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1. The abundance of tyrosine sulfate in secretory proteins and in various classes of cellular proteins has been quantified and compared to protein-bound carbohydrate sulfate. 2. HepG2 cells and fibroblasts, two cell types showing only the constitutive pathway of secretion, and PC12 cells, which show both the constitutive and the regulated pathway of secretion, were subjected to pulse-chase and/ or long-term labelling with [35S]sulfate and [³H]tyrosine, followed by analysis of proteins in the cells and medium. Under both conditions of labelling, 65-92% of the protein-bound tyrosine sulfate and 44-84% of the protein bound carbohydrate sulfate were found to be secretory. In HepG2 cells, the frequency of sulfation of tyrosine residues, which can be determined independently from protein abundance and the rate of protein synthesis, was 8-22 times higher in proteins secreted into the medium than in cellular proteins. 3. All cell lines studied contained significant amounts, not only of carbohydrate sulfate, but also of tyrosine sulfate in specific cellular proteins. As shown for fibroblasts, these tyrosine-sulfated proteins were retained within the cells for at least 100 min of chase following a pulse with [35S]sulfate and were almost completely recovered in a light membrane fraction after subcellular fractionation. 4. Lysosomes were found to contain small, but significant, amounts of protein-bound tyrosine sulfate in addition to protein-bound carbohydrate sulfate. Protein-bound tyrosine sulfate in lysosomes reached a peak at 20 min of chase and rapidly disappeared thereafter, whereas protein-bound carbohydrate sulfate accumulated after 20 min of chase. Examination of the known sequences of eleven lysosomal enzymes revealed the presence of potential tyrosine sulfation sites in five of them. 5. Our results show that secretory proteins are the most abundant, but not exclusive, in vivo substrates for tyrosine sulfation and suggest the presence of soluble tyrosine-sulfated proteins in lysosomes and other, as yet unidentified, organelles of the secretory pathway. In the following paper in this journal we describe the abundance of tyrosine sulfate in integral membrane proteins. [ABSTRACT FROM AUTHOR]

1. The abundance of tyrosine sulfate in membrane proteins was quantified in four different cell lines and compared to that in soluble cellular and secreted proteins. 2. Upon metabolic labelling of HepG2, Ltk-, AtT20 and PC12 cells with [35S]sulfate or [³H]tyrosine, a fraction enriched in integral membrane proteins was found to contain small, but significant, amounts of protein-bound tyrosine sulfate (up to 2.5% of the total cellular plus secreted protein-bound tyrosine sulfate). On the other hand, the frequency of sulfation of tyrosine residues of membrane proteins was within the same order of magnitude as that of secreted proteins, indicating that the low abundance of tyrosine sulfate in membrane proteins was largely a reflection of the low abundance of these proteins themselves. Consistent with this conclusion were the results of an analysis showing that 14 out of 32 selected membrane-spanning proteins contain potential tyrosine sulfation sites. 3. In HepG2 cells, three tyrosine-sulfated integral membrane glycoproteins of molecular mass 100, 125 and 150 kDa were identified. Characterization of the 150-kDa tyrosine-sulfated membrane protein revealed that it was protected from proteolysis in intact cells, suggesting a localization in an intracellular organelle. 4. Together with the results reported in the preceding paper in this journal, our data suggest that tyrosine sulfation occurs in various classes of trans-Golgi-derived proteins, soluble as well as membrane, and extracellularly exposed as well as intracellularly retained, proteins. This suggests that tyrosine sulfation may have a variety of physiological functions, depending on the individual tyrosine-sulfated protein or protein class. [ABSTRACT FROM AUTHOR]

Secretion of haemolysin (HlyA) is secA independent, but depends upon two accessory membrane proteins, HlyB and HlyD. encoded by the hly determinant. A fourth (cytoplasmic) protein, HlyC, is required to activate HlyA post-translationally, but has no role in export. Deletion studies have previously shown that the HlyA molecule contains a targeting signal close to the C-terminus which specifically directs its secretion to the medium. This targeting signal has been variously located within the terminal 27, 53, 60 or 113 amino acids. In this paper, we have sought to confirm the presence of a C-terminal targeting signal and to analyse the specificity of the Hly transport system through fusion of C-terminal fragments of HlyA to heterologous polypeptides. A C-terminal fragment (23 kDa) of HlyA. when fused at the C-terminus, efficiently promoted the secretion of the eukaryotic protein prochymosin (PCM) to the medium via HlyB and HlyD. This result is in contrast to previous findings that prochymosin, preceded by the alkaline phosphatase signal sequence, cannot be translocated across the Escherichia coli inner membrane. The HlyA targeting domain was also used to secrete to the medium varying portions of chloramphenicol acetyltransferase (CAT) and 98 per cent of the β-galactosidase (LacZ) molecule (both E. coli cytoplasmic proteins). In the case of the PCM and CAT fusions the efficiency of secretion was reduced as the proportion of the PCM and CAT molecule increased. This result is consistent with inhibition of secretion through the irreversible folding of the larger passenger protein fragments, or the occlusion of the HlyA targeting signal by upstream sequences. Analysis of the nature of the C-terminal domain promoting secretion of prochymosin, demonstrated that shortening the signal domain from 218 to 113 amino acids significantly reduced the efficiency of secretion. This result may also reflect the importance of maintaining an independent... [ABSTRACT FROM AUTHOR]

