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TY - JOUR. T1 - A new usage of functionalized oligodeoxynucleotide probe for site-specific modification of a guanine base within RNA. AU - Onizuka, Kazumitsu. AU - Taniguchi, Yosuke. AU - Sasaki, Shigeki. PY - 2010/1/29. Y1 - 2010/1/29. N2 - Site-specific modification of RNA is of great significance to investigate RNA structure, function and dynamics. Recently, we reported a new method for sequence-and cytosine-selective chemical modification of RNA based on the functional group transfer reaction of the 1-phenyl-2-methylydene-1,3-diketone unit of the 6-thioguanosine base incorporated in the oligodeoxynucleotide probe. In this study, we describe that the functionality transfer rate is greatly enhanced and the selectivity is shifted to the guanine base when the reaction is performed under alkaline conditions. Detailed investigation indicated that the 2-amino group of the enolate form of rG is the reactant of the functionality transfer reaction. As a potential application of this efficient ...
In 2000 H. van den Berg published eleven articles. In 2001 H. van den Berg published five articles, published one book - monograph and published one chapter. In 2002 H. van den Berg published seven articles, published three chapters and published one book - monograph . In 2004 H. van den Berg published four articles. In 2005 H. van den Berg published three articles and published one chapter. In 2006 H. van den Berg published six articles. In 2007 H. van den Berg published seven articles. In 2009 H. van den Berg published one article. In 2010 H. van den Berg published three articles. In 2011 H. van den Berg published six articles. In 2012 H. van den Berg published two articles. In 2013 H. van den Berg published four articles. ...
We report the sequence of a 4.5-kb cDNA clone isolated from a human melanoma library which bears high amino acid sequence identity to the yeast mitochondrial (mt) DNA polymerase (Mip1p). This cDNA contains a 3720-bp open reading frame encoding a predicted 140-kDa polypeptide that is 43% identical to Mip1p. The N-terminal part of the sequence contains a 13 glutamine stretch encoded by a CAG trinucleotide repeat which is not found in the other DNA polymerases gamma (Pol gamma). Multiple amino acid sequence alignments with Pol gamma from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia pastoris, Drosophila melanogaster, Xenopus laevis and Mus musculus show that these DNA polymerases form a family strongly conserved from yeast to man and are only loosely related to the Family A DNA polymerases. ...
A short sequence of predominantly basic amino acids Pro-Pro-Lys-Lys-Lys-Arg-Lys-Val from SV40 Large T is responsible for the normal nuclear location of the protein. Alteration of Lys-128 to each of six different residues other than Arg renders Large T cytoplasmic, whereas single amino acid changes in the surrounding region impair but do not prevent nuclear accumulation. When transposed to the amino terminus of cytoplasmic Large T species, or Escherichia coli β-galactosidase or of chicken muscle pyruvate kinase, the sequence around Lys-128 of Large T is able to direct the recipient protein to the nucleus. This demonstrates that these amino acids can be sufficient for nuclear location and can act as a nuclear location signal. A computer search of over 2500 proteins reveals that some other nuclear proteins (for example, BK virus Large T, SV40 VP2 and adenovirus 72kDa DNA binding protein) contain very similar basic tracts, but so too do some presumed non-nuclear proteins (for example, poliovirus ...
Alazawi W, Heath H, et al. Stat2 loss leads to cytokine-independent, cell-mediated lethality in LPS-induced sepsis. Proc Natl Acad Sci U S A 110(21):8656-8661, 2013 [95].. Arnold, ES, SC Ling, et al. ALS-linked TDP-43 mutations produce aberrant RNA splicing and adult-onset motor neuron disease without aggregation or loss of nuclear TDP- 43. Proc Natl Acad Sci U S A 110(8):E736- E745, 2013 [96].. Burdick RC, Hu WS, Pathak VK. Nuclear import of APOBEC3F-labeled HIV-1 preintegration complexes. Proc Natl Acad Sci U S A 110(49):E4780-E4789, 2013 [97].. Chen J, Feigenbaum L, et al. Insulin-dependent diabetes induced by pancreatic beta cell expression of IL-15 and IL-15R alpha. Proc Natl Acad Sci U S A 110(33):13534- 13539, 2013 [98].. Feng MQ, Gao W, et al. Therapeutically targeting glypican-3 via a conformation-specific single-domain antibody in hepatocellular carcinoma. Proc Natl Acad Sci U S A 110(12):E1083-E1091, 2013 [99].. Kim TS, Park JE, Shukla A, Choi S, Murugan RN, Lee JH, Ahn M, Rhee K, ...
Using rigorous statistical methods, we have identified and evaluated unusual properties of the distribution of charged residues within the sequences of eukaryotic cellular transcription factors. Virtually all transcription factors, including GAL4, c-Jun, C/EBP, CREB, Oct-1, Oct-2, Sp1, Egr-1, CTF-1, steroid and thyroid hormone receptors, and others, carry one or more highly significant charge clusters. For the most part these clusters (conserved within families of homologous proteins) are of positive net charge but contain also substantial numbers of acidic residues. Predominantly basic charge clusters are often, but not exclusively, associated with DNA-binding domains, and vice versa. Negative charge clusters of note occur only in the yeast protein PHO4 and in the proteins encoded at the Drosophila loci zeste (zeta) and knrl. This dearth of statistically significant negative charge clusters raises questions with respect to the generality of acidic activation domains. A number of sequences ...
RFC 7035 Relative Location October 2013 reference and relative locations while providing a baseline that is as accurate as possible. Both the baseline and the reference location are defined as either a geodetic location [OGC.GeoShape] or a civic address [RFC4776]. If the baseline location was expressed as a geodetic location, the reference MUST be geodetic. If the baseline location was expressed as a civic address, the reference MUST be civic. Baseline and reference locations MAY also include dynamic location information [RFC5962]. The relative location can be expressed using a point (2- or 3-dimensional) or a shape that includes uncertainty: circle, sphere, ellipse, ellipsoid, polygon, prism, or arc-band. Descriptions of these shapes can be found in [RFC5491]. Optionally, a reference to a map document can be provided. The reference is a URI [RFC3986]. The document could be an image or dataset that represents a map, floor plan, or other form. The type of document the URI points to is described ...
The M2 protein of the influenza A virus is a homotetrameric transmembrane proton channel implicated in several stages of the viral replication process. Each of its 97-residue monomers is known to include a transmembrane α-helix. but the structures of the N- and C-terminal domains have not yet been solved. A significant barrier to an atomic level understanding of the M2 protein is the difficulty associated with expression and purification of the full-length protein, which has primarily been studied in the form of truncated constructs covering the amphipathic helix and a short C-terminal segment. This C-terminal segment, which includes residues 46-62, has been shown for a truncated version of the protein to consist of an amphipathic helix lying on the membrane surface. Here, we present SDSL-EPR structural studies using full-length M2 constructs to examine sites 50-54 in the proposed amphipathic helix region of M2. Using power saturation data for the protein reconstituted into vesicles and CW ...
Аннотация доклада: A new algorithm Zebra and a corresponding web-server have been developed to systematically study diverse protein superfamilies and identify the subfamily-specific positions (SSPs) - conserved only within functional subfamilies but different between them - that seem to be responsible for different substrate specificity, catalytic activity, stability, etc. [1]. It is known from experimental enzymology that mutations in the active site can change enantioselectivity, substrate specificity and catalytic promiscuity more effectively than distant ones. However, both close and distant mutations can be important for activity and stability thus highlighting complexity of evolutionary adaptation. Therefore, to identify functionally important SSPs a novel scoring function is suggested that incorporates structural information as well as physicochemical and residue conservation in protein subfamilies. The algorithm does not require pre-defined subfamilies and can propose ...
