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Results for “Functional potential”

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PubMed2002

Immunohistochemical localization of calcitonin receptor-like receptor and receptor activity-modifying proteins in the human cerebral vasculature.

Calcitonin gene-related peptide and adrenomedullin belong to a structurally related neuropeptide family and are potent vasodilators expressed in the trigeminovascular system. The molecular identity of receptors for these proteins has only recently been elucidated. Central to functional binding of these neuropeptides is the G-protein-coupled receptor, the calcitonin receptor-like receptor (CRLR), whose cell surface expression and pharmacology is determined by coexpression of a receptor activity-modifying protein (RAMP). CRLR combined with RAMP binds calcitonin gene-related peptide with high affinity, whereas CRLR coexpression with RAMP2 or -3 confers high-affinity binding of adrenomedullin. The authors investigated the expression of these receptor components in human cerebral vasculature to further characterize neuropeptide receptor content and the potential functions of these receptors. Localization has been carried out using specific antisera raised against immunogenic peptide sequences that were subsequently applied using modern immunohistochemical techniques and confocal microscopy. The results are the first to show the presence of these receptor component proteins in human middle meningeal, middle cerebral, pial, and superficial temporal vessels, and confirm that both calcitonin gene-related peptide and adrenomedullin receptors may arise from the coassembly of RAMPs with CRLR in these vessel types. These novel data advance the understanding of the molecular function of the trigeminovascular system, its potential role in vascular headache disorders such as migraine, and may lead to possible ways in which future synthetic ligands may be applied to manage these disorders.

Autoradiography↗

PubMed1999

Large-scale chromatin structure and function.

Recent results in living cells have now established the existence of levels of chromatin folding above the 30 nm fiber within interphase chromosomes. We discuss the potential functional impact of this large-scale chromatin organization, including its possible role in regulating gene expression.

Animals↗

PubMed1997

Intracellular location, complex formation, and function of the transporter associated with antigen processing in yeast.

Peptide transport across the membrane of the endoplasmic reticulum (ER) gains increasing importance in view of its potential function in selective protein degradation and antigen processing. An example for peptide transport in the ER is the transporter associated with antigen processing (TAP), which supplies peptides for the formation of major-histocompatibility-complex class-I complexes. Here, we have expressed human TAP1 and TAP2 in the yeast Saccharomyces cerevisiae. Expression of both genes resulted in the formation of a stable TAP heterodimer that was localized mainly in the ER. Although a minor fraction of TAP is found in the plasma membrane, TAP is unable to restore a-factor secretion in a mutant cell line that lacks the yeast mating-factor transporter Ste6. Nevertheless, in vitro studies with microsomal vesicles demonstrated that the TAP complex is fully functional in the ER membrane in terms of selective peptide binding, ATP-dependent transport, and specific inhibition by the viral protein of herpes simplex virus ICP47. This offers opportunities for topological, structural and mechanistic studies as well as genetic screenings for TAP functionality.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMedDate not supplied

[Possible configuration of dimers of Gua-Cyt bases. Computation by molecular mechanic models and density functional theory].

The energies of interactions between guanine and cytosine in various mutual positions were calculated by the methods of molecular mechanics with refined atom-atom potential functions and the quantum mechanics theory of density functional. Both methods indicate three types of mutual positions of bases in local energy minima. These types correspond to (1) nearly coplanar base positions with intermolecular hydrogen bond formation (base pairing); (2) arrangements of two bases in nearly parallel planes one above another (base stacking); and (3) nearly perpendicular positions of base planes. According to the calculations, the global energy minimum corresponds to the Watson-Crick base pair with three hydrogen bonds. A specific feature of the pair is a transition from many positions of type (2) to positions of type (1) without any energy barrier. This feature is revealed by both methods. Another special feature of this pair is a deviation, for most of mutual base positions, of the amine group atoms from the ring plane, the deviation being more pronounced for Gua. These features are important for understanding the conformational behavior of DNA fragments and the RNA structure.

