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PubMed1991

[Genetic aspects of some functional proteins in the central nervous system].

There are some functionally important proteins in the central nervous system. We have studied some of these proteins and analyzed the structure and function of their genes and mRNAs. In this review, we briefly described the present state of the studies on 14-3-3 protein, GABA receptor and dopamine receptor from the standpoint of cDNA and genomic DNA analyses. Particularly, we have emphasized the function, heterogeneity, primary structures, nucleotide sequences, gene structures and the distribution of these proteins and mRNAs in the central nervous system.

14-3-3 Proteins↗

PubMed2004

Small is beautiful: what flies tell us about ERM protein function in development.

Actin dynamics is recognized as being a determinant in many developmental processes and pathologies, such as cell polarity, morphogenesis and tumour metastasis. However, how actin interacts with the plasma membrane is poorly understood. Although numerous studies in cell culture point to the crucial role of Ezrin, Radixin and Moesin (ERM) proteins in the actin-membrane link, genetic approaches in mice have not yet revealed their activity during development. Drosophila has recently become an alternative and promising system for the genetic study of ERM protein function. This article focuses on advances made in flies, providing evidence for the evolutionary conservation of functional properties of ERM proteins, in addition to shedding new light on their importance for development.

Actins↗

PubMed2005

Preventing lipid oxidation during recovery of functional proteins from herring (Clupea harengus) fillets by an acid solubilization process.

It has previously been found that a process based on solubilization at pH 2.7 gives high yields of herring muscle proteins with good functionality. In this study, the development of lipid oxidation during acid processing of herring mince was studied. It was tested how modifications of the process conditions and/or additions of antioxidants could prevent lipid oxidation during the actual process and then during ice storage of the protein isolates. Processing parameters evaluated were prewash of the mince, exposure time to pH 2.7, inclusion or exclusion of a high-speed centrifugation, and addition of antioxidants. Antioxidants tested were erythorbate (0.2%, 9.3 mM), sodium tripolyphosphate (STPP; 0.2%, 5.4 mM), ethylenediaminetetraacetic acid (EDTA; 0.044%, 1.5 mM), and milk proteins (4%). The first three antioxidants were added in the prewash or during the homogenization step, whereas milk proteins were added to the final precipitate. At time 0, all isolates were analyzed for pH, moisture content, and thiobarbituric reactive substances (TBARS). Selected isolates were also analyzed for lipid and protein content. Stability during ice storage was followed in terms of odor, TBARS, and color (a/b values). Extensive lipid oxidation took place using the "control" process without high-speed centrifugation. This was not significantly (p < or = 0.05) affected by a prewash or varied exposure time to pH 2.7. Including high-speed centrifugation (20 min, 10,000g) significantly (p < or = 0.05) reduced TBARS values, total lipids, a values and b values. Erythorbate alone, or in combination with STPP/EDTA, significantly (p < or = 0.05) reduced lipid oxidation during processing if added in the prewash or homogenization step. During ice storage, better stability was gained when antioxidants were added in both of these steps and when EDTA was used instead of STPP.

Antioxidants↗

PubMed2005

PDBSite: a database of the 3D structure of protein functional sites.

The PDBSite database provides comprehensive structural and functional information on various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding, protein-protein, protein-DNA and protein-RNA interactions) in the Protein Data Bank (PDB). The PDBSite is available online at http://wwwmgs.bionet.nsc.ru/mgs/gnw/pdbsite/. It consists of functional sites extracted from PDB using the SITE records and of an additional set containing the protein interaction sites inferred from the contact residues in heterocomplexes. The PDBSite was set up by automated processing of the PDB. The PDBSite database can be queried through the functional description and the structural characteristics of the site and its environment. The PDBSite is integrated with the PDBSiteScan tool allowing structural comparisons of a protein against the functional sites. The PDBSite enables the recognition of functional sites in protein tertiary structures, providing annotation of function through structure. The PDBSite is updated after each new PDB release.

Binding Sites↗

PubMed2005

Metastasis suppressor genes: from gene identification to protein function and regulation.