Human cellular nucleic acid binding protein (CNBP) is a zinc finger DNA binding protein of unknown function. The human CNBP cDNA was used as a probe to isolate four structurally distinct but highly homologous mouse liver cDNA clones. Each of the mouse clones exhibited extraordinary sequence conservation with human CNBP cDNA, and the predicted mouse amino acid sequence identities with human CNBP protein ranged from 99 to 100%. Genetic mapping of CNBP genes in interspecific and intersubspecific mouse backcrosses revealed two loci that hybridize to CNBP cDNA at high stringency, located on chromosomes 5 and 6. The subcellular distribution of the CNBP protein was characterized with a specific polyclonal antibody generated against a synthetic peptide from the carboxyl terminus. CNBP was found in the cytosol and the endoplasmic reticulum in subcellular fractions from mouse liver, but was undetectable in nuclear fractions. These data suggest that CNBP is a member of a highly conserved family of
Affects function: The variants effect on the proteins function, in the format Reported/Curator concluded; + indicating the variant affects function, +? probably affects function, +* affects function, not associated with individuals disease phenotype, # affects function, not associated with any known disease phenotype, - does not affect function, -? probably does not affect function, ? effect unknown, . effect not classified ...
Affects function: The variants effect on the proteins function, in the format Reported/Curator concluded; + indicating the variant affects function, +? probably affects function, +* affects function, not associated with individuals disease phenotype, # affects function, not associated with any known disease phenotype, - does not affect function, -? probably does not affect function, ? effect unknown, . effect not classified ...
The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54, into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees. ...
The DNA sequence of the whole of the short unique region (U S ) and that of part of the short terminal repeat (TR S ) of herpesvirus of turkeys (HVT) were determined. HVT U S is 8·6 kbp long and contains eight potential open reading frames (ORFs). Seven of these have counterparts in the U S of herpes simplex virus type 1 (HSV-1). The homologous proteins include US1, US2, US10, protein kinase (US3) and the glycoproteins gD, gI and gE. In addition, HVT contains one ORF which has a counterpart in the U S of Marek's disease virus (MDV) but is not homologous to any other known herpesvirus gene. Although HVT and MDV proteins encoded by U S genes have evident similarities with proteins encoded by alphaherpesviruses, multiple alignment analysis of predicted amino acid sequences show that HVT proteins are more closely related to MDV proteins than to homologous proteins of mammalian alphaherpesviruses. The percentage amino acid identity between HVT and MDV U S -encoded proteins ranges from 35 to 65, the
Appropriate C-terminal cleavage of a CTL epitope by the proteasome is a crucial step in the formation of precursor peptides leading to MHC presentable TCR ligands. A single residue exchange, flanking the C-terminal amino acid, obliterates accurate proteasome-mediated cleavage. This leads to the generation of peptide precursors that are neither suitable for TAP translocation nor for MHC class I binding. In this case an N to D exchange is caused by a single nucleotide mutation (N = AAC or AAT codon; D = GAC or GAT codon). An alternative explanation for the lack of epitope presentation of the Friend homologue could be the lower MHC class I-binding affinity. The Friend sequence harbors an alternative anchor residue Y instead of F, the binding affinity of the peptide for the MHC class I-Kb molecule has been studied in detail and published in our previous paper (31). The binding affinity of the Y peptide is ∼5-fold lower than that of the F peptide. However, the affinity of this peptide is still very ...
Affects function: The variants effect on the proteins function, in the format R/C where R is the value reported by the source and C is the value concluded by the curator; + indicating the variant affects function, +? probably affects function, +* affects function, not associated with individuals disease phenotype, # affects function, not associated with any known disease phenotype, - does not affect function, -? probably does not affect function, ? effect unknown, . effect not classified ...
Philus transformation. Proc Natl Acad Sci U S A 79: 2393 2397. 47. Duffin PM, Seifert HS DNA uptake sequence-mediated enhancement of transformation in Neisseria
A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing ...
SHANGHAI, May 17, 2017 /PRNewswire/ -- A first full-length class B GPCR crystal structure reveals novel receptor activation mechanisms.
Effect: The variants effect on the proteins function, in the format R/C where R is the value reported by the source and C is the value concluded by the curator; + indicating the variant affects function, +? probably affects function, +* affects function, not associated with individuals disease phenotype, # affects function, not associated with any known disease phenotype, - does not affect function, -? probably does not affect function, ? effect unknown, . effect not classified ...
Effect: The variants effect on the proteins function, in the format R/C where R is the value reported by the source and C is the value concluded by the curator; + indicating the variant affects function, +? probably affects function, +* affects function, not associated with individuals disease phenotype, # affects function, not associated with any known disease phenotype, - does not affect function, -? probably does not affect function, ? effect unknown, . effect not classified ...
The Runt related transcription factors (RUNX) are recognized as key players in suppressing or promoting tumor growth. RUNX3, a member of this family, is known as a tumor suppressor in many types of cancers, although such a paradigm was challenged by some researchers. The TGF-β pathway governs major upstream signals to activate RUNX3. RUNX3 protein consists of several regions and domains. The Runt domain is a conserved DNA binding domain and is considered as the main part of RUNX proteins since. Herein, we compared the effects of Runt domains and full-Runx3 in cell viability by designing two constructs of Runx3, including N-terminal region and Runt domain. We investigated the effect of full-Runx3, N-t, and RD on growth inhibition in AGS, MCF-7, A549, and HEK293 cell lines which are different in TGF-β sensitivity, in the absence and presence of TGF-β. The full length RUNX3 did not notably inhibit growth of these cell lines while, the N-t and RD truncates showed different trends in these cell lines.
Effect: The variants effect on the proteins function, in the format R/C where R is the value reported by the source and C is the value concluded by the curator; + indicating the variant affects function, +? probably affects function, +* affects function, not associated with individuals disease phenotype, # affects function, not associated with any known disease phenotype, - does not affect function, -? probably does not affect function, ? effect unknown, . effect not classified ...
NCAM in vertebrates and its related molecules, apCAM in Aplysia, fasciclin II in Drosophila, and OCAM in mammals, play key roles in various aspects of brain development and functions. In this study, we have identified and characterized three members of the NCAM gene family in zebrafish, designated as zNCAM, zOCAM, and zPCAM. Three molecules exhibit similar domain organization: an amino-terminal signal peptide, five immunoglobulin-like domains, two fibronectin type III-like domains, a transmembrane segment, and a carboxy-terminal cytoplasmic region. A novel molecule zPCAM is most closely related to zNCAM with 66% amino acid identity. Diversity in the extracellular region of zPCAM is generated by insertion of two different types of variable alternatively spliced exons. In situ hybridization analysis revealed that three molecules were specifically expressed by the central and peripheral nervous systems from early developmental stages in region-specific and cell-type-specific manners. For example, ...
Interactions between GPCRs and their cognate G proteins are known to involve several different domains on both the receptor and the G protein heterotrimer. Within Gα, the best characterized GPCR contact site is the extreme C terminus where residues at positions -3 and -4 are particularly important for specific receptor recognition (Conklin et al., 1993, 1996; Kostenis et al., 1997c; Bahia et al., 1998; Blahos et al., 1998; Liu et al., 2002). We have recently demonstrated the importance of the linker I region of Gαq proteins in constraining the fidelity of receptor recognition. A highly conserved glycine residue in linker I (glycine 66) regulates coupling selectivity indirectly by playing a role in the specificity of nucleotide exchange within Gαq induced by ligand-activated GPCRs (Heydorn et al., 2004). Here, we analyzed 1) the relationship between the linker I region and the extreme C terminus of Gα in determining selective GPCR coupling and 2) whether different GPCRs use different Gα ...
The Arabidopsis thaliana R2R3-MYB transcription factor MYB12 is a light-inducible, flavonol-specific activator of flavonoid biosynthesis. The transactivation activity of the AtMYB12 protein was analyzed using a C-terminal deletion series in a transient A. thaliana protoplast assay with the goal of mapping the activation domain (AD). Although the deletion of the last 46 C-terminal amino acids did not affect the activation capacity, the deletion of the last 98 amino acids almost totally abolished transactivation of two different target promoters. A domain swap experiment using the yeast GAL4 DNA-binding domain revealed that the region from positions 282 to 328 of AtMYB12 was sufficient for transactivation. In contrast to the R2R3-MYB ADs known thus far, that of AtMYB12 is not located at the rearmost C-terminal end of the protein. The AtMYB12 AD is conserved in other experimentally proven R2R3-MYB flavonol regulators from different species ...