Incorporation of silicon-containing amino acids in peptides is known to endow the peptide with desirable properties such as improved proteolytic stability and increased lipophilicity. In the presented study, we demonstrate that incorporation of β-silicon-β3-amino acids into the antimicrobial peptide alamethicin provides the peptide with improved membrane permeabilizing properties. A robust synthetic procedure for the construction of β-silicon-β3-amino acids was developed and the amino acid analogues were incorporated into alamethicin at different positions of the hydrophobic face of the amphipathic helix by using SPPS. The incorporation was shown to provide up to 20-fold increase in calcein release as compared with wild-type alamethicin. [ABSTRACT FROM AUTHOR]

Background and Purpose: We have investigated the effect of deletions of a postsynaptic density, disc large and zo-1 protein (PDZ) motif at the end of the COOH-terminus of the rat A(2B) adenosine receptor on intracellular trafficking following long-term exposure to the agonist 5'-(N-ethylcarboxamido)-adenosine.Experimental Approach: The trafficking of the wild type A(2B) adenosine receptor and deletion mutants expressed in Chinese hamster ovary cells was studied using an enzyme-linked immunosorbent assay in combination with immunofluorescence microscopy.Key Results: The wild type A(2B) adenosine receptor and deletion mutants were all extensively internalized following prolonged treatment with NECA. The intracellular compartment through which the Gln(325)-stop receptor mutant, which lacks the Type II PDZ motif found in the wild type receptor initially trafficked was not the same as the wild type receptor. Expression of dominant negative mutants of arrestin-2, dynamin or Eps-15 inhibited internalization of wild type and Leu(330)-stop receptors, whereas only dominant negative mutant dynamin inhibited agonist-induced internalization of Gln(325)-stop, Ser(326)-stop and Phe(328)-stop receptors. Following internalization, the wild type A(2B) adenosine receptor recycled rapidly to the cell surface, whereas the Gln(325)-stop receptor did not recycle.Conclusions and Implications: Deletion of the COOH-terminus of the A(2B) adenosine receptor beyond Leu(330) switches internalization from an arrestin- and clathrin-dependent pathway to one that is dynamin dependent but arrestin and clathrin independent. The presence of a Type II PDZ motif appears to be essential for arrestin- and clathrin-dependent internalization, as well as recycling of the A(2B) adenosine receptor following prolonged agonist addition. [ABSTRACT FROM AUTHOR]

γ‐Glutamyl transpeptidase from equine kidney (ekGGT, E.C. 2.3.2.2) is an intrinsic membrane enzyme which transfers the γ‐glutamyl moiety of glutathione to amino acids and peptides, thus producing γ‐glutamyl derivatives. An immobilization study of ekGGT was carried out with the aim to develop a robust biocatalyst for the synthesis of γ‐glutamyl amino acids which are known as kokumi compounds. Heterofunctional octyl‐glyoxyl‐agarose resulted in a high immobilization yield and activity recovery (93 % and 88 %, respectively). Immobilized ekGGT retained more than 95 % activity under reaction conditions (Tris‐HCl, pH 9, 0.05 M) after 6 days, whereas the residual activity after 6 reaction cycles (18 days) was 85 %. The synthesis of γ‐glutamylmethionine catalyzed by octyl‐glyoxyl‐agarose‐ekGGT afforded the product in 42 % yield (101 mg). The immobilized ekGGT was characterized by Raman spectroscopy. The immobilization protocol developed for ekGGT could be of general applicability to membrane proteins. [ABSTRACT FROM AUTHOR]

Background: Due to the unavailability of immunological reagents, the Dombrock blood group is insufficiently explored in African populations and can be a source of alloimmunization. A large study including pygmoid and nonpygmoid ethnic groups from East, Central, and West continental Africa, together with African migrants like Comorians, Afro-Caribbean from Martinique, and Maroons from French Guiana would be helpful to increase transfusion safety.Study Design and Methods: Using genomic DNA extracted from blood samples collected from 336 nonpygmoid and 51 pygmoid Africans as well as 268 samples of African descent, DO coding regions were PCR-amplified and sequenced.Results: DO*A and DO*B alleles were detected in almost all groups, with a clear predominance of DO*B in every cohort tested. DO*JO and DO*HY allele frequencies reached 10% or more in several ethnic groups. DO*B-SH-Gln149Lys, DO*B-Ile5Thr, and DO*DODE variants were identified both in African ethnic groups and outside Africa. Twelve novel variants were characterized on a DO*A or a DO*B background. Five of them were found in both African and migrant cohorts, the others were restricted to either within or outside Africa. No DO*DOYA, DO*DOLG, DO*DOLC, nor DO*DOMR variants were observed. A first phylogenetic tree was proposed including all variant alleles.Conclusion: This study across continental Africa and countries with African migrants provides a useful overview of Dombrock allele diversity and distribution. The identification of 12 new alleles underlines the importance of genotyping for Dombrock alleles, particularly to improve transfusion safety in countries hosting migrant populations of African descent. [ABSTRACT FROM AUTHOR]

