Direct studies of ligand-receptor interactions and ion channel blocking (Review)

Small molecules can activate membrane bound receptors to elicit cellular responses and approximately 80% of all such responses are mediated through membranes. Solid state nuclear magnetic resonance (NMR) methods have been developed for the resolution of specifically labelled ligands, designed to report back structural, dynamic and electronic details of the ligand whilst at its site of action. In particular, ion channel blockers, drugs, inhibitors, prosthetic groups and solutes have been studied when at their target site in functionally competent membranes. A blocker of the channel in the anion transporter of erythrocytes (AE1) has been studied to show that considerable motional freedom within the channel site occurs. The activating agonist of the ligand gated ion channel, the nicotinic acetylcholine receptor, is constrained at its site of action and binds through a cation-pi interaction as revealed in the NMR spectra. The footprint for the inhibitor binding site of the digitalis receptor, the Na(+)/K(+)-ATPase has been resolved as well as the molecular conformation of digitalis showing a bent structure whilst at its site of action. For the gastric proton pump, however, a planar conformation is observed for a reversible substituted imidazopyridine. In all cases not only the structure, but also some indications about the electronic interactions of ligand and target have been resolved using these approaches.     

Molecular cytogenetic insights into the ageing syndrome Hutchinson-Gilford Progeria (HGPS)

Hutchinson-Gilford Progeria Syndrome (HGPS) is an extremely rare genetic disorder characterized by premature ageing in childhood and serves as a valuable model for the human ageing process in general. Most recently, point mutations in the lamin A (LMNA) gene on chromosome 1q have been associated with the disease, however how these mutations relate to the complex phenotype of HGPS remains to be established. It has been shown that fibroblasts from HGPS patients are frequently resistant to immortalization with telomerase (hTERT), consistent with the idea that the loss of a dominant acting HGPS gene is a pre-requisite for immortalization. In this study we report the first detailed cytogenetic analysis of hTERT-immortalised HGPS cell lines from three patients and one corresponding primary fibroblast culture. Our results provide evidence for a cytogenetic mosaicism in HGPS with a distinctive pattern of chromosome aberrations in all the HGP clones. Chromosome 11 alterations were observed at a high frequency in each immortalised HGPS cell line but were also present at a lower frequency in the corresponding primary cells. Moreover, we were able to identify the 11q13-->q23 region as a potential site of breakage. Our results are therefore consistent with a role of chromosome 11 alterations in the escape from senescence observed in HGPS cells. In addition to this defined rearrangement, we consistently observed complex chromosomal rearrangements, suggesting that HGPS displays features of chromosomal instability.     

The surprising proton channel: Novel insights into its structure and function

Commentary to: Tombola F, Ulbrich M, Isacoff I. The voltage-gated proton channel Hv1 has two pores, each controlled by one voltage sensor. Neuron 2008; 58:546-66.

Commentary to: Lee S-Y, Letts JA, MacKinnon R. Dimeric subunit stoichiometry of the human voltage-dependent proton channel Hv1. Proc Natl Acad Sci 2008; 105:7692-5.     

Structural insights into protein-metal ion partnerships

New metalloprotein structures continue to provide discoveries regarding protein-metal ion partnerships. Many recent structures reveal metal ion sites that control or are controlled by protein conformational change, including modulation by alternative splice variants and striking conformational changes. Only a few novel catalytic metal centers have been revealed recently, such as the surprising Ni-hook superoxide dismutase catalytic site and the cubane-like Mn(3)CaO(4) photosynthetic oxygen-evolving center. However, important new variations on old heme themes, breakthroughs in the fields of metal ion regulation and metallochaperones, and captivating insights into partnerships between proteins and minerals have also been described. Very high resolution metal site structures and metalloprotein design will be increasingly important in order to leverage the wealth of native metalloprotein structures into a deep understanding of metal ion site specificity and activity.     

Molecular and functional characterization of acid-sensing ion channel (ASIC) 1b.