In the past decade, findings from various disciplines of research have stimulated a reevaluation of fundamental concepts of the biology of metastasis. The convergence of two avenues of research has largely been responsible for this shift. First, clinical and experimental studies of specific steps of the metastatic cascade have shown that cancer cells often disseminate early in the natural history of disease and can persist at secondary sites for extended periods of time. These findings suggest that disseminated cells remain subject to growth regulation at distant sites as "dormant" single cells or microscopic metastases consisting of small numbers of cells. Second, complementary functional, biochemical, and signal transduction studies have identified a specific class of proteins that suppress the formation of overt metastases. These proteins are encoded by metastasis suppressor genes, which are operationally defined as genes that suppress in vivo metastasis without inhibiting primary tumor growth when expressed ectopically in metastatic cell lines. While metastasis suppressor proteins may affect many steps in metastatic development, recent evidence specifically implicates several of these proteins in the regulation of growth of disseminated cells at secondary sites. This review describes the evolving understanding of rate-limiting steps of metastatic growth, and the role of metastasis suppressor proteins in the regulation of these processes. We will give an overview of the studies of metastasis suppressor protein function, which have shifted our attention toward mechanisms of growth control at the secondary site (i.e., "metastatic colonization"). Emphasis is placed upon the complimentary research in the fields of metastasis and signal transduction that has identified signaling pathways controlling metastatic colonization. We also discuss the regulation of metastasis suppressor proteins and the potential biological and biochemical mechanisms responsible for their organ-type specificity. Finally, the implication of these emerging concepts on the development of therapeutic strategies will be presented.

Gene Expression Regulation, Neoplastic↗

PubMed2001

Evolution of Ftz protein function in insects.

The Drosophila gene fushi tarazu (ftz) encodes a homeodomain-containing transcriptional regulator (Ftz) required at several stages during development. Drosophila melanogaster ftz (Dm-ftz) is first expressed in seven stripes defining alternate parasegments of the embryo--a "pair-rule" segmentation function [1, 2]. It is then expressed in specific neural precursor cells in the central nervous system and finally in the developing hindgut [3]. An Orthopteran ortholog of ftz (Sg-ftz, formally Dax) has been isolated from the grasshopper Schistocerca gregaria [4]. The pattern of Sg-ftz expression in Schistocerca embryos suggests that some developmental roles of the ftz gene are likely to be conserved between these two species (e.g., CNS functions) while others may have diverged (e.g., segmentation functions). To test whether the function of the Ftz protein itself differs between these two species, here we compare the functions of Sg-Ftz and Dm-Ftz proteins by expressing both in Drosophila embryos. Sg-ftz mimics only poorly several segmentation roles of Dm-ftz (engrailed activation, wingless repression, and embryonic cuticle transformation). However, the two proteins are similarly active in the rescue of a CNS-specific ftz mutant. These findings argue that this ftz CNS function is mediated by conserved parts of the protein, while efficient pair-rule function requires sequences present specifically in the Drosophila protein.

Amino Acid Sequence↗

PubMed1992

Accessory protein function in the DNA polymerase III holoenzyme from E. coli.

DNA polymerases which duplicate cellular chromosomes are multiprotein complexes. The individual functions of the many proteins required to duplicate a chromosome are not fully understood. The multiprotein complex which duplicates the Escherichia coli chromosome, DNA polymerase III holoenzyme (holoenzyme), contains a DNA polymerase subunit and nine accessory proteins. This report summarizes our current understanding of the individual functions of the accessory proteins within the holoenzyme, lending insight into why a chromosomal replicase needs such a complex structure.

DNA Polymerase III↗

PubMed1992

Alterations of G protein function in cardiac tissues from streptozotocin-induced chronic diabetic rats.

1. This study was performed to investigate G protein function in cardiac tissues from chronic diabetic rats by using pertussis toxin (PTX) and cholera toxin (CTX) as probes for G(i) and Gs proteins, respectively. 2. In the 10-week control group, i.v. injection of PTX significantly elevated the basal heart rate without having any effect on the chronotropic response of right atria to increasing concentrations of isoproterenol (ISO). In the 10-week diabetic rats, PTX treatment had no effect on the basal heart rate or on the response of right atria to ISO. In the 6-month groups, PTX did not exert any effects on basal or ISO-stimulated heart rate in either control or diabetic rat. 3. The inhibitory effect of carbachol (CCH) on cardiac tension in ISO-stimulated left atria was completely abolished by i.v. injection of PTX in the 10-week groups (both control and diabetic rats). The same treatment, however, only slightly reduced the effect of CCH on left atria contraction in rats from 6-month groups. 4. In both control and diabetic rats in the 10-week groups, incubation with CTX caused a significant increase in heart rate in right atria, and in developed cardiac tension in left atria preparations. The magnitude of the increase was the same in both control and diabetic rats. 5. Studies carried out using ADP-ribosylation technique indicated that the amount of G(i) protein was not changed in the ventricular muscle of the 10-week diabetic rat. Labelling of Gs protein could not be detected in either control or diabetic rat heart.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenosine Diphosphate Ribose↗

PubMed2005

Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery.