Cytosine↗

PubMed2002

On the existence of CuI pairs in ZSM-5--a computational study.

The siting and coordination of Cu(I) pairs in zeolite ZSM-5 have been studied by means of a combined quantum mechanics/interatomic potential function technique (QM-Pot). It couples a density functional theory (DFT) description employing a hybrid functional (B3LYP) for copper ions, including their local environment, with a DFT-parameterized shell model ion-pair potential for the periodic ZSM-5 structure. A missing Cu(I)-Cu(I) interaction potential term in the force field has been parameterized on the basis of DFT results. Several distinct coordination sites for Cu(I) pairs have been identified within the ZSM-5 framework. These have been classified as open, nest, open-nest, and cage pairs, owing to the shape of their local environment in the crystal. A nest-shaped, bridged eight-membered ring constitutes the most probable site for the existence of Cu(I) ion pairs. It is energetically favored over all isolated Cu(I) sites. The excitation and emission energies for the singlet-triplet transition of the Cu(I) pairs have been studied. Earlier assignment of an emission band at 520 nm to Cu(I) pairs by others is not supported by our computed results.

Journal Article↗

PubMed2006

Association of cytokine gene polymorphisms with malignant melanoma in Caucasian population.

It has been hypothesized that polymorphisms expected to result in functional changes in cytokine genes may influence susceptibility to cancer, including malignant melanoma (MM). Here, we have screened 24 potentially functional polymorphisms in five cytokine genes by PCR-SBT and PCR-SSP methods in 122 MM cell lines derived from Caucasian patients. The polymorphic positions studied were: TNFA -1031, -863, -857, -851, -574, -376, -308, -238, +488; TGFB1 -988, -800, -509, +869, +915, +652, +673, +713, +788; IL10 -1082, -819, -592; IL6 -174; IFNG -333, +874. The frequencies of cytokine genotypes of melanoma tumours were compared with those published for healthy Caucasians. It was found that TNFA -238 GA, TGFB1 -509 CT, -800 GG, IFNG +874 AT, IL6 -174 GG, IL10 -1082 GA genotypes were significantly decreased, while TNFA -238 AA, -857 CC, TGFB1 -509 TT, IFNG +874 AA, IL6 -174 CC, IL10 -1082 AA, -819 TT, -592 AA genotypes were significantly increased, in MM. This suggests that genotypes provisionally associated with low expression of pro-inflammatory and immunomodulatory TNF-alpha, IFN-gamma and IL-6 and anti-inflammatory IL-10 and TGF-beta1 could be involved in the mechanisms of cancer progression and escape from immunosurveillance.

Cell Line, Tumor↗

PubMed2001

The Yin Yang 1 transcription factor associates with ribonucleoprotein (mRNP) complexes in the cytoplasm of Xenopus oocytes.

Yin Yang 1 (YY1) is a multifunctional transcription factor that activates, represses, or initiates transcription of a diverse assortment of genes. Previous studies suggest a role for YY1 in cellular growth and differentiation, but its biological function during development of the vertebrate oocyte or embryo remains to be determined. We recently showed that YY1 is abundantly expressed throughout oogenesis and early embryonic stages of Xenopus, but it is sequestered in the cytoplasm and does not function directly in transcriptional regulation. In the present study we used a series of biochemical analyses to explore the potential function of YY1 in the oocyte cytoplasm. YY1 was isolated from oocyte lysates by oligo(dT)-cellulose chromatography, suggesting that it associates with maternally expressed mRNA in vivo. RNA mobility shift assays demonstrate that endogenous YY1 binds to labeled histone mRNA. Size exclusion chromatography of oocyte lysates revealed that YY1 exists in high molecular mass complexes in the range of 480 kDa. Destruction of endogenous RNA by RNase treatment of lysates, abolished the binding of YY1 to oligo(dT)-cellulose and resulted in redistribution from 480-kDa complexes to the monomeric form. Microinjection of RNase directly into the cytoplasm released YY1 from 480-kDa complexes and unmasked its DNA-binding activity, but did not promote translocation to the nucleus. These results provide evidence that YY1 is a component of ribonucleoprotein (mRNP) complexes in the Xenopus oocyte, indicating a novel function for YY1 in the storage or metabolism of maternal transcripts.

