Cyclic nucleotide-gated channels: structural basis of ligand efficacy and allosteric modulation

Most working proteins, including metabolic enzymes, transcription regulators, and membrane receptors, transporters, and ion channels, share the property of allosteric coupling. The term 'allosteric' means that these proteins mediate indirect interactions between sites that are physically separated on the protein. In the example of ligand-gated ion channels, the binding of a suitable ligand elicits local conformational changes at the binding site, which are coupled to further conformational changes in regions distant from the binding site. The physical motions finally arrive at the site of biological activity: the ion-permeating pore. The conformational changes that lead from the ligand binding to the actual opening of the pore comprise 'gating'. In 1956, del Castillo and Katz suggested that the competition between different ligands at nicotinic acetylcholine receptors (nAChRs) could be explained by formation of an intermediate, ligand-bound, yet inactive state of the receptor, which separates the active state of the receptor from the initial binding of the ligand (del Castillo & Katz, 1957). This 'binding-then-gating', two-step model went beyond the then-prevailing drug-receptor model that assumes a single bimolecular binding reaction, and paralleled Stephenson's conceptual dichotomy of 'affinity' and 'efficacy' (Stephenson, 1956). In 1965 Monod, Wyman and Changeux presented a simple allosteric model (the MWC model) (Monod et al. 1965) that explained the cooperative binding of oxygen to haemoglobin; it was adopted as an important paradigm for ligand-gated channels soon after its initial formulation (Changeux et al. 1967; Karlin, 1967; Colquhoun, 1973)

Amine, Amido, and Imido Complexes of Tantalum Supported by a Pyridine-Linked Bis(phenolate) Pincer Ligand: Ta−N π-Bonding Influences Pincer Ligand Geometry

A series of tantalum imido and amido complexes supported by a pyridine-linked bis(phenolate) ligand has been synthesized. Characterization of these complexes via X-ray crystallography reveals both C_s and C_2 binding modes of the bis(phenolate)pyridine ligand, with complexes containing two or fewer strong π-donor interactions from ancillary ligands giving C_s symmetry, whereas three strong π-donor interactions (e.g., three amido ligands or one amido ligand and one imido ligand) give C_2-symmetric binding of the bis(phenolate)pyridine ligand. DFT calculations and molecular orbital analyses of the complexes have revealed that the preference for C_s-symmetric ligand binding is a result of tantalum−phenolate π-bonding, whereas in cases where tantalum−phenolate π-bonding is overridden by stronger Ta−N π-bonding, C_2-symmetric ligand binding is preferred, likely because conformationally this is the lowest-energy arrangement. This electronically driven change in geometry indicates that, unlike analogous metallocene systems, the bis(phenolate)pyridine pincer ligand is not a strong enough π-donor to exert dominant control over the electronic and geometric properties of the complex

A model study of cooperative binding of ionic surfactants to oppositely charged flexible polyions

A novel statistical model for the cooperative binding of monomeric ligands to a linear lattice is developed to study the interaction of ionic surfactant molecules with flexible polyion chain in dilute solution. Electrostatic binding of a ligand to a site on the polyion and hydrophobic associations between the neighboring bound ligands are assumed to be stochastic processes. Ligand association separated by several lattice points within defined width is introduced for the flexible polyion. Model calculations by the Monte Carlo method are carried out to investigate the binding behavior. The hypothesis on the ligand association and its width on the chain are of importance in determining critical aggregation concentration and binding isotherm. The results are reasonable for the interpretations of several surfactant-flexible polyion binding experiments. The implications of the approach are presented and discussed.Comment: 11 pages, 9 figure

Conformational selection in protein binding and function

Protein binding and function often involves conformational changes. Advanced NMR experiments indicate that these conformational changes can occur in the absence of ligand molecules (or with bound ligands), and that the ligands may 'select' protein conformations for binding (or unbinding). In this review, we argue that this conformational selection requires transition times for ligand binding and unbinding that are small compared to the dwell times of proteins in different conformations, which is plausible for small ligand molecules. Such a separation of timescales leads to a decoupling and temporal ordering of binding/unbinding events and conformational changes. We propose that conformational-selection and induced-change processes (such as induced fit) are two sides of the same coin, because the temporal ordering is reversed in binding and unbinding direction. Conformational-selection processes can be characterized by a conformational excitation that occurs prior to a binding or unbinding event, while induced-change processes exhibit a characteristic conformational relaxation that occurs after a binding or unbinding event. We discuss how the ordering of events can be determined from relaxation rates and effective on- and off-rates determined in mixing experiments, and from the conformational exchange rates measured in advanced NMR or single-molecule FRET experiments. For larger ligand molecules such as peptides, conformational changes and binding events can be intricately coupled and exhibit aspects of conformational-selection and induced-change processes in both binding and unbinding direction.Comment: review article; 10 pages, 4 figures, Protein Sci. 201

Influence of ligand shape and steric hindrance on the composition of the nanocrystal ligand shell