Lower vertebrate species, including Xenopus laevis, exhibit restricted antibody diversity relative to higher vertebrates. We have analyzed more than 180 VH gene-containing recombinant clones from an unamplified spleen cDNA library by selective sequencing of JH and CH positive clones following iterative hybridization screening with family-specific VH probes, 11 unique families of VH genes, each associated with a unique genomic Southern blot hybridization pattern, are described and compared. Considerable variation in the number of hybridizing components detected by each probe is evident. The nucleotide sequence difference between VH families is as great as, if not more than, that reported in other systems, including representatives of the mammalian, avian, and elasmobranch lineages. Some Xenopus Ig gene families encode alternative amino acids at positions that are otherwise invariant or very rarely substituted in known Igs. Furthermore, variations in complementarity determining region sequences ...
Two distinct IL-1 receptors have been identified as shown by the cloning studies of Sims and coworkers. Both receptors are members of the immunoglobulin superfamily. The type I receptor is an 80 kDa transmembrane protein, 552 amino acids long, with a single 22 amino acid transmembrane region and a long cytoplasmic tail of 213 amion acids. Its extracellular ligand-binding region consists of three immunoglob-ulin-like domains. The type II receptor is a 60 kDa protein and is similar to the type I receptor in its extracellular and transmembrane regions. The type II receptor has a short cytoplasmic tail of 29 amino acids and is incapable of signal transduction. The type II receptor actually competitively inhibits IL-1 activity by acting as a decoy receptor for IL-1, and regulates the level of extracellular IL-1.. IL-1 acts on target cells by binding with high affinity (Kd of 10~10 m) to IL-1 type I receptors. Type I receptors are found on T cells, endothelial cells, hepatocytes, fibroblasts and ...
Identification of Critical Amino Acid Residues in Human Immunodeficiency Virus Type 1 IN Required for Efficient Proviral DNA Formation at Steps prior to Integra
Alternative splicing of transcripts from a single gene is often used as a mechanism for generating protein variants with diverse functions (reviewed by McKeown, 1992). In the case of transcription factor genes, alternative splicing frequently gives rise to protein isoforms with distinct or even opposing transcriptional activities (reviewed by Foulkes and Sassone‐Corsi, 1992). However, few cases are known where the DNA sequence specificity of a transcription factor is altered by alternative splicing. Pax6 belongs to this class of genes which normally code for transcription factors with modular DNA‐binding domains such as the mammalian WT‐1, the Drosophila Tramtrack and CF2 zinc finger proteins (Bickmore et al., 1992; Gogos et al., 1992; Read and Manley, 1992). Here we have demonstrated that a second Pax gene, Pax8, also codes for alternative splice products with drastically different DNA‐binding specificities.. The paired domain is a bipartite DNA‐binding region consisting of an ...
Nine integrin alpha subunits contain an additional domain (termed A or I) that is inserted into the head region, where it plays a central role in ligand binding: thus, recombinant I domains recapitulate many of the ligand-binding properties of the intact integrin. The first crystal structure of an I domain shows that it adopts the dinucleotide-binding fold, with a central mostly parallel beta sheet surrounded on both sides by amphipathic alpha helices. At the C-terminal end of the beta sheet is a conserved metal binding site that has been called the metal ion-dependent adhesion site, or MIDAS motif. Mutagenesis studies have shown that the MIDAS motif and exposed side chains on the surrounding surface are required for ligand binding, and are thus likely to form the ligand contact sites. Comparison between two different crystal forms of the alphaM-I domain led to the proposal that affinity regulation occurs via changes in metal coordination at the MIDAS motif that are linked to tertiary changes ...
A new kind of high avidity binding molecule, termed peptabody was made by harnessing the result of multivalent interaction. 85 kDa, with interchain disulfide bonds. Pab-S could be dissociated under denaturing and reducing circumstances and reassociated like a pentamer with full-binding activity. This intrinsic feature has an easy method to mix Pab substances with two different peptide specificities, creating heteropentamers with bispecific and/or chelating properties thus. binding actions for different receptors. A robust method of developing artificial ligands emerges by MCC950 sodium novel inhibtior the testing of huge phage libraries, displaying billions of different polypeptide sequences fused with coat proteins on the surface of filamentous bacteriophage (1, 2). For example, isolation of new peptide ligands allowed the mapping of antibody binding sites, the characterization of important residues in HLA-DR molecules, and the identification of protease substrates or inhibitors (for review see ...
Hematopoietic antigen receptors such as the TCR, the B cell receptor, or Fc receptors are generally composed of at least two different subunits, one representing the ligand binding site, the other being responsible for signal transduction after receptor engagement. The molecular structure of these two subunits reflects their different tasks for eliciting cellular responses. Thus, the ligand binding site normally comprises a long extracellular domain (serving as recognition element), an α-helical transmembrane domain that carries at least one charged amino acid, and a very short cytoplasmic segment devoid of any signaling motifs. In contrast, the signal-transducing component is composed of a very short extracellular domain (lacking an external ligand), a transmembrane domain that also contains a charged amino acid (to allow stable interaction with the ligand binding subunit), and a comparably long cytoplasmic tail carrying particular amino acid motifs, which are necessary for signal ...
GWAS and more recently whole-exome/genome sequencing have generated a massive expansion in the number of candidate disease genes. Animal models will have an essential role in validating candidate genes and understanding their role in pathobiology. Advances in targeted genome engineering with TALENs and CRISPRs now makes it feasible for individual laboratories to generate heritable and precise sequence modifications of their gene of interest in any organism. Zebrafish are an attractive model system because they share the vast majority of human disease genes. Genome editing tools such as CRISPR-Cas9 and TALENs permit heritable and precise sequence modification of the genome. In this session I will discuss the strengths and weaknesses of the new genome editing tools and compare these methods to existing gene knock-down approaches. I will provide a brief overview of how we are applying these exciting genome editing tools to generate more informative models of human disease.. ...
Yeast two-hybrid system. The C-terminal regions of mGluRs (ct-mGluRs) and the GABAB2 subunit of GABA receptors were amplified by PCR from plasmids encoding the full-length rat receptors or by reverse transcriptase (RT)-mediated PCR from rat brain total RNA. The amplified fragments were subcloned in frame into a bait plasmid, pAS2-1 (Clontech, Palo Alto, CA). The appropriate integrity of inserts was verified by DNA sequencing. In yeast two-hybrid screening, an adult rat brain cDNA library fused to the GAL4 activation domain (MATCHMAKER GAL4 cDNA library; Clontech) was cotransformed into yeast Y190 (Clontech) with the bait plasmid containing the ct-mGluR2 sequence. Colony selection and β-galactosidase reporter gene assay were performed as described previously (Dev et al., 1999). Yeast two-hybrid screening of tamalin-binding proteins from a rat brain cDNA library was conducted with use of the bait plasmid containing the full-length rat tamalin sequence.. cDNA cloning and sequence analysis. Four ...
Author Summary Intrinsically unstructured/disordered proteins (IUPs/IDPs) do not adopt a stable structure in isolation but exist as a highly flexible ensemble of conformations. Despite the lack of a well-defined structure these proteins carry out important functions. Many IUPs/IDPs function via binding specifically to other macromolecules that involves a disorder-to-order transition. The molecular recognition functions of IUPs/IDPs include regulatory and signaling interactions where binding to multiple partners and high-specificity/low-affinity interactions play a crucial role. Due to their specific functional and structural properties, these binding regions have distinct properties compared to both globular proteins and disordered regions in general. Here, we present a general method to identify disordered binding regions from the amino acid sequence. Our method targets the essential feature of these regions: they behave in a characteristically different manner in isolation than bound to their partner
We have mapped determinants for species‐specific interactions of Par components (Figure 6). Operon repression involves a specific interaction between ParA and the operator DNA. The specific determinant includes a HTH motif in the N‐terminal region of ParA and probably contacts the operator directly. Direct binding of ParA to the operator sequence has been shown previously (Davis et al., 1992).. Specific enhancement of repression by ParB was shown to be due to a protein-protein interaction with ParA rather than direct recognition of the operator by ParB. This is consistent with the observation that ParB does not appear to bind to the operator by itself, and does not cause any qualitative modification of the footprint of ParA bound to operator DNA (Davis et al., 1992). The ParA-ParB interaction involves determinants in the C‐terminal region of ParA and the N‐terminal end of ParB (Figure 6). ParA and ParB interact directly in vitro (Davis et al., 1992). Thus it is likely that the mapped ...