Active Transport, Cell Nucleus↗

PubMed2001

Oligomeric structures of poliovirus polymerase are important for function.

Central to the replication of poliovirus and other positive-strand RNA viruses is the virally encoded RNA-dependent RNA polymerase. Previous biochemical studies have suggested that direct polymerase- polymerase interactions might be important for polymerase function, and the structure of poliovirus polymerase has revealed two regions of extensive polymerase-polymerase interaction. To explore potential functional roles for the structurally observed polymerase-polymerase interactions, we have performed RNA binding and extension studies of mutant polymerase proteins in solution, disulfide cross-linking studies, mutational analyses in cells, in vitro activity analyses and RNA substrate modeling studies. The results of these studies indicate that both regions of polymerase-polymerase interaction observed in the crystals are indeed functionally important and, furthermore, reveal specific functional roles for each. One of the two regions of interaction provides for efficient substrate RNA binding and the second is crucial for forming catalytic sites. These studies strongly support the hypothesis that the polymerase- polymerase interactions discovered in the crystal structure provide an exquisitely detailed structural context for poliovirus polymerase function and for poliovirus RNA replication in cells.

Amino Acid Substitution↗

PubMed1992

Experimental tests of the cortical imaging technique--applications to the response to median nerve stimulation and the localization of epileptiform discharges.

In a previous paper a method for simulating the electric potentials on the surface of the brain was introduced. This method consisted of the construction of a layer of radially oriented current dipoles in a conducting sphere that simulated the head so that the voltages generated by the layer would take the values measured on the surface of the medium (the scalp). The harmonic potential function for this layer was then evaluated in the interior of the medium in an attempt to approximate the potentials that would be generated by the actual neural sources but which could not be observed without recourse to invasive recording techniques. This method, the cortical imaging technique (CIT), has been previously tested by applying it to artificially generated data where the "cortical surface" potentials were known and could be compared with CIT-generated potentials. In this paper the method is tested by applying it to the scalp-recorded potentials evoked by right median nerve stimulation, where direct cortical recordings are available for comparison, and to the scalp-recorded epileptiform discharges from two patients where the spike foci were well defined. The effects of varying the "noise ratio," an input parameter in CIT which allows one to account for noise in scalp-recorded data, is discussed.

Cerebral Cortex↗

PubMed2006

Adenovirus type 5 early region 1B 156R protein promotes cell transformation independently of repression of p53-stimulated transcription.

Early region 1B (E1B) of adenovirus type 5 (Ad5) encodes at least five different polypeptides generated by alternative splicing of a common mRNA precursor. Two of these gene products, E1B-19K and E1B-55K, are individually capable of cooperating with the Ad5 E1A proteins to completely transform rodent cells in culture. Substantial evidence suggests that these two E1B proteins contribute to cell transformation by antagonizing growth arrest and apoptosis. Here, we performed genetic and biochemical analyses to assess the attributes of the remaining E1B proteins (E1B-156R, E1B-93R, and E1B-84R). Our results show that E1B-156R, which comprises the 79 amino-terminal and 77 carboxy-terminal amino acids of E1B-55K, also enhances focal transformation of primary rat cells in cooperation with E1A. Since E1B-156R seemed unable to relocalize p53 and inhibit its transactivating function, it must be assumed that it contributes to transformation independently of repression of p53-stimulated transcription. Furthermore, we discovered that E1B-156R contains a functional transcriptional repression domain and binds Ad5 E4orf6 and the cellular apoptosis regulator Daxx. While the ability to bind E4orf6 could indicate further biological functions of E1B-156R in viral infection, the interaction with Daxx might also be linked to its transforming potential. Taken together, these analyses introduce E1B-156R as a novel transformation-promoting E1B protein that acts without repressing p53 transactivation. Moreover, identification of the interaction partners E4orf6 and Daxx provides a first glance of E1B-156R's potential functions.