Microbes are abundant in nature and often highly adapted to local conditions. While great progress has been made in understanding the ecological factors driving their distribution in complex environments, the underpinning molecular-evolutionary mechanisms are rarely dissected. Therefore, we scrutinized the coupling of environmental and molecular adaptation in Thaumarchaeota, an abundant archaeal phylum with a key role in ammonia oxidation. These microbes are adapted to a diverse spectrum of environmental conditions, with pH being a key factor shaping their contemporary distribution and evolutionary diversification. We integrated high-throughput sequencing data spanning a broad representation of ammonia-oxidizing terrestrial lineages with codon modelling analyses, testing the hypothesis that ammonia monooxygenase subunit A (AmoA) - a highly conserved membrane protein crucial for ammonia oxidation and classical marker in microbial ecology - underwent adaptation during specialization to extreme pH environments. While purifying selection has been an important factor limiting AmoA evolution, we identified episodic shifts in selective pressure at the base of two phylogenetically distant lineages that independently adapted to acidic conditions and subsequently gained lasting ecological success. This involved nonconvergent selective mechanisms (positive selection vs. selection acting on variants fixed during an episode of relaxed selection) leading to unique sets of amino acid substitutions that remained fixed across the radiation of both acidophilic lineages, highlighting persistent adaptive value in acidic environments. Our data demonstrates distinct trajectories of AmoA evolution despite convergent phenotypic adaptation, suggesting that microbial environmental specialization can be associated with diverse signals of molecular adaptation, even for marker genes employed routinely by microbial ecologists. [ABSTRACT FROM AUTHOR]

SUMMARY The Frizzled proteins (FZDs) are a family of trans-membrane receptors that play pivotal roles in Wnt pathways and thus in animal development. Based on evaluation of the Amphimedon queenslandica genome, it has been proposed that two Fzd genes may have been present before the split between demosponges and other animals. The major purpose of this study is to go deeper into the evolution of this family of proteins by evaluating an extended set of available data from bilaterians, cnidarians, and different basally branching animal lineages (Ctenophora, Placozoa, Porifera). The present study provides evidence that the last common ancestor of metazoans did possess two Fzd genes, and that the last common ancestor of cnidarians and bilaterians may have possessed four Fzd. Furthermore, amino acid analyses revealed an accurate diagnostic motif for these four FZD subfamilies facilitating the assignation of Frizzled paralogs to each subfamily. By highlighting conserved amino acids for each FZD subfamily, our study could also provide a framework for further research on the precise mechanisms that have driven FZD neo-functionalization. [ABSTRACT FROM AUTHOR]

A monofluoro-substituted amino acid was designed to serve as a conformationally restricted label for solid-state 19F NMR distance measurements in membrane-bound peptides. The aromatic cis and trans isomers of 1-amino-3-(4-fluorophenyl)cyclobutanecarboxylic acid were synthesized in five steps from diethyl 2-(4-fluorophenyl)propanedioate. They were incorporated into the antimicrobial peptide gramicidin S to replace a native DPhenylalanine residue. Because the Cα-tetrasubstituted amino acid cannot racemize, it showed full compatibility with solid-phase peptide synthesis protocols. According to circular dichroism analysis and molecular modeling, the 19F-labeled analogues of the known helix-inducing amino acid (1-aminocyclobutane-1-carboxylic acid) do not disrupt the peptide conformation when substituted for Phe, neither in a β-turn nor in an α-helix. [ABSTRACT FROM AUTHOR]

An extensive series of bis-oligobenzamides and bis-oligopyridylamides have been efficiently prepared and studied by X-ray analysis and computational methods. A modular synthesis led to double α-helix mimics bearing between two and ten branched side-chains. The inter-helix angle and distance can be tuned by varying the length and rigidity of the spacer, thereby reproducing the recognition domains of a range of super-secondary structures. [ABSTRACT FROM AUTHOR]

Background and Purpose: ClC-K kidney Cl(-) channels are important for renal and inner ear transepithelial Cl(-) transport, and are potentially interesting pharmacological targets. They are modulated by niflumic acid (NFA), a non-steroidal anti-inflammatory drug, in a biphasic way: NFA activates ClC-Ka at low concentrations, but blocks the channel above approximately 1 mM. We attempted to identify the amino acids involved in the activation of ClC-Ka by NFA.Experimental Approach: We used site-directed mutagenesis and two-electrode voltage clamp analysis of wild-type and mutant channels expressed in Xenopus oocytes. Guided by the crystal structure of a bacterial CLC homolog, we screened 97 ClC-Ka mutations for alterations of NFA effects.Key Results: Mutations of five residues significantly reduced the potentiating effect of NFA. Two of these (G167A and F213A) drastically altered general gating properties and are unlikely to be involved in NFA binding. The three remaining mutants (L155A, G345S and A349E) severely impaired or abolished NFA potentiation.Conclusions and Implications: The three key residues identified (L155, G345, A349) are localized in two different protein regions that, based on the crystal structure of bacterial CLC homologs, are expected to be exposed to the extracellular side of the channel, relatively close to each other, and are thus good candidates for being part of the potentiating NFA binding site. Alternatively, the protein region identified mediates conformational changes following NFA binding. Our results are an important step towards the development of ClC-Ka activators for treating Bartter syndrome types III and IV with residual channel activity. [ABSTRACT FROM AUTHOR]