Acid-sensing ion channels (ASICs) are activated by extracellular protons and are involved in neurotransmission in the central nervous system, in pain perception, as well as in mechanotransduction. Six different ASIC subunits have been cloned to date, which are encoded by four genes (ASIC1-ASIC4). Proton-gated currents have been described in isolated neurons from sensory ganglia as well as from central nervous system. However, it is largely unclear which of the cloned ASIC subunits underlie these native proton-gated currents. Recently, a splice variant, ASIC-beta, has been described for ASIC1a. In this variant about one-third of the protein is exchanged at the N terminus. Here we show that ASIC-beta has a longer N terminus than previously reported, extending the sequence divergence between ASIC1a and this new variant (ASIC1b). We investigated in detail kinetic and selectivity properties of ASIC1b in comparison to ASIC1a. Kinetics is similar for ASIC1b and ASIC1a. Ca(2+) permeability of ASIC1a is low, whereas ASIC1b is impermeable to Ca(2+). Currents through ASIC1a resemble currents, which have been described in sensory and central neurons, whereas the significance of ASIC1b remains to be established. Moreover, we show that a pre-transmembrane 1 domain controls the permeability to divalent cations in ASIC1, contributing to our understanding of the pore structure of these channels.     

Model organisms: new insights into ion channel and transporter function. L-type calcium channels regulate epithelial fluid transport in Drosophila melanogaster

The neuropeptide CAP2b stimulates fluid transport obligatorily via calcium entry, nitric oxide, and cGMP in Drosophila melanogaster Malpighian (renal) tubules. We have shown by RT-PCR that the Drosophila L-type calcium channel alpha1-subunit genes Dmca1D and Dmca1A (nbA) are both expressed in tubules. CAP2b-stimulated fluid transport and cytosolic calcium concentration ([Ca2+]i) increases are inhibited by the L-type calcium channel blockers verapamil and nifedipine. cGMP-stimulated fluid transport is verapamil and nifedipine sensitive. Furthermore, cGMP induces a slow [Ca2+]i increase in tubule principal cells via verapamil- and nifedipine-sensitive calcium entry; RT-PCR shows that tubules express Drosophila cyclic nucleotide-gated channel (cng). Additionally, thapsigargin-induced [Ca2+]i increase is verapamil sensitive. Phenylalkylamines bind with differing affinities to the basolateral and apical surfaces of principal cells in the main segment; however, dihydropyridine binds apically in the tubule initial segment. Immunocytochemical evidence suggests localization of alpha1-subunits to both basolateral and apical surfaces of principal cells in the tubule main segment. We suggest roles for L-type calcium channels and cGMP-mediated calcium influx in both calcium signaling and fluid transport mechanisms in Drosophila.     

Molecular insights into eukaryotic chemotaxis.

Many cells display directed migration toward specific compounds. The best-studied eukaryotic models of chemotaxis are polymorphonuclear leukocytes, which respond to formylated peptides and Dictyostelium amoebas, which respond to extracellular cAMP. In both cell types, chemoattractants bind to surface receptors that contain seven transmembrane domains and interact with G proteins. Some cells, such as fibroblasts, undergo chemotaxis toward compounds whose receptors lack this motif and transmit their signals by other mechanisms. The cytosolic changes elicited by chemoattractants include increased levels of cAMP, cGMP, inositol phosphates, and calcium. These changes are correlated with actin polymerization and other cytoskeletal events that result in preferential extension of pseudopods toward the chemoattractant. Dictyostelium cell lines in which specific genes have been disrupted have demonstrated the necessity of a cAMP receptor (cAR1) and a G protein alpha-subunit (G alpha 2) for responsiveness to cAMP. Other proteins, such as myosin heavy chain and several actin binding proteins, are dispensible although their absence does affect the details of chemotaxis. The disruption of other relevant genes and the genetic reconstitution of chemotaxis in cells lacking crucial proteins should reveal many clues about this complicated and fascinating process.     