Adaptor Proteins, Signal Transducing↗

PubMed1998

Human-specific integrations of the HERV-K endogenous retrovirus family.

Several distinct families of endogenous retrovirus-like sequences (HERVs) exist in the genomes of humans and other primates. One of these families, the HERV-K group, contains members that encode functional proteins and that have been implicated in the etiology of insulin-dependent diabetes mellitus (IDDM). Because of potential functional and disease relevance, it is important to determine if there are HERV-K-associated genetic differences between individuals. In this study, we have investigated the divergence and evolutionary age of HERV-K long terminal repeats (LTRs). Thirty-seven LTRs, taken primarily from random human clones in GenBank, were aligned and grouped into nine clusters with decreasing sequence divergence. Cluster 1 sequences are 8.6% divergent, on average, whereas cluster 9 LTRs, represented by the LTRs of the fully sequenced HERV-K10 clone, show an average of only 1.1% divergence from each other. The evolutionary age of 18 LTRs from different clusters was then investigated by genomic PCR to determine presence or absence of the retroviral element in different primate species. LTRs from clusters of higher divergence were detected in monkeys and apes, whereas LTRs in clusters with lower divergence were acquired later in evolution. Notably, LTRs of cluster 9 were found only in humans at all nine loci examined. Genomic Southern analysis with an oligonucleotide probe specific for cluster 9 LTRs suggests that HERV-K elements with this type of LTR expanded independently in the genomes of humans and the great apes. This is the first report of endogenous retroviral integrations that are specific to humans and indicates that some HERVs have amplified much later than previously thought. These elements may still be actively transposing and may therefore represent a source of genetic variation linked to disease development.

Animals↗

PubMed2003

Functional comparison of DCs generated in vivo with Flt3 ligand or in vitro from blood monocytes: differential regulation of function by specific classes of physiologic stimuli.

Dendritic cells (DCs) are a family of leukocytes that initiate T- and B-cell immunity against pathogens. Migration of antigen-loaded DCs from sites of infection into draining lymphoid tissues is fundamental to the priming of T-cell immune responses. In humans, the major peripheral blood DC (PBDC) types, CD1c+ DCs and interleukin 3 receptor-positive (IL-3R+) plasmacytoid DCs, are significantly expanded in vivo with the use of Flt3 ligand (FL). DC-like cells can also be generated from monocyte precursors (MoDCs). A detailed comparison of the functional potential of these types of DCs (in an autologous setting) has yet to be reported. Here, we compared the functional capacity of FL-expanded CD1c+ PBDCs with autologous MoDCs in response to 3 different classes of stimuli: (1) proinflammatory mediators, (2) soluble CD40 ligand trimer (CD40L), and (3) intact bacteria (Escherichia coli). Significant differences in functional capacities were found with respect to changes in phenotype, migratory capacity, cytokine secretion, and T-cell stimulation. MoDCs required specific stimuli for the expression of functions. They responded vigorously to CD40L or E coli, expressing cytokines known to regulate interferon-gamma (IFN-gamma) in T cells (IL-12p70, IL-18, and IL-23), but required prostaglandin E2 (PGE2) during stimulation to migrate to chemokines. In contrast, PBDCs matured in response to minimal stimulation, rapidly acquired migratory function in the absence of PGE2-containing stimuli, and were low cytokine producers. Interestingly, both types of DCs were equivalent with respect to stimulation of allogeneic T-cell proliferation and presentation of peptides to cytotoxic T lymphocyte (CTL) lines. These distinct differences are of particular importance when considering the choice of DC types for clinical applications.