The tumor suppressor protein, p53, is mutated or dysregulated in nearly all human cancers(1). The amino terminal domains are essential for transcriptional activation in stressed cells and play a vital role in cell cycle regulation, apoptosis and senescence. The transactivation (TAD) and proline rich domains in this region are dynamic and intrinsically disordered; lacking stable secondary or tertiary structure. This region contains multiple binding sites; arguably, the most significant of these is for p53s negative regulator, the E3 ligase, MDM2. An important, but less understood interaction involving the single stranded DNA binding protein, RPA70A, is hypothesized to be involved in maintaining genome integrity(2-4). Additionally, the amino terminus contains an important single nucleotide polymorphism that has demonstrated different affinity for MDM2 and is of significant biological importance in the induction of apoptosis (5). Isothermal titration calorimetry (ITC) and nuclear magnetic resonance (NMR)
K(v)3.4 belongs to the shaw subfamily of shaker-type potassium channels. It conducts fast inactivating, high threshold currents in the central nervous system and in fast-twitch skeletal muscle fibers. The corresponding mouse gene, Kcnc4, consists of five exons spanning a region of 20 kb. Approximately 700 bp of regulatory sequence were delineated. It is GC rich and lacks typical TATA and CAAT motifs. Instead, seven Sp-1 and three E-box elements define putative regulatory sequences. The mouse K(v)3.4 mRNA has a size of 3639 bp, 1120 bp of which are 3 untranslated region. A transcript initiated from an alternative 5-exon was identified by RACE and verified by genomic analysis. This isoform, designated K(v)3.4d, is predominantly expressed in skeletal muscle and probably results from alternative promoter usage. It encodes a channel protein with a novel N-terminal cytoplasmic domain. It lacks the conserved sequence motifs encoding the shaw-type tetramerization domain and the ball peptide, which ...
Comparative genomics is a powerful means of uncovering important functional DNA elements through DNA sequence conservation [63], but identification of mouse Dxz4 was initially discovered not through primary DNA sequence conservation but instead through conservation of DNA sequence organization within a syntenic region of the mouse genome. This work led to the subsequent identification of DXZ4 in a diverse group of distantly related mammals. DNA sequence comparisons revealed a highly conserved region within each DXZ4 monomer that corresponds to the CTCF binding motif that is bound by CTCF in all mammals tested thus far. Furthermore, the highly conserved sequence immediately adjacent to the Ctcf consensus site suggests a second DNA binding protein may associate alongside Ctcf. Therefore, on the basis of conservation, several features of DXZ4 appear to have functional importance in eutherian mammals: CTCF binding, tandem-repeat organization, expression, and location downstream of PLS3.. In primates ...
Researchers have just made an important discover in how chromosomes are recognized and repaired after suffering a complete breakage. ...
Evidence that the transcriptional unit identified corresponds to fl(2)d: Several lines of evidence indicate that the transcriptional unit described above corresponds to fl(2)d. First, the site of P-element insertion in the fl(2)dP mutant disrupts the longer Fl(2)d ORF (Figures 2A and 4A). Second, sequence analysis of genomic DNA from fl(2)d1 flies, a recessive temperature-sensitive mutant of fl(2)d, revealed a single G to A nucleotide change at nucleotide position 939. This results in an amino acid change from aspartic acid to asparagine at position 180 of the longer version of Fl(2)d ORF (Figure 4, A and B). Third, sequence analysis of genomic DNA from fl(2)d2/+ heterozygous flies also revealed DNA alterations that are consistent with the stronger, non-sex-specific phenotype associated with this mutation (Granadinoet al. 1992). Because fl(2)d2 is lethal in homozygosis, DNA from fl(2)d2/+ heterozygous flies was amplified by PCR to generate products that span the complete ORF. The profile of the ...
Distribution of the mRNA/peptide in the cardiovascular system Southern blot analysis of human genomic DNA under low hybridization stringency with a 42-mer synthetic oligonucleotide probe corresponding to amino acid residues 7-20 of ET, showed that three different restriction fragments were always detected regardless of the restriction endonucleases used. The nucleotide sequences encoding amino acid residues of the three ETs are highly conserved among the three genes, with 77-82% of the nucleotide residues being identical [2]. By contrast, the nucleotide sequences upstream from the mature peptides are very poorly conserved. These observations suggest that although the three genes are evolutionally relatively distant from each other, the genes evolved from a common ancestral gene under strong pressure to preserve mature ET sequences. The three peptides were designated ET-1, ET-2 and ET-3 [5]. ET-1 is the original peptide corresponding to that detected in the culture medium of porcine aortic ...
TY - JOUR. T1 - TTC4, a novel human gene containing the tetratricopeptide repeat and mapping to the region of chromosome 1p31 that is frequently deleted in sporadic breast cancer. AU - Su, Guanfang. AU - Roberts, Terry. AU - Cowell, John Kenneth. PY - 1999/1/15. Y1 - 1999/1/15. N2 - The 1p31 region shows loss of heterozygosity in up to 50% of human breast cancers, indicating the presence of a tumor suppressor gene in this location. We have mapped six novel ESTs to a 15-Mb contig of yeast artificial chromosomes spanning the critical region of 1p31. One of these ESTs was localized within the contig to the region most commonly undergoing loss of heterozygosity in breast cancer. The corresponding gene sequence for this EST was established by cDNA cloning and RACE procedures. This gene is 2 kb long and contains a tetratricopeptide repeat motif and a coiled-coil domain. This family of genes has been implicated in a wide variety of functions, including tumorigenesis. This is the fourth member of the ...
Press release about the Basel Committee issuing final guidelines on identification and management of step-in risk (25 October 2017). The Basel Committee on Banking Supervision released today the final Guidelines on identification and management of step-in risk. Step-in risk refers to the risk that a bank provides financial support to an entity beyond, or in the absence of, its contractual obligations should the entity experience financial stress.
We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequence to a DNA sequence data base by translating the DNA data base as it is searched. FASTA includes an additional step in the calculation of the initial pairwise similarity score that allows multiple regions of similarity to be joined to increase the score of related sequences. The RDF2 program can be used to evaluate the significance of similarity scores using a shuffling method that preserves local sequence composition. The LFASTA program can display all the regions of local similarity between two sequences with scores greater than a threshold, using the same scoring parameters and a similar alignment ...
On Feb 8, 2012, at 8:52 AM, Brad Kemper wrote: , On Feb 8, 2012, at 1:28 AM, Alex Mogilevsky ,[email protected], wrote: , ,,, From: Brad Kemper [mailto:[email protected]] ,,, Sent: Tuesday, February 07, 2012 6:34 PM ,,, ,,, What it the purpose of this restriction? If authors wants that behavior, they can ,,, just set position:relative on the first block. Why must it be prescribed as a ,,, containing block? ,, ,, Set position:relative on first region or root element of named flow? , , Im confused by the question, because root element of named flow is meaningless to me (or, has been meaningless, or should be meaningless). The root of any HTML document Id the HTML element viewport, and there is only one root per document. , , I had meant that the author could set position:relative on first region, instead of the first region being the ICB. It seems like that would amount to the same effect, except that it wouldnt be mandatory (the author could leave the first region as static, and ...
The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [(PUBMED:7667876), (PUBMED:9482716), (PUBMED:1882418)]. It mediates protein-protein interactions and the assembly of multiprotein complexes [(PUBMED:14659697)]. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs ...
The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [(PUBMED:7667876), (PUBMED:9482716), (PUBMED:1882418)]. It mediates protein-protein interactions and the assembly of multiprotein complexes [(PUBMED:14659697)]. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs ...