Organic ligands play a key role in the synthesis of colloidal semiconductor nanocrystals or quantum dots. Generally they consist of a functional group and an aliphatic chain, with carboxylic acids, thiols and phosphonic acids as typical examples. The functional group ensures the binding to the nanocrystal surface, while the stability of the dispersion strongly depends on the interactions between the organic chains of the adjacent ligands. A number of studies already addressed the binding strength and the type of binding between the nanocrystal surface and the ligand yet none discuss the effect of the organic chain on the ligand exchange. By means of NMR spectroscopy, we examine the ligand shell composition of CdSe nanocrystals originally capped with oleic acid (OA), when exposed to a linear carboxylic acid. Regardless of chain length, we see a one-to-one exchange between the carboxylic acids. The composition of the ligand shell closely matches that of the ligand mixture in solution, indicating that the ligand shell can be seen as an ideal mixture of both ligands. As a consequence, a mixed ligand shell can easily be prepared by adding a ligand mixture with desired composition to the nanocrystal dispersion. On the other hand, when the CdSe nanocrystals are exposed to a branched carboxylic acid with two long aliphatic chains, like 2-hexyldecanoic acid, the ligand shell mainly consists of OA moieties. We interpret these results using an exchange process where the incoming ligand not only displaces oleic acid but also occupies additional space in the ligand shell to accommodate both aliphatic chains. Hence, given a one-for-one exchange reaction, steric hindrance in a fully packed ligand shell will prevent complete ligand exchange. These results can be very useful in view of producing nanocrystals with lower ligand densities by means of synthesis with these branched carboxylic acids

A tight coupling between β\u3csub\u3e2\u3c/sub\u3eY97 and β\u3csub\u3e2\u3c/sub\u3eF200 of the GABA\u3csub\u3eA\u3c/sub\u3e receptor mediates GABA binding

The GABAA receptor is an oligopentameric chloride channel that is activated via conformation changes induced upon the binding of the endogenous ligand, GABA, to the extracellular inter-subunit interfaces. Although dozens of amino acid residues at the α/β interface have been implicated in ligand binding, the structural elements that mediate ligand binding and receptor activation are not yet fully described. In this study, double-mutant cycle analysis was employed to test for possible interactions between several arginines (α1R67, α1R120, α1R132, and β2R207) and two aromatic residues (β2Y97 and β2F200) that are present in the ligand-binding pocket and are known to influence GABA affinity. Our results show that neither α1R67 nor α1R120 is functionally coupled to either of the aromatics, whereas a moderate coupling exists between α1R132 and both aromatic residues. Significant functional coupling between β2R207 and both β2Y97 and β2F200 was found. Furthermore, we identified an even stronger coupling between the two aromatics, β2Y97 and β2F200, and for the first time provided direct evidence for the involvement of β2Y97 and β2F200 in GABA binding. As these residues are tightly linked, and mutation of either has similar, severe effects on GABA binding and receptor kinetics, we believe they form a single functional unit that may directly coordinate GABA

The hepta-β-glucoside elicitor-binding proteins from legumes represent a putative receptor family

The ability of legumes to recognize and respond to β-glucan elicitors by synthesizing phytoalexins is consistent with the existence of a membrane-bound β-glucan-binding site. Related proteins of approximately 75 kDa and the corresponding mRNAs were detected in various species of legumes which respond to beta-glucans. The cDNAs for the beta-glucan-binding proteins of bean and soybean were cloned. The deduced 75-kDa proteins are predominantly hydrophilic and constitute a unique class of glucan-binding proteins with no currently recognizable functional domains. Heterologous expression of the soybean beta-glucan-binding protein in tomato cells resulted in the generation of a high-affinity binding site for the elicitor-active hepta-β-glucoside conjugate (K-d = 4.5 nM). Ligand competition experiments with the recombinant binding sites demonstrated similar ligand specificities when compared with soybean. In both soybean and transgenic tomato, membrane-bound, active forms of the glucan-binding proteins coexist with immunologically detectable, soluble but inactive forms of the proteins. Reconstitution of a soluble protein fraction into lipid vesicles regained beta-glucoside-binding activity but with lower affinity (K-d = 130 nM). We conclude that the beta-glucan elicitor receptors of legumes are composed of the 75 kDa glucan-binding proteins as the critical components for ligand-recognition, and of an as yet unknown membrane anchor constituting the plasma membrane-associated receptor complex

Metal-ion binding and metal-ion induced folding of the adenine-sensing riboswitch aptamer domain

Divalent cations are important in the folding and stabilization of complex RNA structures. The adenine-sensing riboswitch controls the expression of mRNAs for proteins involved in purine metabolism by directly sensing intracellular adenine levels. Adenine binds with high affinity and specificity to the ligand binding or aptamer domain of the adenine-sensing riboswitch. The X-ray structure of this domain in complex with adenine revealed an intricate RNA-fold consisting of a three-helix junction stabilized by long-range base-pairing interactions and identified five binding sites for hexahydrated Mg2+-ions. Furthermore, a role for Mg2+-ions in the ligand-induced folding of this RNA was suggested. Here, we describe the interaction of divalent cations with the RNA–adenine complex in solution as studied by high-resolution NMR spectroscopy. Paramagnetic line broadening, chemical shift mapping and intermolecular nuclear Overhauser effects (NOEs) indicate the presence of at least three binding sites for divalent cations. Two of them are similar to those in the X-ray structure. The third site, which is important for the folding of this RNA, has not been observed previously. The ligand-free state of the RNA is conformationally heterogeneous and contains base-pairing patterns detrimental to ligand binding in the absence of Mg2+, but becomes partially pre-organized for ligand binding in the presence of Mg2+. Compared to the highly similar guanine-sensing riboswitch, the folding pathway for the adenine-sensing riboswitch aptamer domain is more complex and the influence of Mg2+ is more pronounced