Antigens, CD1↗

PubMed2006

CARD tricks: controlling the interactions of CARD6 with RICK and microtubules.

In recent years, a number of proteins have been identified that contain a homotypic interaction motif called the caspase recruitment domain (CARD). Most proteins containing a CARD are involved in pathways regulating apoptosis or adaptive or innate immunity. Examples of prominent CARD proteins are caspase-9 and Apaf1, which are involved in the intrinsic death pathway; BCL10 and CARD11, which mediate antigen receptor-induced NF-kappaB activation; and receptor-interacting protein (RIP)-like interacting caspase-like apoptosis regulatory protein kinase (RICK) and the nucleotide-binding oligomerization domain (NOD) proteins, which induce NF-kappaB activation in response to intracellular bacterial peptidoglycan. The most recently discovered pathway involving CARD proteins senses virally-derived double-stranded (ds) RNA and initiates a host defense signaling program. CARD6 is a CARD-containing protein with a domain structure not shared by any other CARD protein. Although the CARD6 cDNA was deposited in GenBank five years ago, the physiological function of full-length CARD6 has yet to be reported. Here we review our initial characterization of CARD6 and discuss the functional implications of various conserved modules found in the CARD6 protein sequence. We conclude that CARD6 is structurally and potentially functionally related to the superfamily of interferon (IFN)-inducible GTPases, a growing family of host defense proteins that confer cell-autonomous immunity.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Voltage- and site-dependent control of the somatic impact of dendritic IPSPs.

Inhibitory interneurons target specific subcellular compartments of cortical pyramidal neurons, where location-specific interactions of IPSPs with voltage-activated ion channels are likely to influence the inhibitory control of neuronal output. To investigate this, we simulated IPSPs as a conductance source at sites across the somato-apical dendritic axis (up to 750 microm) of neocortical layer 5 pyramidal neurons. Analysis revealed that the electrotonic architecture of cortical pyramidal neurons is highly voltage dependent, resulting in a significant site-dependent disparity between the amplitude, kinetics, and dendro-somatic attenuation of IPSPs generated from depolarized (-50 mV) and hyperpolarized (-80 mV) membrane potentials. At the soma, the time course of IPSPs evoked from depolarized potentials was greatest when generated from proximal dendritic sites and decreased as events were generated more distally, whereas the somatic time course of IPSPs evoked from hyperpolarized potentials was independent of the dendritic site of generation. This behavior resulted from the concerted actions of axo-somatic sodium channels that increased the duration of proximal dendritic IPSPs generated at depolarized potentials and distal dendritic hyperpolarization-activated channels that mediated site independence of somatic IPSP time course at hyperpolarized potentials. Functionally, this voltage-dependent control of IPSPs shaped the spatial and temporal profile of inhibition of axonal action potential firing and dendritic spike generation. Together, these findings demonstrate that the somatic impact of dendritic IPSPs is highly voltage dependent and controlled by classes of ion channels differentially distributed across axodendritic domains, directly revealing site-dependent inhibitory synaptic processing in cortical pyramidal neurons.

Action Potentials↗

PubMed1980

Psychotic depression: the common therapeutic principle.

Cholinergic prevalence together with a monaminergic deficit characterize the neurotransmitter imbalance underlying psychotic depression. Correction of this neurotransmitter imbalance is the principal purpose and goal of all treatment methods for the relief of psychotic depression. This can be accomplished by reducing the acetylcholine predominance or increasing the level of monaminergic functioning, or a combination of both approaches. The antidepressant tricyclic drugs combine a central anticholinergic action with an aminergic potentiating function. Electroconvulsive therapy is effective through activation of both cholinergic and aminergic systems, with removal of excess acetylcholine into the cerebrospinal fluid. Psychiatric surgery restores neurotransmitter balance by blocking excessive acetylcholine synthesis and activity.

Acetylcholine↗

PubMed2003

Structure-function relationships of the extracellular domain of the autosomal dominant polycystic kidney disease-associated protein, polycystin-1.