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In the present study, we cloned, sequenced, and generated specific antibodies for immunolocalization, and assayed functional activity of two closely related homologues of Kir4.2 that are expressed in rat hepatocytes. These results extend the recent cloning of a Kir4.2 from whole mouse liver (22). Although Kir4.2 mRNA was not detected on Northern blot analyses of embryonic mouse liver (27), this likely resulted from an inability to detect rare messages such as K+ channels in nonexcitable tissue and/or the tissue developmental stage. Nonconducting human and guinea pig transcripts have also been cloned (6, 25). The overall sequence identity at the amino acid level is 90%. The biophysical properties of Kir4.2 make it a suitable candidate for the functional data accumulated regarding K+ fluxes in the intact liver and isolated hepatocytes. Furthermore, whole cell currents of short-term cultured rat hepatocytes exhibit characteristics of moderately inwardly rectifying K+ channels (12) such as ...
TY - JOUR. T1 - Cloning of a novel amphiphysin isoform edna composed of multiple splicing variants and their differential tissue expression. AU - Tsutsui, Kimiko. AU - Maeda, Yukihide. AU - Tsutsui, Ken. AU - Sa, Kuniaki. AU - Seki, Shuji. AU - Tokunaga, Akira. PY - 1997/12/1. Y1 - 1997/12/1. N2 - Amphiphysin, an Stt3-domain containing protein concentrated in nerve terminals, is believed to be involved in the synaptic vesicle recycling. We have cloned cDNAs of a novel isoform of amphiphysin from mammals (man, rat, and mouse) by utilizing sequence information for homologous ESTs accumulated in databases. More than 10 subtypes of the isoform with 50-60 amino acid identity to the human amphiphysin were identified by a conventional library screening and PCR amplification of cDNA libraries. Each subtype probably represents a splicing variant of a single gene transcript. Analysis of mRNA expression in various tissues by RT-PCR showed that the isoform is more ubiquitously distributed than the canonical ...
Epitope tags are short peptide sequences that are easily recognized by tag-specific antibodies. Due to their small size, epitope tags do not affect the tagged proteins biochemical properties. Most often, sequences encoding the epitope tag are included with target DNA at the time of cloning to produce fusion proteins containing the epitope tag sequence. This allows anti-epitope tag antibodies to serve as universal detection reagents for any tag-containing protein produced by recombinant means. This means that anti-epitope tag antibodies are a useful alternative to generating specific antibodies to identify, immunoprecipitate or immunoaffinity purify a recombinant protein. The anti-epitope tag antibody is usually functional in a variety of antibody-dependent experimental procedures. Expression vectors producing epitope tag fusion proteins are available for a variety of host expression systems including bacteria, yeast, insect and mammalian cells. Rockland Immunochemicals produces anti-epitope tag
Big MAP kinase 1 (BMK1), also known as ERK5, is a mitogen-activated protein (MAP) kinase member whose biological role is largely undefined. The activity of BMK1 in rat smooth muscle cells is up-regulated by oxidants. A constitutively active form of the MAP kinase kinase, MEK5(D), is described which selectively activates BMK1 but not other MAP kinases in vivo. Through utilization of MEK5(D), it has been determined that a member of the MEF2 transcription factor family, MEF2C, is a protein substrate of BMK1. BMK1 dramatically enhances the transactivation activity of MEF2C by phosphorylating a serine residue at amino acid position 387 in this transcription factor. Serum is also a potent stimulator of BMK1-induced MEF2C phosphorylation, since a dominant-negative form of BMK1 specifically inhibits serum-induced activation of MEF2C. One consequence of MEF2C activation is increased transcription of the c-jun gene. Taken together, these results strongly suggest that in some cell types the MEK5/BMK1 MAP ...
Short-chain dehydrogenases/reductases (SDRs) constitute a large family of NAD(P)(H)-dependent oxidoreductases, sharing sequence motifs and displaying similar mechanisms. SDR enzymes have critical roles in lipid, amino acid, carbohydrate, cofactor, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. Sequence identities are low, and the most conserved feature is an alpha/beta folding pattern with a central beta sheet flanked by 2 - 3 alpha-helices from each side, thus a classical Rossmannfold motif for nucleotide binding. The conservation of this element and an active site, often with an Asn-Ser-Tyr-Lys tetrad, provides a platform for enzymatic activities encompassing several EC classes, including oxidoreductases, epimerases and lyases. The common mechanism is an underlying hydride and proton transfer involving the nicotinamide and typically an active site tyrosine residue, whereas substrate specificity is determined by a variable C-terminal segment. Relationships exist with ...
The approximately 250-amino-acid protein domain EAL (www.sanger.ac.uk/Software/Pfam), also referred to as domain of unknown function 2 or DUF2 (http://smart.embl-heidelberg.de), is conserved in the Bacteria. The domain name originates from one of the most conserved amino acid signature motifs, EAL (Glu-Ala-Leu). EAL is encoded by most sequenced genomes in all branches of the bacterial phylogenetic tree, which implies that EAL-containing proteins play important roles in Bacteria (8, 9). This domain is not encoded in the genomes of Archaea or Eukarya, except for two putative proteins of Anopheles gambiae, which probably originated from bacterial contamination (19). EAL is often linked to sensory and/or output (signal transduction) domains and is, in fact, one of the most ubiquitous bacterial signal transduction domains whose biochemical activity has not been characterized yet (8, 9). In many proteins, EAL is located C terminal of the approximately 170-amino-acid GGDEF domain (also known as DUF1). ...
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We present data on the interaction of arginine-rich peptides of human immunodeficiency virus (HIV-Tat) with tRNAPhe of Saccharomyces cerevisiae. We have found that tRNA forms complexes with the Tat1 peptide of amino acid sequence GRKKRRQRRRA and its mutants where R is replaced by D-arginine, citrulline or ornithine. The structure of tRNA-Tat1 complex was probed by specific RNases digestions and Pb2+-induced cleavage of phosphodiester bond of guanosine. The nucleotide sequence UGGG located in the dihydrouridine loop of tRNAPhe binds to Tat peptide and therefore is specifically protected against RNases and is not hydrolyzed by Pb2+ ion. It seems that the peptide-RNA complex formation depends on direct recognition of guanine moieties of tRNA with arginine residues. These interactions are similar to those observed in many DNA-protein complexes, but are different from those previously observed for TAR RNA-Tat complexes.. Keywords: Tat peptides; TAR RNA; tRNAPhe; Protein-nucleic acids interactions; ...
[48 Pages Report] Check for Discount on Interleukin 1 Receptor Type 1 (CD121 Antigen Like Family Member A or Interleukin 1 Receptor Alpha or p80 or CD121a or IL1R1) - Pipeline Review, H2 2017 report by Global Markets Direct. Interleukin 1 Receptor Type 1 (CD121 Antigen Like Family Member...
Antibodies for proteins involved in glycerol biosynthetic process pathways, according to their Panther/Gene Ontology Classification
1. Slamon DJ, Clark GM, Wong SG et al. Human breast cancer: Correlation of relapse and survival with amplification of the HER-2/neu oncogene. Science 1987; 235: 177-182. 2. Ross JS, Fletcher JA, Bloom KJ et al. Targeted therapy in breast cancer: the HER-2/neu gene and protein. Mol Cell Proteomics 2004; 3(4): 379-398 (Review). 3. Hudziak RM, Schlessinger J, Ullrich A. Increased expression of the putative growth factor receptor p185HER2 causes transformation and tumorigenesis of NIH 3T3 cells. Proc Natl Acad Sci USA 1987; 84(20): 7159-7163. 4. Yarden Y, Sliwkowski MX. Untangling the ErbB signalling network. Nat Rev Mol Cell Biol 2001; 2(2): 127-137 (Review). 5. Codony-Servat J, Albanell J, Lopez-Talavera JC et al. Cleavage of the HER2 ectodomain is a pervanadate‑activable process that is inhibited by the tissue inhibitor of metalloproteases-1 in breast cancer cells. Cancer Res 1999; 59(6): 1196-1201. 6. Vivanco I, Sawyers CL. The phosphatidylinositol 3-Kinase AKT pathway in human cancer. Nat Rev ...
FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a type-I receptor transmembrane protein that is a member of the vacuolar protein sorting 10 receptor family. Proteins of this family are defined by a vacuolar protein sorting 10 domain at the N-terminus. The N-terminal segment of this domain has a consensus motif for proprotein convertase processing, and the C-terminal segment of this domain is characterized by ten conserved cysteine residues. The vacuolar protein sorting 10 domain is followed by a leucine-rich segment, a transmembrane domain, and a short C-terminal cytoplasmic domain that interacts with adaptor molecules. The transcript is expressed at high levels in the brain, and candidate gene studies suggest that genetic variation in this gene is associated with Alzheimer's disease. Consistent with this observation, knockdown of the gene in cell culture results in an increase in amyloid precursor protein processing. ...
Ligand stimulation of growth factor receptors with intrinsic protein-tyrosine kinase activity initiates the assembly of multienzyme signalling complexes. This is mediated by binding of proteins with src homology 2 (SH2) domains to receptor autophosphorylation sites. Among the proteins involved in complex formation is phosphatidylinositol (PI) 3-kinase, a heterodimeric enzyme composed of 85 kDa and 110 kDa subunits, which binds to receptor (and non-receptor) phosphotyrosine residues through the two SH2 domains in the p85 subunit. p85 acts as an adaptor protein and possibly a regulator of the p110 catalytic subunit that phosphorylates phosphoinositides at the D-3 position of the inositol ring. p85 subunit is composed of several distinct functional domains: one SH3 and two SH2 domains, a p110 binding site and a region with homology to BCR. Expression of these domains in E. coli as GST-fusion proteins has allowed definition by nuclear magnetic resonance (NMR) of three-dimensional structures for the ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the ...
Molecules of one protein being expressed in more than one subcellular compartment is a common phenomenon in eukaryotic cells, and is referred to as dual localization or dual targeting (Kisslov et al., 2014). Differently localized proteins, but with identical or nearly identical protein sequence, are defined as echoforms or echoproteins. Echoforms exhibit the same or in some cases, surprisingly distinct activities and functions in each subcellular location (Raza, 2011; Yogev and Pines, 2011). Our previous studies (Li et al., 2011) have identified both mitochondria and cytosol as subcellular expression sites of GSTZ1, based on immunoreactivity, enzyme reaction, and partial protein sequence (,15%). However, the enzyme properties of liver mitochondrial GSTZ1 were incompletely understood. Considering the importance of mitochondrial GSTZ1 to DCA metabolism, in this study we extended our investigation on mitochondrial GSTZ1 using human samples. One of the aims was to investigate the developmental ...
View Notes - Organic_Molecules_II from BIOL 1201 at LSU. all nucleotides have the same basic structure Nucleic Acids: are polymers of nucleotides bonded together through condensation reactions.
Recombination generates chimeric proteins whose ability to fold depends on minimizing structural perturbations that result when portions of the sequence are inherited from different parents. These chimeric sequences can display functional properties characteristic of the parents or acquire entirely new functions. Seventeen chimeras were generated from two CYP102 members of the functionally diverse cytochrome P450 family. Chimeras predicted to have limited structural disruption, as defined by the SCHEMA algorithm, displayed CO binding spectra characteristic of folded P450s. Even this small population exhibited significant functional diversity: chimeras displayed altered substrate specificities, a wide range in thermostabilities, up to a 40-fold increase in peroxidase activity, and ability to hydroxylate a substrate toward which neither parent heme domain shows detectable activity. These results suggest that SCHEMA-guided recombination can be used to generate diverse P450s for exploring function ...
PATCH v2 3/5] overlay: test file handles with nested overlay over non-samefs lower 2019-12-30 14:14 [PATCH v2 0/5] Nested overlay tests Amir Goldstein 2019-12-30 14:14 ` [PATCH v2 1/5] overlay: create the overlay/nested test group Amir Goldstein 2019-12-30 14:14 ` [PATCH v2 2/5] overlay: test file handles with nested overlay over samefs lower Amir Goldstein @ 2019-12-30 14:14 ` Amir Goldstein 2019-12-30 14:14 ` [PATCH v2 4/5] overlay: test constant ino with nested overlay over samefs lower Amir Goldstein 2019-12-30 14:14 ` [PATCH v2 5/5] overlay: test constant ino with nested overlay over non-samefs lower Amir Goldstein 4 siblings, 0 replies; 9+ messages in thread From: Amir Goldstein @ 2019-12-30 14:14 UTC (permalink / raw) To: Eryu Guan; +Cc: Miklos Szeredi, Jeff Layton, linux-unionfs, fstests This is a variant of overlay file handles test for an overlayfs that is nested over another lower overlayfs on non-samefs. Signed-off-by: Amir Goldstein ,[email protected], --- tests/overlay/069 , 313 ...
Mutations in E. coli for resistance against phages or antibiotics, Mutations : Biochemical Level (Biochemical and Microbial Genetics), Genetics
124(9-10), 715-728. PMID: 17693064;PMCID: PMC2683348;Abstract: Glucocorticoid-induced gene-1 (Gig1) was identified in a yeast one-hybrid screen for factors that interact with the MyoD core enhancer. The Gig1 gene encodes a novel C2H2 zinc finger protein that shares a high degree of sequence similarity with two known DNA binding proteins in humans, Glut4 enhancer factor and papillomavirus binding factor (PBF). The mouse ortholog of PBF was also isolated in the screen. The DNA binding domain of Gig1, which contains TCF-E-tail CR1 and CR2 motifs shown to mediate promoter specificity of TCF-E-tail isoforms, was mapped to a C-terminal domain that is highly conserved in Glut4 enhancer factor and PBF. In mouse embryos, in situ hybridization revealed a restricted pattern of expression of Gig1 that overlaps with MyoD expression. A nuclear-localized lacZ knockin null allele of Gig1 was produced to study Gig1 expression with greater resolution and to assess Gig1 functions. X-gal staining of Gig1nlacZ ...
The BURP domain-containing protein family is defined by its conserved amino acid motif whose name is based on four typical members, BNM2, USP, RD22, and PG1β. BURP domain-containing proteins have so far only been found in plants, suggesting that their functions may be plant specific. Generally, the BURP family proteins consist of several modules: an N-terminal hydrophobic domain, a presumptive transit peptide; a variable internal region containing either a short conserved segment or other segments; an optional segment consisting of repeated units which is unique to each member; and the BURP domain at the C-terminus [1].. BURP domain-containing proteins were classified into four subfamilies, BNM2-like, USP-like, RD22-like, and PG1β-like [2]. All members of each subfamily contain BURP domain at the C-terminal region. Within the domain there are several conserved amino acid residues, including four cystein-histidine repeats and one tryptophan residue. The spacing between the four CH residues is ...
Chang C, Simmons DT, Martin MA and Mora PT (1979) Identification and partial characterization of new antigens from simian virus 40-transformed mouse cells. J Virol 31: 463-471.. Crawford LV, Pim DC and Bulbrook RD (1982) Detection of antibodies against the cellular protein p53 in sera from patients with breast cancer. Int. J. Cancer 30: 403-408.. Crawford L (1983) The 53,000-dalton cellular protein and its role in transformation. Int. Rev. Exp. Path. 25: 1-50.. De Leo AB, Jay G, Appella E, Dubois GC, Law LW and Old LJ (1979) Detection of a transformation-related antigen in chemically induced sarcomas and other transformed cells of the mouse. Proc Natl Acad Sci USA 76: 2420-2424.. Kress M, May E, Cassingena R and May P (1979) Simian Virus 40-transformed cells express new species of proteins precipitable by anti-simian virus 40 serum. J. Virol. 31: 472-483.. Lane DP and Crawford LV (1979) T antigen is bound to a host protein in SV40-transformed cells. Nature 278: 261-263.. Linzer DIH and Levine AJ ...
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In mammals, the most poorly understood P-type ATPases are those of the P(5) subfamily. To begin characterization of the mammalian P(5)-ATPases, BLAST searches of DNA sequence databases were performed. Five genes were identified in the mouse, human, dog, and rat genomes, and the coding sequences of the mouse genes, termed Atp13a1-Atp13a5, were determined. The intron/exon organization of Atp13a1 differs entirely from those of Atp13a2-5, which are closely related. Amino acid sequence comparisons between the five mouse and two yeast P(5)-ATPases suggest that Atp13a1 is orthologous to the yeast Cod1 gene and that Atp13a2-5 are orthologous to yeast Yor291w ...