Molecular insights into the structure and function of plant K(+) transport mechanisms

Our understanding of plant potassium transport has increased in the past decade through the application of molecular biological techniques. In this review, recent work on inward and outward rectifying K(+) channels as well as high affinity K(+) transporters is described. Through the work on inward rectifying K(+) channels, we now have precise details on how the structure of these proteins determines functional characteristics such as ion conduction, pH sensitivity, selectivity and voltage sensing. The physiological function of inward rectifying K(+) channels in plants has been clarified through the analysis of expression patterns and mutational analysis. Two classes of outward rectifying K(+) channels have now been cloned from plants and their initial characterisation is reviewed. The physiological role of one class of outward rectifying K(+) channel has been demonstrated to be involved in long distance transport of K(+) from roots to shoots. The molecular structure and function of two classes of energised K(+) transporters are also reviewed. The first class is energised by Na(+) and shares structural similarities with K(+) transport mechanisms in bacteria and fungi. Structure-function studies suggest that it should be possible to increase the K(+) and Na(+) selectivity of these transporters, which will enhance the salt tolerance of higher plants. The second class of K(+) transporter is comprised of a large gene family and appears to have a dual affinity for K(+). A suite of molecular techniques, including gene cloning, oocyte expression, RNA localisation and gene inactivation, is now being used to fully characterise the biophysical and physiological function of plants K(+) transport mechanisms.     

Molecular insights into NF2/Merlin tumor suppressor function

The FERM domain protein Merlin, encoded by the NF2 tumor suppressor gene, regulates cell proliferation in response to adhesive signaling. The growth inhibitory function of Merlin is induced by intercellular adhesion and inactivated by joint integrin/receptor tyrosine kinase signaling. Merlin contributes to the formation of cell junctions in polarized tissues, activates anti-mitogenic signaling at tight-junctions, and inhibits oncogenic gene expression. Thus, inactivation of Merlin causes uncontrolled mitogenic signaling and tumorigenesis. Merlin’s predominant tumor suppressive functions are attributable to its control of oncogenic gene expression through regulation of Hippo signaling. Notably, Merlin translocates to the nucleus where it directly inhibits the CRL4^DCAF1 E3 ubiquitin ligase, thereby suppressing inhibition of the Lats kinases. A dichotomy in NF2 function has emerged whereby Merlin acts at the cell cortex to organize cell junctions and propagate anti-mitogenic signaling, whereas it inhibits oncogenic gene expression through the inhibition of CRL4^DCAF1 and activation of Hippo signaling. The biochemical events underlying Merlin’s normal function and tumor suppressive activity will be discussed in this Review, with emphasis on recent discoveries that have greatly influenced our understanding of Merlin biology.     

Molecular insights into the history of plague

Because of the limits inherent in historical sources on ancient plague epidemics, many questions concerning their etiology and epidemiology remain unanswered. Molecular biology tools and the use of dental pulp as a preserved source of bacterial DNA enabled us to demonstrate that Yersinia pestis was the etiologic agent of the 1347 European Black Death and of two additional epidemics in 1590 and 1722 in southern France.     

Molecular regulation of Nogo-A in neural cells: Novel insights into structure and function

Nogo-A is part of the reticulon family of proteins localized to the myelin and oligodendroglial plasma membranes. Nogo-A specifically initiates signal transduction cascades limiting axonal regrowth following injury and disease in the adult mammalian central nervous system (CNS). Recent novel data support the contention that neuronal Nogo-A plays an important role in regulating cytoskeletal re-organization without the requirement of signaling through its cognate receptor (Nogo receptor). These data, along with the recent findings that the N-terminus of Nogo-A can interact with integrins and that NgR1 interacts with the amyloid precursor protein extracellularly, as well as novel findings showing ubiquitin ligases binding with Nogo-A intracellularly add a layer of complexity to its functional role in the CNS.     

Molecular regulation of cardiac ryanodine receptor ion channel

The release of Ca(2+) ions from intracellular stores is a key step in a wide variety of cellular functions. In striated muscle, the release of Ca(2+) from the sarcoplasmic reticulum (SR) leads to muscle contraction. Ca(2+) release occurs through large, high-conductance Ca(2+) release channels, also known as ryanodine receptors (RyRs) because they bind the plant alkaloid ryanodine with high affinity and specificity. The RyRs are isolated as 30S protein complexes comprised of four 560 kDa RyR2 subunits and four 12 kDa FK506 binding protein (FKBP12) subunits. Multiple endogenous effector molecules and posttranslational modifications regulate the RyRs. This review focuses on current research toward understanding the control of the isolated cardiac Ca(2+) release channel/ryanodine receptor (RyR2) by Ca(2+), calmodulin, thiol oxidation/reduction and nitrosylation, and protein phosphorylation.     

