fundamentally alike. In either system, the strict control of the mobility and specificity of the carrier, a prerequisite for active transport, depends on the utilization of substrate binding forces to alter the protein conformation; and whether the driving substrate is transported or not and whether reversibly bound or covalently bound (like the phosphate group derived from ATP), the force producing the conformational change is derived from non-covalent interactions between the substrate (held at the substrate site) and other sections of the protein. The protein probably encloses the substrate, with a resulting increase in the binding force; the favourable energy of interaction balances the unfavourable energy involved in distorting the protein structure. The postulated complex can account for the 'occluded state' of transported cations and for the favourable reaction of inorganic phosphate with the calcium pump.

Coupling mechanisms in active transport

In primary and secondary active transport, the mobility and specificity of the carrier are controlled, over the course of the transport reaction, in accordance with a set of 'rules'. The rules are shown to depend on two mechanisms: a substrate--either the driving substrate (a transported ion or ATP) or the driven substrate--may shift a conformational equilibrium or accelerate a rate-limiting conformational change. From an analysis of coupling mechanisms the following conclusions emerge. (i) The ratio of coupled to uncoupled flux, which should be large, cannot be greater than the ratio of substrate dissociation constants in an initial complex and a conformationally altered state. A minimum value for the increased binding force can be estimated from steady-state constants. (ii) In an ordered mechanism, slippage is expected at high concentrations of the substrate adding to the carrier second, while slippage of the first substrate should remain low. (iii) Slippage in coupled transport is minimized if the driven substrate is last on in loading the carrier and last off in unloading, while the reverse order makes the affinity high in loading and low in unloading, as required for efficient transfer from one compartment to another; hence the preferred mechanism may depend on prevailing physiological conditions. (iv) A coupled transport system can be transformed into a facilitated system for one substrate or both if the control of carrier mobility is undermined through modification of the carrier.