Background and Purpose: Cardiac I(Ks) is enhanced by protein kinase A (PKA) stimulation. And PKA-stimulated I(Ks) is about threefold less sensitive to quinidine block than basal current. In this study, we further tested two competing hypotheses: I(Ks) phosphorylation either (i) modulates access of blocking drugs to a binding site; or (ii) destabilizes the drug-channel interaction.Experimental Approach: To distinguish between these hypotheses, we studied quinidine block of I(Ks) channels in which three PKA site residues of the alpha-subunit KCNQ1 were mutated with a bulky negative charged aspartic acid (D). To study alleviation of I(Ks) block by quinidine, we compared activating current at +60 mV, either with or without 5 s hyperpolarizing prepulses to -120 mV.Key Results: Without PKA stimulation, quinidine (100 microM) blocked wild-type current to a similar extent with and without the prepulse (93 +/- 2% of pre-drug current at +60 mV vs. 95 +/- 1%). With PKA-stimulated wild-type channels, however, there was less block with the hyperpolarization to -120 mV: at +60 mV, block was 71 +/- 2% (-prepulse) versus 58 +/- 3% (+prepulse). Individual D-mutations and the triple-D mutant were resistant to quinidine block similar to that seen with PKA-stimulated wild-type I(Ks).Conclusions and Implications: We conclude that phosphorylation-induced insertion of bulky negative charges alleviates quinidine block and that PKA-induced stimulation, by conferring negative charges to the channels, blunts I(Ks) block as the interaction between the channels and blockers becomes destabilized. These effects would be of clinical significance in providing protective mechanisms against pro-arrhythmias caused by drug-induced inhibition of I(Ks) and I(Kr). [ABSTRACT FROM AUTHOR]

A computational model, IMP-TYPE, is proposed for the classification of five types of integral membrane proteins from protein sequence. The proposed model aims not only at providing accurate predictions but most importantly it incorporates interesting and transparent biological patterns. When contrasted with the best-performing existing models, IMP-TYPE reduces the error rates of these methods by 19 and 34% for two out-of-sample tests performed on benchmark datasets. Our empirical evaluations also show that the proposed method provides even bigger improvements, i.e., 29 and 45% error rate reductions, when predictions are performed for sequences that share low (40%) identity with sequences from the training dataset. We also show that IMP-TYPE can be used in a standalone mode, i.e., it duplicates significant majority of correct predictions provided by other leading methods, while providing additional correct predictions which are incorrectly classified by the other methods. Our method computes predictions using a Support Vector Machine classifier that takes feature-based encoded sequence as its input. The input feature set includes hydrophobic AA pairs, which were selected by utilizing a consensus of three feature selection algorithms. The hydrophobic residues that build up the AA pairs used by our method are shown to be associated with the formation of transmembrane helices in a few recent studies concerning integral membrane proteins. Our study also indicates that Met and Phe display a certain degree of hydrophobicity, which may be more crucial than their polarity or aromaticity when they occur in the transmembrane segments. This conclusion is supported by a recent study on potential of mean force for membrane protein folding and a study of scales for membrane propensity of amino acids. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [ABSTRACT FROM AUTHOR]

Etiolated Arabidopsis thaliana seedlings, lacking a functional prephenate dehydratase1 gene ( PD1), also lack the ability to synthesize phenylalanine (Phe) and, as a consequence, phenylpropanoid pigments. We find that low doses of ultraviolet (UV)-C (254 nm) are lethal and low doses of UV-B cause severe damage to etiolated pd1 mutants, but not to wild-type (wt) seedlings. Furthermore, exposure to UV-C is lethal to etiolated gcr1 (encoding a putative G protein-coupled receptor in Arabidopsis) mutants and gpa1 (encoding the sole G protein α subunit in Arabidopsis) mutants. Addition of Phe to growth media restores wt levels of UV resistance to pd1 mutants. The data indicate that the Arabidopsis G protein-signalling pathway is critical to providing protection from UV, and does so via the activation of PD1, resulting in the synthesis of Phe. Cotyledons of etiolated pd1 mutants have proplastids (compared with etioplasts in wt), less cuticular wax and fewer long-chain fatty acids. Phe-derived pigments do not collect in the epidermal cells of pd1 mutants when seedlings are treated with UV, particularly at the cotyledon tip. Addition of Phe to the growth media restores a wt phenotype to pd1 mutants. [ABSTRACT FROM AUTHOR]

The potential mechanisms for driving a ligand to and through a transporter are examined for the leucine transporter using the recently published X-ray structure. Through analyses with computational methods, including investigation of electrostatic properties, site and channel identification, and docking studies, a picture emerges whereby dipolar patches which characterize the electrostatic field serve as the primary driving force to attract the ligand to the protein and begin propagation into it. The electrostatic forces are then augmented by hydrophobic forces in the transport stages, with conformational changes in the protein helping to accommodate the migration. We identify 12 sites that might be involved in ligand recognition and migration. One of these sites corresponds to the tricyclic antidepressant binding site observed in the recently published X-ray structures. [ABSTRACT FROM AUTHOR]

G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure–function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein. [ABSTRACT FROM AUTHOR]

