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Results for “Protein Modification, Translational”

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PubMed1991

DBcAMP effect on the expression of GFAP and of its encoding mRNA in astroglial primary cultures.

Short term and chronic dBcAMP effects on the expression of glial fibrillary acidic protein (GFAP) in astroglial primary cultures are investigated. Short (48 h) and long (more than 7 days) treatments with the cAMP derivative induce both cell shape changes and an increase in GFAP immunolabelling. Such effects are only associated with an increase in GFAP and in GFAP-mRNA levels in the long term treatment. These results suggest that the short term effect of dBcAMP induces post-translational modifications of the protein whereas the long term effect is associated with an increase in GFAP mRNA transcription and/or stability.

Animals↗

PubMed1999

Selective beta1-adrenoceptor blockade enhances the activity of the stimulatory G-protein in human atrial myocardium.

1. Chronic selective beta1-adrenoceptor (beta1AR) blocker treatment enhances the sensitivity of beta2-adrenoceptor (beta2AR) in human heart (Hall et al., 1990; 1991). To clarify the mechanism of the cross-sensitization between beta1AR and beta2AR, we determined whether the stimulatory G-protein (G(s)alpha) function is increased in atria from beta1AR-blocker treated patients compared with non-beta-blocked patients, and investigated whether this change is caused by an alteration of post-translational modification of Gsalpha protein. 2. G(s)alpha function was determined by reconstitution of human atrial G(s)alpha into S49 cyc- cell membranes. In the reconstitution system, GTPgammaS stimulated cyclic AMP generation in a dose-dependent manner. Upon 10(-4) M GTPgammaS stimulation, G(s)alpha activity in the beta1AR-blocker, atenolol, treated group (78.2+/-10. 3 pmol cyclic AMP mg(-1) min(-1) 10(-3)) was 65% higher than that in non-beta-blocked patients (47.3+/-6.3 pmol cyclic AMP mg(-1) min(-1) 10(-3), n=15, P=0.02). 3. Isoelectric point (pI) valu G(s)alpha were measured by two dimensional gel electrophoresis (2D-E) and the amount of each isoform quantified by image analysis of a Western blot of the gel using specific antibody. Multiple isoforms of G(s)alpha were detected by 2D-E with different pI values. There were no significant differences between the groups of patients in either pI values or the proportions of the acidic isoforms of G(s)alpha to the main basic form (n=12, P>0.05). 4. The results suggest that chronic beta1AR-blockade enhances Gsalpha function in human atrium, and this may account in part for the hypersensitivity of beta2AR and other Gs-coupled receptors during beta1AR-blockade. The increased G(s)alpha function is unlikely to be caused directly by blockade of protein kinase A phosphorylation of G(s)alpha protein.

Adenylyl Cyclases↗

PubMed2001

The Twisted gastrulation family of proteins, together with the IGFBP and CCN families, comprise the TIC superfamily of cysteine rich secreted factors.

AIMS: To analyse the similarities between the Twisted gastrulation (TSG) proteins known to date; in addition, to determine phylogenetic relations among the TSG proteins, and between the TSGs and other protein families--the CCN (for example, CCN2 (CTGF), CCN1 (CYR61), and CCN3 (NOV)) and IGFBP (insulin-like growth factor binding protein) families. METHODS: TBLASTN and FASTA3 were used to identify new tsg genes and relatives of the TSG family. The sequences were aligned with ClustalW. The predictions of sites for signal peptide cleavage, post-translational modifications, and putative protein domains were carried out with software available at various databases. Unrooted phylogenetic trees were calculated using the UPGMA method. RESULTS: Several tsg genes from vertebrates and invertebrates were compared. Alignment of protein sequences revealed a highly conserved family of TSG proteins present in both vertebrates and invertebrates, whereas the slightly less well conserved IGFBP and CCN proteins are apparently present only in vertebrates. The TSG proteins display strong homology among themselves and they are composed of a putative signal peptide at the N-terminus followed by a cysteine rich (CR) region, a conserved domain devoid of cysteines, a variable midregion, and a C-terminal CR region. The most striking similarity between the TSGs and the IGFBP and CCN proteins occurs in the N-terminal conserved cysteine rich domain and the characteristic 5' cysteine rich domain(s), spacer region, and 3' cysteine rich domain structure. CONCLUSION: The family of highly conserved TSG proteins, together with the IGFBP and CCN families, constitute an emerging multigene superfamily of secreted cysteine rich factors. The TSG branch of the superfamily appears to pre-date the others because it is present in all species examined, whereas the CCN and IGFBP genes are found only in vertebrates.

Animals↗

PubMed1986

Post-translational modification of the major human surfactant-associated proteins.