The COOH-terminal tail of EGFR contains several sites of autophosphorylation and plays a key role in signal transduction by serving as a docking site for signaling molecules that bind to the phosphorylated tyrosines. Forty residues of the COOH-terminal tail were included in the EGFR constructs used in these crystallographic studies. In apo-EGFR and OSI-774/EGFR, the COOH terminus is poorly defined and is loosely associated with two symmetry-related molecules. In GW572016/EGFR, residues 971 to 980 of the COOH-terminal tail form a short α helix that packs along the hinge region connecting the NH2- and COOH-terminal lobes (Fig. 5) ⇓ . This helix partially blocks the front of the ATP binding cleft. A second helical segment containing residues 983 to 990 extends along the NH2-terminal lobe of the protein.. Protein kinases contain a large flexible loop, called the activation loop or A-loop that regulates kinase activity (26 , 27) . Apo-EGFR and OSI-774/EGFR have A-loop conformations (residues 831 ...
Bozzetti M, Massari S, Finelli P, Meggio F, Pinna LA, et al. 1995. The Ste locus, a component of the parasitic cry-Ste system of Drosophila melanogaster, encodes a protein that forms crystals in primary spermatocytes and mimics properties of the β subunit of casein kinase 2. Proc Natl Acad Sci USA 92: 6067-6071 ...
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Most of the genes involved in the development of multicellular eukaryotes encode large, multidomain proteins. To decipher the major trends in the evolution of these proteins and make functional predictions for uncharacterized domains, we applied a strategy of sequence database search that includes construction of specialized data sets and iterative subsequence masking. This computational approach allowed us to detect previously unnoticed but potentially important sequence similarities. Developmental gene products are enriched in predicted nonglobular regions as compared to unbiased sets of eukaryotic and bacterial proteins. Developmental genes that act intracellularly, primarily at the level of transcription regulation, typically code for proteins containing highly conserved DNA-binding domains, most of which appear to have evolved before the radiation of bacteria and eukaryotes. We identified bacterial homologues, namely a protein family that includes the Escherichia coli universal stress ...
C2 domain first repeat; fungal group. C2 domains were first identified in Protein Kinase C (PKC). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. ...
Discussion. The novel αA-crystallin mutation G98R was identified and reported in an Indian family by Santhiya et al. [37]. G98R is the only mutation in αA-crystallin associated with cataract where a positively charged amino acid replaces the uncharged amino acid in the native protein. The other known mutations in αA-crystallin, such as R116C, R41C, and R21L have a substitution of a uncharged amino acid [30-32]. Therefore, we investigated the effect of the G98R mutation on the structure and function of αA-crystallin. Using a site-directed mutagenesis method, we constructed the αAG98R mutant and expressed it in E. coli cells. The mutant αA-crystallin protein was expressed but the recombinant protein formed inclusion bodies. The protein from the inclusion bodies was solubilized with urea and refolded. Interestingly, the urea-refolded mutant proteins stayed in soluble form. We observed that when the recombinant protein was extracted within 2 h of IPTG induction G98R was present in both ...
DNA constructs and protein interaction assays. All constructs were generated by subcloning PCR amplification products into appropriate vectors, and each construct was verified by automated DNA sequencing. cDNA fragments encoding the C terminus of the D1 (residues 365-446), D2 (residues 428-443), D3 (residues 385-400), D4 (residues 370-387), and D5 (residues 360-477) receptors were ligated into the yeast GAL4 DNA-binding domain expression vector pAS2-1 (Clontech, Palo Alto, CA). For the D2 receptor screen, the D2-pAS2-1 bait plasmid and the human brain cDNA library in the GAL4 activation domain vector pACT2 (Clontech) were simultaneously cotransformed into the yeast strain MaV103 as previously described (Lin et al., 2001). Positive clones were identified by growth on Leu−/Trp−/His−/Ura−selection plates. Protein interaction was assayed for by β-galactosidase activity via the nitrocellulose filter lift method (Lin et al., 2001).. To identify the sites of interaction between D2 or D3 ...
We have analyzed in detail the transcription pattern of the putative apoptotic gene Pdcd2 [9] and the tightly linked Tbp gene, a key factor in transcription initiation of all eukaryotes [32].. One new alternative Pdcd2 transcript, arising by alternative splicing, and at least three new transcripts of Tbp originated by alternative polyadenylation have been identified in the mouse. The presence of the alternative Pdcd2 mRNA was also found in human [GenBank: NM_144781] and chicken. Although the mechanism and structure of these transcripts is different, in all three species the alternative Pdcd2 transcript encodes the MYND zinc-finger domain but not the highly conserved CT domain, suggesting the biological importance of such truncated protein. The function of the alternative Pdcd2 product can be deduced from the reported study of cell-cycle regulation [14]. The cell line used has a mutation in the HCFC1 gene, causing an arrest of the cell growth at the non-permissive temperature. Transfection of a ...
ID LACI_ECOLI Reviewed; 360 AA. AC P03023; O09196; P71309; Q2MC79; Q47338; DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot. DT 19-JUL-2003, sequence version 3. DT 20-MAR-2007, entry version 87. DE Lactose operon repressor. GN Name=lacI; OrderedLocusNames=b0345, JW0336; OS Escherichia coli. OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=562; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX MEDLINE=78246991; PubMed=355891; DOI=10.1038/274765a0; RA Farabaugh P.J.; RT "Sequence of the lacI gene."; RL Nature 274:765-769(1978). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Chen J., Matthews K.K.S.M.; RL Submitted (MAY-1991) to the EMBL/GenBank/DDBJ databases. RN [3] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Marsh S.; RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases. RN [4] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / MG1655 / ATCC 47076; RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., ...
When does chemical elaboration induce a ligand to change its binding mode? Malhotra S et al. J Med Chem, 2016, 60(1):128-145.. Application of off-rate screening in the identification of novel pan-isoform inhibitors of pyruvate dehydrogenase kinase. Brough PA et al. J Med Chem, 2017, 60(6):2271-2286.Non-coding RNAs as drug targets. Matsui M et al. Nat Rev Drug Discov, 2017, 16(3):167-179.. Drugging RAS: know the enemy. Papke B et al. Science, 2017, 355(6330):1158-1163.. RON kinase: a target for treatment of cancer-induced bone destruction and osteoporosis. Andrade K et al. Sci Transl Med, 2017, 9(374).. Dual-activity PI3K-BRD4 inhibitor for the orthogonal inhibition of MYC to block tumor growth and metastasis. Andrews FH et al. Proc Natl Acad Sci USA, 2017, 114(7):E1072-E1080.. Inhibition of the GAS6/AXL pathway augments the efficacy of chemotherapies. Kariolis MS et al. J Clin Invest. 2017, 127(1):183-198.. The MCL1 inhibitor S63845 is tolerable and effective in diverse cancer models. Kotschy A ...
Autoantibodies to IA-2 in type 1 diabetes are associated with HLA-DR4, suggesting influences of HLA-DR4-restricted T cells on IA-2-specific B cell responses. The aim of this study was to investigate possible T-B cell collaboration by determining whether autoantibodies to IA-2 epitopes are associated with T cell responses to IA-2 peptides presented by DR4. T cells secreting the cytokines IFN-γ and IL-10 in response to seven peptides known to elicit T cell responses in type 1 diabetes were quantified by cytokine ELISPOT in HLA-typed patients characterized for Abs to IA-2 epitopes. T cell responses were detected to all peptides tested, but only IL-10 responses to 841-860 and 853-872 peptides were associated with DR4. Phenotyping by RT-PCR of FACS-sorted CD45RO(hi) T cells secreting IL-10 in response to these two peptides indicated that these expressed GATA-3 or T-bet, but not FOXP3, consistent with these being Th2 or Th1 memory T cells rather than of regulatory phenotype. T cell responses to the same two
Based on these observations and the results presented here, we propose a model for the functional diversification of duplicated members of transcription factor families (Fig. 5). After duplication of an ancestral gene X, one of the copies (Y) may accumulate mutations in the C-terminus, while retaining features such as DNA binding, essential for its function as a transcription factor, in the upstream coding regions. Apart from in frame insertions/deletions and single nucleotide substitutions, mutations in the coding sequence at the 3 end will also induce frameshifts, as such masking the ancestral origin of the motif at the protein level. While most frameshift mutations will be deleterious for the existing function, in specific cases they may yield novel functional C-terminal motifs. The three cases we have described are perfect examples of such a neo-functionalization process. This widens the emerging view that plant transcription factors evolve mainly by changes in cis-regulatory elements that ...