The penta-subunit retromer complex of yeast mediates selective retrieval of membrane proteins from the prevacuolar endosome to the trans Golgi network. In this study, we set out to generate a panel of vps35 dominant-negative mutants that disrupt retromer-mediated cargo sorting. Mapping of the mutations revealed two types of alterations leading to dominant-negative behavior of the 944-amino acid protein: (i) mutations at or near the R98 residue or (ii) C-terminal truncations exemplified by a nonsense mutation at codon 733. Both could be suppressed by overexpression of wild-type Vps35p, suggesting that these dominant-negative mutants compete for interactions with other retromer subunits. Interestingly, Vps35-R98W expression destabilized Vps26p while having no effect on Vps29p stability, while Vps35-Q733* expression affected Vps29p stability but had no effect on Vps26p. Measurement of Vps35/Vps26 and Vps35/Vps29 pairwise associations by coimmunoprecipitation in the presence or absence of other retromer subunits indicated that the R98 residue, which is part of a conserved PRLYL motif, is critical for Vps35p binding to Vps26p, while both R98 and residues 733–944 are needed for efficient binding to Vps29p. [ABSTRACT FROM AUTHOR]

In this work we discover that a specific recognition of the N-terminal lectin domain of FimH adhesin by the usher FimD is essential for the biogenesis of type 1 pili in Escherichia coli. These filamentous organelles are assembled by the chaperone–usher pathway, in which binary complexes between fimbrial subunits and the periplasmic chaperone FimC are recognized by the outer membrane protein FimD (the usher). FimH adhesin initiates fimbriae polymerization and is the first subunit incorporated in the filament. Accordingly, FimD shows higher affinity for the FimC/FimH complex although the structural basis of this specificity is unknown. We have analysed the assembly into fimbria, and the interaction with FimD in vivo, of FimH variants in which the N-terminal lectin domain of FimH was deleted or substituted by different immunoglobulin (Ig) domains, or in which these Ig domains were fused to the N-terminus of full-length FimH. From these data, along with the analysis of a FimH mutant with a single amino acid change (G16D) in the N-terminal lectin domain, we conclude that the lectin domain of FimH is recognized by FimD usher as an essential step for type 1 pilus biogenesis. [ABSTRACT FROM AUTHOR]

Background and purpose:GPRC6A is a novel member of family C of G protein-coupled receptors with so far unknown function. We have recently described both human and mouse GPRC6A as receptors for L-α-amino acids. To date, functional characterization of wild-type GPRC6A has been impaired by the lack of activity in quantitative functional assays. The aim of this study was thus to develop such an assay and extend the pharmacological characterization of GPRC6A.Experimental approach:We have engineered a novel cell-based inositol phosphate turnover assay for wild-type mouse GPRC6A based on transient co-expression with the promiscuous GαqG66D protein, known to increase receptor signalling sensitivity. This assay allowed for measurements of L-α-amino acid potencies. Furthermore, in combination with an assay measuring inward currents at Ca2+-activated chloride channels in Xenopus oocytes, the divalent cation-sensing ability of the receptor was examined.Key results:Using our novel assay, we demonstrate that the basic L-α-amino acids ornithine, lysine, and arginine are the most potent agonists at wild-type mouse GPRC6A. Using two different assay systems, we show that divalent cations do not activate the Gq signalling pathway of mouse GPRC6A per se but positively modulate the amino-acid response.Conclusions and Implications:This is the first reported assay for a wild-type GPRC6A successfully applied for quantitative pharmacological characterization of amino acid and divalent cation responses at mouse GPRC6A. The assay enables further search for GPRC6A ligands such as allosteric modulators, which may provide essential information about the physiological function of GPRC6A.British Journal of Pharmacology (2007) 150, 798–807. doi:10.1038/sj.bjp.0707121; published online 22 January 2007 [ABSTRACT FROM AUTHOR]

NECAPs (adaptin ear-binding clathrin-associated protein) are a new family of clathrin accessory proteins identified through a proteomic analysis of clathrin-coated vesicles (CCVs) from the brain. One member of this family, NECAP 1, is found primarily in tissues from the central nervous system and has been shown to be complexed tightly with a substantial portion of adaptor protein-2 (AP-2) in brain extracts. However, the function and intracellular location of this protein is unknown. In this study, we find that endogenous and epitope-tagged NECAP 1 co-localizes well with clathrin and AP-2 in punctate structures, many of which also contain the presynaptic markers synaptophysin, synaptotagmin or synaptic vesicle protein 2 (SV2). NECAP 1 was also detected by western blot in synaptic vesicle preparations. Overexpression of a truncation mutant of NECAP 1 (BC-NECAP 1) in neurons inhibited transferrin endocytosis but not epidermal growth factor (EGF) endocytosis, and this inhibition was dependent on an AP-2-binding WVQF motif. Moreover, overexpression of BC-NECAP 1 results in inhibition of synaptotagmin endocytosis both in unstimulated neurons and in neurons stimulated with potassium chloride. This inhibition was abrogated by truncation of the WVQF domain. We conclude from these observations that NECAP 1 plays a role in clathrin-mediated neuronal endocytosis, including a role in presynaptic endocytosis. [ABSTRACT FROM AUTHOR]