Every entirely sequenced genome reveals 100 s to 1000 s of protein sequences for which the only annotation available is 'hypothetical protein'. Thus, in the human genome and in the genomes of pathogenic agents there could be 1000 s of potential, unexplored drug targets. Computational prediction of protein function can play a role in studying these targets. We shall review the challenges, research approaches and recently developed tools in the field of computational function-prediction and we will discuss the ways these issues can change the process of drug discovery.

Computational Biology↗

PubMed2001

Immunomodulation of phytohormones and functional proteins in plant cells.

Recombinant antibodies expressed ectopically in plant cells recognize their corresponding antigens and can therefore bind specifically to phytohormones and proteins in vivo. The generation of antibody-antigen complexes interferes with the functions of the targets and affects the phenotype of transgenic plants. Recombinant antibodies can accumulate in different cell compartments and organs of transgenic plants at different stages of development. High levels of expression of specific, high-affinity antibodies are required for immunomodulation. Here, we discuss several models and examples of the antibody-mediated modulation of phytohormone and protein functions in terms of their potential for plant research.

Abscisic Acid↗

PubMedDate not supplied

[Alterations in functional proteins. Calpaine-3 deficiency].

INTRODUCTION: Muscular dystrophies due to calpain deficiency are the first example of a muscular dystrophy due to the mutation of a gene codifying for a non-structural enzymatic protein of unknown function and substrate. DEVELOPMENT: More than 70 mutations have been described in the gene structure, localized to chromosome 15. Although the time course and topography is fairly homogeneous, correlation between the different mutations and the phenotype has still to be analyzed. The age of onset of symptoms is usually between 8 and 14, with no difference between the sexes. There is a slow but uniformly progressive course starting in the pelvis and extending to the shoulder and the distal musculature. Almost all patients are confined to a wheelchair twenty years after onset of the disease. There is no facial, oculomotor or bulbar involvement and gemellar pseudohypertrophy is rare. However, a winged scapula and marked lumbar hyperlordosis is universal. No cardiac or cognitive changes have been observed. Muscle CT shows a pattern of atrophy, mainly of the posterior and medial muscle compartments and of the posterosuperficial group of the legs, which varies depending on the time the disorder has been present. This condition is the commonest etiological group of the dystrophy syndromes, especially of those of late infancy or juvenile onset, in the open populations studied to date. Muscle biopsy, stained by all methods available, is essential to rule out other types of progressive dystrophies secondary to deficiencies of structural proteins.

Adult↗

PubMedDate not supplied

Regulation of G protein function: implications for heart disease.

Heterotrimeric GTP-binding and -hydrolyzing proteins (G proteins) link members of a family of seven-helix transmembrane receptors (G protein-coupled receptors, GPCR) to intracellular effectors. The coupling mechanism involves the G protein completing a cycle of activation, dissociation into alpha and beta gamma subunits, deactivation, and reassociation. At the center of this cycle is the alpha subunit, in which activation by GPCR, GTPase activity, and regulation of effector are combined. Whereas G alpha's functional domains and residues had already been inferred from mutagenesis studies, the recent solution of the crystal structure has elucidated the structural basis of alpha subunit function. It is now clear that an irregularity in any GPCR pathway component could cause a physiological defect. This is confirmed by the identification of mutations in GPCR and G alpha's in various human diseases. Although several cardiomyopathies are associated with abnormal GPCR function, mutations are unlikely in these disorders. The last few years, other aspects of G protein function have moved into focus: e.g. posttranslational modifications; effector regulation by beta gamma subunits; GTPase activating protein (GAP) activity of effectors; G protein expression levels etc. When comparing the regulation of G protein functional activity in cAMP and in inositol phosphate generating pathways, an extrapolation can be made to data on the status of these pathways in some cardiovascular diseases.

Adenylyl Cyclases↗

PubMed1997

"Spot 14" protein functions at the pretranslational level in the regulation of hepatic metabolism by thyroid hormone and glucose.