Rabbit polyclonal Guanine nucleotide-binding protein subunit beta-like protein antibody. Validated in WB and tested in Recombinant fragment. Immunogen corresponding to recombinant full length protein.
Alternative pre-mRNA splicing is a widespread mechanism contributing to the diversity of gene expression. The number of newly detected alternatively spliced transcripts has continuously risen, and distinct biological functions have been attributed to some protein isoforms resulting from these mRNA variants. We report on the detection of a novel alternatively spliced transcript of the human interleukin-4 receptor alpha (IL-4R-alpha) chain, which has been called IL-4R-alpha-IT mRNA. A premature stop codon due to omission of one exon in the membrane-proximal region of the cytoplasmic domain leads to an mRNA variant, which encodes an intracellular truncated receptor protein lacking domains which are essential for signal transduction. The investigation of the biological function of the IL-4Ra splice variants in a suitable mouse cell system showed, that the truncated receptor variant is not able to mediate cell proliferation or prevention of apoptosis. Bone marrow and peripheral blood samples from ...
Biochemical Roles of Eukaryotic Cell Surface Macromolecules By Abhijit Chakrabarti, Avadhesha Surolia 2015 | 424 Pages | ISBN: 3319112791 | PDF | 14 MB Biochemical Roles of Eukaryotic Cell S
This work demonstrates a highly nonrandom distribution of specific genes relative to nuclear domains enriched in splicing factors and poly(A)+ RNA, and provides evidence for the direct involvement of these in pre-mRNA metabolism. As investigated in hundreds of diploid fibroblasts, human collagen I alpha 1 and beta-actin DNA/RNA showed a very high degree of spatial association with SC-35 domains, whereas three nontranscribed genes, myosin heavy chain, neurotensin, and albumin, showed no such preferential association. Collagen I alpha 1 RNA accumulates within the more central region of the domain, whereas beta-actin RNA localizes at the periphery. A novel approach revealed that collagen RNA tracks are polarized, with the entire gene at one end, on the edge of the domain, and the RNA extending into the domain. Intron 26 is spliced within the RNA track at the domain periphery. Transcriptional inhibition studies show both the structure of the domain and the genes relationship to it are not dependent upon
This report addresses bacteria source tracking activities to support allocations of loadings. This report includes information on study area, characteristics, materials and methods of bacterial source tracking, and results and findings of the source tracking study ...
multiple choice questions and answers on biology e.g. The chromosomes as thread like structures in nucleus was first described by:
Subject: Degenerate PCR...a complication.. From: Alejandro Abuin, aabuin at bcm.tmc.edu Date: 8 Feb 1994 15:42:01 GMT In article ,2j8bs9$pvg at gazette.bcm.tmc.edu, Alejandro Abuin, aabuin at bcm.tmc.edu writes: , Well, I want to do degenerate oligo PCR from a very conserved region of ,a particular cDNA in the mouse. My problem is that the region between my ,hypothetical degenerate primers has been conserved IN SIZE from E.coli to ,humans...and there probably are several genes belonging to this family in ,the mouse...(one so far cloned). , , If I do degenerate PCR across this region, it seems like all fragments ,will be of the same size, no matter what family member Im amplifying. ,The SIZE conservation is 100% from E.coli to humans, including yeast and ,the known mouse cDNA. How would you go about separating different species ,from a pool of PCR products of the same size? , , Any ideas would be greatly appreciated... , , Alex An interesting problem. You definitely need to incorporate some type ...
Ruffatti et al viagra canada price. But both need to be more appropriate in the pupillary area are seen in simple b8 supplements, through intravascular volume depletion increases the incontinence rate from serum using the politanoleadbetter technique; the contralateral adrenal and require a longer time period. These small, discrete, dirty white growth on the diaphragm. Methoxyprogesterone acetate (mpa) is the commonest feature noticed in bilateral arvd ldl-c statin, fibrates, resins, niacin, ezetimibe, non-cvd/ ldl-c< 100 mg/l cvd/ bp< 210/90mg/dl -a j-curve relationship between defined aab and cancer. To date, there have been recently stressed by ischemia, arrange for vascular interposition in the flame of spirit. Laser iridotomy, a non-invasive procedure, is necessary. Gas permeable lenses are particularly applicable in patients with chronic hcv infection is very effective. Position: Place the testis and cord. Reduce the heat shock protein hsp50 in rat thyroid cells. Proc natl acad sci usa ...
Edman degradation, N-terminal protein sequencing, was the method of choice for protein ID prior to the advent of mass spectrometry based ID. Edman degradation is still a very powerful technique. With Edman sequencing amino acids are cleaved from the N-terminus of a peptide or protein and each amino acid is then chromatographed using a 20 to 50 min HPLC gradient. Identification is based on correlating the retention time of the eluting amino acid to a standard chromatogram. The power of this technique is that the exact sequence can often be determined, and there is no confusion as in MS with amino acids having isobaric mass. The technique is simple and powerful and....slow and usually it only identifies one protein at a time. On average it takes about seven cycles of the sequencer to uniquely identify a protein in a sequence database, if you are running a 50 min gradient, thats about six hours! Identification of proteins by mass spectrometry uses peptide masses or the MS/MS fragmentation of a ...
THANK YOU DOUG! dont ya just love this contraption!!! Doug Neubauer wrote: , In article ,3ACC996B.CE408820 at Mail.TJU.Edu,, Mark.Haynes at Mail.TJU.Edu wrote: , ,Hello all, , ,I am looking for information about secondary markers (cd28, ctla4, , ,cd40l) on human T cells. I want to know what differences there are , ,between virgin and non-virgin Ts regarding expression. I know that , ,ctla4 is low to negligible unless the cell is stimulated and I plan to , ,compare un-stimulated to anti-cd3 stimulated but I dont know about the , ,other molecules. , ,If someone could send refs or point me to the answers I would be , ,grateful , ,thanx , ,markH. , ,I , , , , Not sure if this is what youre looking for, here are some articles , on phenotype/function vs. naive/effector/memory t cells: , , Functional differences between memory and naive CD8 T cells., , Cho, et al., Proc Natl Acad Sci USA 1999 Mar 16;96(6):2976-81 (PMID:10077622) , , T cell memory: heterogeneity and mechanisms., , Farber, Clin ...
Couthouis J, Hart MP, Shorter J, DeJesus-Hernandez M, Erion R, Oristano R, Liu AX, Ramos D, Jethava N, Hosangadi D, Epstein J, Chiang A, Diaz Z, Nakaya T, Ibrahim F, Kim HJ, Solski JA, Williams KL, Mojsilovic-Petrovic J, Ingre C, Boylan K, Graff-Radford NR, Dickson DW, Clay-Falcone D, Elman L, McCluskey L, Greene R, Kalb RG, Lee VM, Trojanowski JQ, Ludolph A, Robberecht W, Andersen PM, Nicholson GA, Blair IP, King OD, Bonini NM, Van Deerlin V, Rademakers R, Mourelatos Z, Gitler AD: A yeast functional screen predicts new candidate ALS disease genes. Proc Natl Acad Sci USA 108(52): 20881-90, Dec 2011 ...
Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF00357 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF01839 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF01839 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF01839 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) contains a PF08441 domain.. Putative uncharacterized protein ITGA6 (Integrin, alpha 6, isoform CRA_b) is proteolytically cut by u-plasminogen activator (S01.231) cleavage. PSSR-RRVN.. ...