The Ca2+-ATPase of skeletal muscle sarcoplasmic reticulum (SERCA), an integral membrane protein, becomes irreversibly inactivated in vitro by the addition of a single bolus of peroxynitrite with a K0.5 of 200–300 µ m, and this results in a large decrease of the ATP-dependent Ca2+ gradient across the sarcoplasmic reticulum (SR) membranes. The inactivation of SERCA is raised by treatment of SR vesicles with repetitive micromolar pulses of peroxynitrite. The inhibition of the SERCA is due to the oxidation of thiol groups and tyrosine nitration. Scavengers that react directly with peroxynitrite, such as cysteine, reduced glutathione, NADH, methionine, ascorbate or Trolox, a water-soluble analog of α-tocopherol, afforded significant protection. However, dimethyl sulfoxide and mannitol, two hydroxyl radical scavengers, and α-tocopherol did not protect SERCA from inactivation. Our results showed that the target of peroxynitrite is the cytosolic globular domain of the SERCA and that major skeletal muscle intracellular reductants (ascorbate, NADH and reduced glutathione) protected against inhibition of this ATPase by peroxynitrite. [ABSTRACT FROM AUTHOR]

γ-Hydroxybutyric acid is a naturally occurring substance that may act as a neurotransmitter or neuromodulator to elicit several biological effects. Although the existence of a specific γ-hydroxybutyric acid receptor has been postulated, the receptor protein itself has not been cloned yet. The current study was designed to elucidate whether γ-hydroxybutyric acid receptors are functionally coupled with heterotrimeric G-proteins, especially Gi/Go family, by means of high-affinity GTPase activity and guanosine 5′- O-(3-[35S]thiotriphosphate) ([35S]GTPγS) binding assays in rat brain membranes. The stimulatory effects of GABAB receptor activation were always determined in parallel as a positive control. The selective GABAB receptor agonist (±)-baclofen stimulated the high-affinity GTPase activity in cerebral cortical, hippocampal, and striatal membranes, whereas γ-hydroxybutyric acid was inactive up to 1 mM in these brain regions. The optimum assay conditions for [35S]GTPγS binding to detect a receptor-mediated activation of G-proteins at the greatest signal to noise ratio were then probed as to the concentrations of constituents in the assay mixture (GDP, MgCl2, and NaCl) and incubation period. Even under such an optimized experimental condition, [35S]GTPγS binding was not altered by γ-hydroxybutyric acid in the membranes prepared from cerebral cortex or hippocampus. On the other hand, the specific [35S]GTPγS binding was increased by GABAB receptor agonists in a concentration-dependent manner, which was competitively inhibited by CGP54626, a selective GABAB receptor antagonist. These results indicate that γ-hydroxybutyric acid receptors, if any, are not associated with G-proteins, at least Gi/Go family. [ABSTRACT FROM AUTHOR]

The human anion exchanger AE1 (Band 3) is an abundant glycoprotein localized in plasma membrane of red cells and is responsible for the electro-neutral exchange of chloride for bicarbonate. In order to determine the role of the carboxyl-terminal tail of AE1 in its expression, function and trafficking to the plasma membrane, we generated a series of five constructs encoding truncation mutants missing the last 5 (Δ5), 11 (Δ11), 15 (Δ15), 20 (Δ20) or 35 (Δ35) amino-acids. In transiently transfected HEK 293 cells, immunoblotting of whole cell extracts showed that all the proteins were expressed at the same level as full-length AE1, except Δ20 and particularly Δ35, which showed a reduced expression. Furthermore, the last 15 amino-acids were not required for AE1 folding in the membrane, since Δ5, Δ11 and Δ15 were able to bind to an inhibitor affinity matrix, while Δ20 and Δ35 exhibited poor binding. Immunofluorescence and deglycosylation results showed that Δ15 and Δ11 were retained intracellularly, whereas a lower amount of Δ5 compared with WT trafficked to the plasma membrane. These results indicate that an intact C-terminal tail of human AE1 is important for efficient AE1 trafficking to the plasma membrane. [ABSTRACT FROM AUTHOR]

The rate at which a membrane protein is internalized from the plasma membrane can be regulated by revealing a latent internalization signal in response to an appropriate stimulus. Internalization of the synaptic vesicle membrane protein, synaptotagmin 1, is controlled by two distinct regions of its intracytoplasmic C2B domain, an internalization signal present in the 29 carboxyterminal (CT) amino acids and a separate regulatory region. We have now characterized the internalization motif by mutagenesis and found that it involves an essential tryptophan in the last beta strand of the C2B domain, a region that is distinct from the AP2-binding site previously described. Internalization through the tryptophan-based motif is sensitive to eps15 and dynamin mutants and is therefore likely to be clathrin mediated. A tryptophan-to-phenylalanine mutation had no effect on internalization of the CT domain alone, but completely inhibited endocytosis of the folded C2B domain. This result suggests that recognition of sorting motifs can be influenced by their structural context. We conclude that endocytosis of synaptotagmin 1 requires a novel type of internalization signal that is subject to regulation by the rest of the C2B domain. [ABSTRACT FROM AUTHOR]