Polycystin-1 (PC-1) is a member of a novel family of proteins that have a multidomain structure. Although the C-terminal intracellular segments have been extensively studied, mainly with respect to their putative involvement in cell signalling, the potential function of the extracellular domains has received less attention. Mutations in PC-1 result in autosomal dominant polycystic kidney disease (ADPKD) which is characterised by perturbation of transport resulting in fluid accumulation, cell proliferation and modification of the extracellular matrix. The possibility that the interaction of a component of the extracellular matrix or some external factor with PC-1 may be important in the initiation or progression of ADPKD cannot currently be ruled out. The purpose of this review is to assess current evidence for the function of the PC-1 extracellular domains, and their potential implications for ADPKD.

Humans↗

PubMed2026

Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential.

Incomplete functional annotation limits biological interpretation in microbiome studies and their translational potential. Poor annotation arises from multiple causes, with incomplete gene-protein-reaction mapping being one tractable yet under-examined contributor. We address this gap by developing a comprehensive hierarchical framework that systematically integrates gene families in UniRef, proteins in UniProt, and metabolic reactions in MetaCyc and BioCyc through UniProtKB accession, EC number, and Pfam-domain matching. Applied to a human gut metagenome dataset via HUMAnN3, our MetaCyc-based mapping recovers up to 2.3-fold more unique reaction identifiers than the default pipeline and increases reaction prevalence across samples from ≈32% to 52% core reactions, addressing the data sparsity that limits statistical and machine-learning applications in microbiome research. Biological plausibility for the tested functions was supported by positive and negative controls: gut-microbial hormone-metabolism reactions previously linked to this dataset were recovered, while vertebrate-specific hormone-metabolism reactions remained correctly undetected. These gains derive from systematic database integration alone, without predictive algorithms, indicating that a tractable, mapping-related component of functional dark matter and data sparsity in microbiome studies is directly addressable. Because Pfam- and BioCyc-derived mappings trade specificity for coverage, confidence in any individual reaction assignment depends on the supporting evidence tier and source database.

Humans↗

PubMed2004

Lipopolysaccharide-induced paw edema model for detection of cytokine modulating anti-inflammatory agents.

Cytokines are critical to pathogenesis of inflammatory disorders. So inhibition of their action provides therapeutic benefits in various diseases. Although inhibition of inflammation caused by intraperitoneally administered LPS can identify cytokine modulators, this inflammatory test-agent does not allow one to determine overall anti-inflammatory potential. Functional characteristics of Carrageenan (Cara)-induced edema were valuable for identification of nonsteroidal anti-inflammatory drugs (NSAIDS). Hence, the potential of LPS-induced paw inflammation was investigated and compared to that by Cara. Stimulation of isolated rat peritoneal exudates cells (PEC) with 10 ng/ml LPS, but not Cara, induced IL-6 (3.04+/-0.2 ng/ml) and TNFalpha (1.030.09 ng/ml). At least 100 mg/ml Cara was necessary for detection of IL-6 (2.03+/-0.1 ng/ml) and TNFalpha (0.6+0.09 ng/ml) in PEC. Similar to Cara, subplantar administration of LPS-induced inflammatory paw edema in rats. LPS, but not Cara, induced TNFalpha (2.14+/-0.6 ng/ml) and IL-6 (2.9+/-0.5 ng/ml) in serum at 1 and 3 h, respectively, which returned to basal levels by 5 h. LPS-induced serum TNFalpha (sTNFalpha) levels closely paralleled paw swelling and its neutralization by anti-TNFalpha antibody or inhibition by pentoxifylline and nimesulide correlated with inhibition of inflammation. Similar to earlier reports, rofecoxib induced sTNFalpha at 30 mg/kg and exhibited pro-inflammatory effect by enhancing paw swelling. LPS-induced edema provides a useful functional model for identification of cytokine modulating anti-inflammatory agents.

Animals↗