Outer membrane translocons: structural insights into channel formation

Gram-negative bacteria need to maintain the integrity of their outer membrane while also regulating the secretion of toxins and other macromolecules. A variety of dedicated outer membrane proteins (OMPs) facilitate this process. Recent structural work has shown that some of these proteins adopt classical β-barrel transmembrane structures and rely on structural changes within the barrel lumen to allow passage of substrate proteins. Other secretion systems have OMP components which use transmembrane α-helices and appear to function in a different way. Here we review a selection of recent structural studies which have major ramifications for our understanding of the passage of macromolecules across the outer membrane.     

Molecular insights into X;BTA5 chromosome rearrangements in the tribe Antilopini (Bovidae)

For a clade that includes Antilope, Gazella,Nanger and Eudorcas (Antilopinae), X;BTA5 translocation is a synapomorphy. Using a combination of fluorescence in situ hybridization (FISH) probes and polymerase chain reaction techniques, we provide (i) the first insight into the X;BTA5 architecture which differs in the species under study: Antilope cervicapra (genus Antilope), Gazella leptoceros (genus Gazella) and Nanger dama ruficollis (genus Nanger), (ii) determination of interstitial satellite DNA at the X;BTA5 junctions, and (iii) determination of repetitive sequences occupying constitutive heterochromatin of Xp arms in the studied species. The distribution of 2 repetitive DNA families in the centromeric regions of all chromosomes has been investigated by FISH with probes representing satellite I and satellite II DNA in all studied species. In this context, we discuss a markedly smaller centromere in the BTA5 (Y2) unfused chromosomes in males in the XY1Y2 determining system in comparison with other acrocentrics. An analysis of karyotypic data described in current published studies revealed a disparity with the data determined by FISH. In this report, we document chromosomal fusions in the 3 species mentioned resulting from FISH with painting probes prepared from cattle (Bos taurus). The number and chromosomal location of nucleolus organizer regions were determined by FISH. In the present study, we emphasize the importance of chromosomal rearrangement verification, particularly, if they are used for phylogenetic analysis.     

New insights into creatine function and synthesis

The text-book view of the role of the creatine/creatine phosphate system as an energy buffer has been expanded to include functions such as energy shuttling, proton buffering and regulating cytosolic ADP levels. There is continuous need for creatine replacement due to creatinine formation. Replacement involves a combination of diet and de novo synthesis. Creatine synthesis makes very significant demands on amino acid metabolism, in particular that of glycine, arginine and methionine. It uses about 40% of all methyl groups transferred from S-adenosylmethionine. Although the traditional view of the function of the creatine/creatine phosphate system is largely concerned with its role in skeletal and cardiac muscle, recent work obliges us to take a broader view. In particular, its role in the brain is brought into sharp focus by the neurological symptoms displayed by children suffering from inborn errors of creatine synthesis and transport, as well as by suggestions that brain creatine status may play a role in cognitive performance in adults.     

New insights into fish ion regulation and mitochondrion-rich cells

Compared to terrestrial animals, fish have to cope with more-challenging osmotic and ionic gradients from aquatic environments with diverse salinities, ion compositions, and pH values. Gills, a unique and highly studied organ in research on fish osmoregulation and ionoregulation, provide an excellent model to study the regulatory mechanisms of ion transport. The present review introduces and discusses some recent advances in relevant issues of teleost gill ion transport and functions of gill ionocytes. Based on accumulating evidence, a conclusive model of NaCl secretion in gills of euryhaline teleosts has been established. Interpretations of results of studies on freshwater fish gill Na+/Cl- uptake mechanisms are still being debated compared with those for NaCl secretion. Current models for Na+/Cl- uptake are proposed based on studies in traditionally used model species. Many reported inconsistencies are claimed to be due to differences among species, various experimental designs, or acclimation conditions. Having the benefit of advanced techniques in molecular/cellular biology, functional genomics, and model animals, several new notions have recently been raised concerning relevant issues of Na+/Cl- uptake pathways. Several new windows have been opened particularly in terms of molecular mechanisms of ionocyte differentiation and energy metabolite transport between gill cells during environmental challenge.