F-pilin, the 70-amino-acid F-pilus subunit, accumulates in the cell envelope of F+ strains in a process that requires interactions between its precursor (the traA gene product) and other host and F-encoded proteins. Here, we have used a set of Φ(traA-phoA) genes to explore the effects of different TraA domains on the synthesis and membrane insertion of TraA--PhoA fusion proteins, particularly in relation to other F-encoded gene products. The 51-amino-acid TraA leader peptide fused directly to alkaline phosphatase was synthesized at comparable rates and incorporated rapidly and efficiently into the inner membrane in F' and F- cells. A second fusion gene encoded the TraA leader peptide and the first 51 amino acids of F-pilin itself fused to PhoA (TraA'-'PhoA-102 polypeptide). Alkaline phosphatase activities and patterns of pulse-labelled polypeptides indicated that TraA'--'PhoA-102 was synthesized at comparable rates in F' and F- cells, but in neither was the TraA'-'PhoA-102 polypeptide efficiently processed as a membrane protein. A third gene encoded the entire 121-amino-acid TraA polypeptide fused to PhoA (TraA-'PhoA-121 polypeptide). About 70% of the pulse-labelled TraA-PhoA-121 polypeptide was rapidly processed in F' cells, where it accumulated in the cell envelope as active alkaline phosphatase, whereas in F- cells, <5% of the pulse-labelled polypeptide was processed. Additionally, the apparent rate of TraA-'PhoA-121 polypeptide synthesis was threefold higher in F' cells. The traQ gene alone could not substitute for F in restoring TraA-'PhoA-121 (or wild-type F-pilin) accumulation. [ABSTRACT FROM AUTHOR]

We show that the so-called 'positive inside' rule, i.e. the observation that positively charged amino acids tend to be more prevalent in cytoplasmic than in extra-cytoplasmic segments in transmembrane proteins (von Heijne, G. (1986) EMBO J. 5, 3021-3027), seems to hold for all polar segments in multi-spanning eukaryotic membrane proteins irrespective of their position in the sequence and hence can be used in conjunction with hydrophobicity analysis to predict their transmembrane topology. Further, as suggested by others, we confirm that the net charge difference across the first transmembrane segment correlates well with its orientation (Hartmann, E., Rapoport, T. A. and Lodish H. F. (1989) Proc. Natl Acad. Sci. USA 86, 5786-5790), and that the overall amino-acid composition of long polar segments can also be used to predict their cytoplasmic or extra-cytoplasmic location (Nakashima, H. and Nishikawa, K. (1992) FEBS Lett. 303, 141-146). We present an approach to the topology prediction problem for eukaryotic membrane proteins based on a combination of these methods. [ABSTRACT FROM AUTHOR]

We have analyzed the amino acid distribution in seven nuclearly encoded and five mitochondrially encoded inner membrane proteins with experimentally well characterized topologies. The mitochondrially encoded proteins conform to the ‘positive inside’ rule, i.e. they have many more positively charged residues in their non-translocated as compared to translocated domains. However, most of the nuclearly encoded proteins do not show such a bias but instead have a surprisingly skewed distribution of Glu residues with an almost ten times higher frequency in the intermembrane space than in the matrix domains. These findings suggest that some, but possibly not all, nuclearly encoded inner membrane proteins may insert into the membrane by a mechanism that does not depend on the distribution of positively charged amino acids. [ABSTRACT FROM AUTHOR]

The nucleotide binding center of the uncoupling protein from brown adipose tissue (UCP) was probed by photoaffinity labeling with 8-azido-ATP. The isolated dimeric UCP in non-ionic detergent was used. 8-azido-ATP binds to UCP with a Kd = 3 µM, i.e. with an only threefold lower affinity than ATP and a maximum number of binding sites of about 12 µmol/g protein corresponding to about I mol/mol dimer UCP. UCP is rapidly degraded by ultraviolet radiation, and therefore only near ultraviolet and visible light can be used for photoaffinity labeling. The total covalent incorporation is shown to be dependent on the concentration of azido-ATP and on competing phospholipids. The specific, i.e. ATP-sensitive incorporation only to the binding site depends on the presence of cysteine. With CNBr cleavage the 8-azido-[γ-32P]ATP insertion within the primary structure was located by identifying ATP-sensitive labeled peptides in SDS/PAGE. A major specific 8-azido-ATP incorporation was found by autoradiography in the smallest CNBr fragments. Identification of the radioactive peptides was difficult since 8-azido-ATP insertion causes a distinct shift in the gels from the stained peptides. Identification was possible by specific disulfide formation at the C-terminal within the UCP dimer which only removed the CB7 (CB, CNBr fragment) portion of the lowmolecular-mass peptides but did not move the radioactive band. This excludes the C-terminal CB7 and identifies the labeled peptide as CB6. Also, limited tryptic cleavage of intact UCP at Lys293 did not remove the radioactivity. Cleavage of tryptophanes support localization of 8-azido-ATP between residues 173-280 which includes CB6. Solid-phase sequencing of the labeled CB6 both after serine lactone and carboxyl coupling suggest incorporation into Thr260. These results indicate that the adenine-binding site is within the third domain of the tripartite UCP structure at a putative hydrophilic channel which can be assessed both from the cytosol and matrix of mitochondria. [ABSTRACT FROM AUTHOR]