"Spot 14" protein appears rapidly in nuclei of hepatocytes exposed to glucose and thyroid hormone. Exposure of glucose- and T3-treated hepatocytes to a spot 14 antisense oligonucleotide inhibited induction of mRNAs encoding malic enzyme, ATP citrate-lyase, fatty acid synthase, liver-type pyruvate kinase, phosphoenolpyruvate carboxykinase, and type I deiodinase but not hydroxymethylglutaryl-CoA reductase, cytochrome c, and actin mRNAs. Induction of spot 14, ATP citrate-lyase, and fatty acid synthase polypeptides, but not propionyl-CoA carboxylase and mitochondrial pyruvate carboxylase, was inhibited. Antisense treatment of hepatocytes transfected with a reporter controlled by a glucose- and T3-inducible fragment of the pyruvate kinase gene promoter inhibited reporter activity, as did cotransfection of the reporter and a spot 14 antisense plasmid. Spot 14 protein acts in the induction of mRNAs coding for key lipogenic (malic enzyme, ATP citrate-lyase, fatty acid synthase), glycolytic (pyruvate kinase), and gluconeogenic enzymes (phosphoenolpyruvate carboxykinase), as well as the diet-responsive type I deiodinase, but not those involved in mitochondrial respiration (cytochrome c) or cholesterol synthesis (hydroxymethylglutaryl-CoA reductase). Transfection experiments indicated that these effects are mediated at the transcriptional level. The protein functions in the activation of genes involved in metabolic switching between the fasted and fed states in liver.

ATP Citrate (pro-S)-Lyase↗

PubMed1991

Transient anticardiolipin antibodies, functional protein S deficiency, and deep vein thrombosis.

A 30-year-old man presented with an episode of deep vein thrombosis. He was found to have primary antiphospholipid syndrome with anticardiolipin antibodies and protein S deficiency. All other investigations were negative. Three months later, anticardiolipin antibodies were negative and protein S levels were normal. The transient presence of anticardiolipin antibodies and functional protein S deficiency in this patient suggests a new mechanism for the association between anticardiolipin antibodies and venous thrombosis.

Adult↗

PubMed1992

Contractile protein function in failing and nonfailing human myocardium.

Isometric heat and force measurements were used to relate mechanical performance to function of contractile proteins in muscle strips from failing and nonfailing human hearts (37 degrees C, 60 beats per minute). Compared to control myocardium, crossbridge behavior was altered in myocardium from hearts with end-stage failing dilated and ischemic cardiomyopathy, resulting in increased crossbridge force-time integral by 33% and 36%, respectively. Peak isometric twitch tension was reduced significantly by 46% in muscle strips from hearts with dilated cardiomyopathy. In myocardium from hearts with ischemic cardiomyopathy peak isometric twitch tension was comparable to values from nonfailing hearts. Including all three types of myocardium, there was a close correlation between the number of crossbridge interactions during the isometric twitch (tension-dependent heat) and peak twitch tension (r = 0.88; p less than 0.001). Compared to control, in failing myocardium from dilated cardiomyopathic hearts, tension-independent heat (calcium cycling) was significantly reduced. This indicates that in dilated cardiomyopathy reduced peak twitch tension results from decreased calcium activation of contractile proteins with reduced number of crossbridge interactions during the isometric twitch. In ischemic cardiomyopathy mechanisms different from those observed in dilated cardiomyopathy seem to be involved in the development of heart failure.

Actomyosin↗

PubMed2006

Expression of small hairpin RNAs for S100A9 used in the protein function research.

To study the function of S100A9 protein in HL-60 cells treated with all-trans retinoic acid (ATRA), we had designed and constructed retroviral vectors for expression of small hairpin RNAs (shRNAs), and silenced S100A9 expression in HL-60 cells treated with ATRA. The silence efficiency of siRNA was detected with RT-PCR and Western blotting. The differentiation of HL-60 was monitored by nitro blue tetrazolium (NBT) reduction experiment. Western blot showed that shRNAs remarkably reduce of S100A9 expression in HL-60 cells when they were induced to differentiation by ATRA. But NBT positive percentage of differentiated HL-60 cells was no remarked change with S100A9 expression. The data indicated S100A9 could be no important action during differentiation of HL-60 treated with ATRA.

Calgranulin B↗

PubMed2004

What are the structural features of the active site that define binuclear copper proteins function?

The structural basis that define the physiological functions of binuclear copper enzymes is discussed in the frame of the data generated by a broad spectroscopic approach, spanning from paramagnetic NMR and pulsed EPR to x-ray absorption spectroscopies. The structural features discussed for the different oxidation and ligation states accessible to a binuclear copper sites are the coordination geometry for the first and second shell, the metal-metal distance and the role of the bridging exogenous ligand(s). A structural model will be presented to rationalize both the differentiation in function within the protein families and the reaction mechanism of those proteins that are enzymatically active.

Animals↗

PubMed1996

Threading your way to protein function.

It is still very difficult to determine the function of a protein from its sequence. One potential solution to the problem combines the concept of enzyme superfamilies with modern methods of protein structure prediction. Active-site templates can be used as search tools to identify new members of the superfamilies.

Amino Acid Sequence↗