To investigate the role of the cell surface-exposed regions of outer membrane protein PhoE of Escherichia coli in the biogenesis of the protein, deletions were generated in two presumed cell surface-exposed regions of the protein. Intact cells expressing these mutant proteins were recognized by PhoE-specific monoclonal antibodies, which recognize conformational epitopes on the cell surface-exposed parts of the protein and/or were sensitive to a PhoE-specific phage. This shows that the polypeptides were normally incorporated into the outer membrane. When the deletions extended four amino acid residues into the seventh presumed membrane-spanning segment, the polypeptides accumulated in the periplasm. In conclusion, exposed regions of PhoE protein apparently do not play an essential role in outer membrane localization, which is consistent with the observation that these regions are hypervariable when PhoE is compared to the related proteins OmpF and OmpC. In contrast, the membrane-spanning segments are essential for the assembly process. [ABSTRACT FROM AUTHOR]

Amino acid residue arginine-1 58 of the outer membrane protein PhoE of Eseherichia coli K-I 2 has been shown to be cell-surface-exposed [Korteland et al. (1985) Eur. J. Biochem. 152, 691 -697]. To study the effects of small insertions in this region of the protein on its biogenesis and characteristics, a unique restriction site was created by site-directed mutagenesis in a plasmid carrying the phoE gene and oligonucleotides of 12-74 bp were inserted. The insertions did not interfere with incorporation into the outer membrane since (a) several monoclonal antibodies, directed against the cell-surface-exposed part of PhoE protein, bound to whole cells producing the altered proteins and (b) the proteins formed functional pores for the uptake of β-lactam antibiotics. The binding of one monoclonal antibody and of the PhoE-specific phages TC45 and TC45hrN3 was disturbed by the insertions, showing that this region of the protein is immunogenic and is involved in the binding of both of these phages. The functioning of the mutant pores was characterized both in vivo by studying the uptake of β-lactam antibiotics and in vitro after the reconstitution of the proteins in black lipid films. The pore characteristics changed depending on the nature of the inserted amino acids. Addition of a negatively charged amino acid resulted in decreased anion-selectivity, whereas insertion of a positive charge and deletion of a negative charge had only a small influence. [ABSTRACT FROM AUTHOR]

The sequence of the gene encoding major outer membrane protein (MOMP) P2 of antigenic variants of non-encapsulated Haemophilus influenzae isolated from persistently infected chronic bronchitis patients was analysed. Antigenic drift was shown to result from single base changes in the P2 gene, all generating amino acid changes in the surface-exposed loops of MOMP P2, predominantly in loop 6. Similar single base changes were observed in H. influenzae persistently present in a subcutaneous cage implanted in rabbits, as well as in a spontaneous H. influenzae mutant that had survived MOMP P2 specific monocional- antibody-dependent bactericidal killing in vitro. We hypothesize that accumulation of point mutations under the selection pressure of immunity is a mechanism of antigenic drift of a surface-exposed protein during persistent H. influenzae infection. [ABSTRACT FROM AUTHOR]

The major outer membrane protein of Haemophilus influenzae type b (Hib) is porin (Mr, 38000, 341 amino acids). To identify antigenic determinants on Hib porin that might be exposed at the bacterial cell surface, seven mouse monoclonal anti-Hib porin antibodies were generated. The monoclonal antibodies were tested for their binding to intact cells by flow cytometry; all but one bound to the cell surface. Digestions of Hib porin with cyanogen bromide, hydroxylamine or trypsin generated fragments, the identities of which were confirmed by microsequencing of the amino termini. Following electrophoresis and immunoblotting of the fragments, the specificities of the monoclonal antibodies for their cognate sequences were determined. The porin gene ompP2 was expressed in the baculovirus expression vector system; the recombinant porin was recognized by all of the monoclonal antibodies. Deletions were created by omega mutagenesis of ompP2, generating proteins truncated after amino acids 139, 174, 182, and 264. These deletion proteins were tested for reactivities with the monoclonal antibodies, thereby establishing the boundaries of three antigenic determinants that were recognized by the monoclonals: domain (i), amino acids 104-139; domain (ii) amino acids 162-174; and domain (iii), amino acids 267-341. The biological activities of monoclonal antibodies that were representative of these three classes were tested for their bactericidal activity in complement-mediated lysis of whole cells. The monoclonal antibodies were also tested for their immunoprotective properties in the infant rat model of bacteraemia. Although the monoclonal antibodies were surface-binding, they were neither bactericidal nor protective. [ABSTRACT FROM AUTHOR]

The rate of synthesis of the OmpA and OmpF proteins, two of the major outer membrane proteins of Escherichia coli K12, was determined. At 25 °C both proteins were translated at 6.5 amino acids/s. and the OmpF protein was translated at 15 amino acids/s at 37 °. The former rate corresponded to a synthesis time of just over 50 s for both proteins, which is significantly faster than their reported rates of assembly into the outer membrane at 25 °C. The kinetics of processing of the pro-OmpF protein were also investigated in detail, and the pro-OmpF half-life estimated to be 3-5 s at 25 °C. However a fraction of the precursor was processed more slowly, which may explain the discrepancy between these data and our earlier published estimate of 30 s. Pro-OmpA protein was processed with similar kinetics. These results demonstrate that the rate-limiting step in the assembly of both proteins into the outer membrane is post-translational and follows the processing step. [ABSTRACT FROM AUTHOR]