The major protein in human pulmonary surfactant is a sialoglycoprotein of 32-36 kDa (PSP-A) that has been shown by translation of lung mRNA in vitro to be derived from precursor molecules of 29-31 kDa [Floros, Phelps & Jaeusch (1985). J. Biol. Chem. 260, 495-500]. We show here that two-dimensional gel patterns of PSP-A similar to that of the primary translation products are obtained by incorporation of [35S]methionine in the presence of tunicamycin or by N-glycanase digestion of the 32-36 kDa group. Additional gel patterns are also observed in which the isoelectric-point heterogeneity is similar to that of either tunicamycin-treated tissue or primary translation products, but with higher molecular masses. The gel patterns showing higher-molecular-mass components are obtained when terminal sialic acid addition is prevented by the incubation of lung tissue with monensin or when terminal sialic acids are digested from the fully processed protein with neuraminidase. The 32-36 kDa forms have been shown to contain [14C]mannose. Pulse-chase experiments indicate that the acidic isoforms in the protein group arise from basic isoforms that are detectable within 10 min.

Electrophoresis, Polyacrylamide Gel↗

PubMed1978

Potential for variability through multiple gene products of bacteriophage phiX174.

The small single-stranded DNA phages phiX174 and S13 produce multiple products of certain phage genes, as observed by electrophoresis on SDS-polyacrylamide slab gels. Two A protein products, two A products and four G products are observed. The multiple gene products may arise from multiple sites for initiation or termination of translation, or by protein modification. Some of the variant products may provide a substitute for heterozygosity without a concomitant increase in the size of the genome.

Chromosome Mapping↗

PubMed2000

Serotype classification and characterisation of the rotavirus SA11 VP6 protein using mass spectrometry and two-dimensional gel electrophoresis.

VP6, which makes up the inner capsid of rotavirus, is the major structural protein of this virus. Whilst VP6 has been sequenced at the DNA level in several rotavirus strains, there has been less effort to characterise the protein at the amino acid level. This paper reports the use of peptide mass fingerprinting and post-source decay fragmentation studies using MALDI-TOF and electrospray ionisation mass spectrometry to identify and characterise, in detail, the VP6 protein. We show that mass spectrometric analysis of VP6 peptides successfully distinguished SA11 from other rotavirus serotypes, and identify unique peptides that can be used for serotypic differentiation. For VP6 characterisation, the ExPASy FindMod tool was used to predict post-translational modifications on the protein. Analysis of trypsin and AspN digests predicted that the N-terminal methionine of VP6 was acetylated and this was confirmed using post source decay and electrospray ionisation mass spectrometry-mass spectrometry. An asparagine residue (aa107), which is followed by a glycine residue, was shown to undergo partial deamidation to aspartic acid. VP6 has two additional asparagine-glycine sequences and, in this sequence context, asparagine is known to be particularly susceptible to deamidation. Two-dimensional gel electrophoresis revealed a complex series of VP6 isoforms with an apparent molecular mass of approximately 45,000 Da and a pI ranging from 5.25 to 5.8. This pattern could partly be explained by the potential for deamidation at several sites within the protein.

Acetylation↗

PubMed2005

Dynamic and reversibility of heterochromatic gene silencing in human disease.

In eukaryotic organisms cellular fate and tissue specific gene expression are regulated by the activity of proteins known as transcription factors that by interacting with specific DNA sequences direct the activation or repression of target genes. The post genomic era has shown that transcription factors are not the unique key regulators of gene expression. Epigenetic mechanisms such as DNA methylation, post-translational modifications of histone proteins, remodeling of nucleosomes and expression of small regulatory RNAs also contribute to regulation of gene expression, determination of cell and tissue specificity and assurance of inheritance of gene expression levels. The relevant contribution of epigenetic mechanisms to a proper cellular function is highlighted by the effects of their deregulation that cooperate with genetic alterations to the development of various diseases and to the establishment and progression of tumors.

Chromatin↗

PubMed1987

Antigenic comparison of five species of mammalian zonae pellucidae.

A comparison of glycoproteins of the zona pellucida (ZP) of five different mammalian species (cat, dog, rabbit, pig, and rat) has been made using polyclonal and monoclonal antibodies. In an enzyme-linked immunosorbent assay (ELISA), polyclonal antisera against total rabbit and pig ZP recognize their homologous ZP to the greatest extent but also detect crossreactive antigenic determinants in the ZP of all other species tested. Polyclonal antibodies against each of two purified rabbit ZP glycoproteins or one purified pig ZP glycoprotein also show some recognition of heterologous (pig, cat, and dog) ZP, but not rat ZP. Monoclonal antibodies (McR5-rabbit ZP protein determinant; McPSI-determinant associated with post-translational modifications of pig ZP proteins such as carbohydrates) further demonstrate that specific determinants are shared between some but not all of these mammalian species. For example, both of these antibodies recognize distinct determinants which are most abundant in pig and cat ZP. However, McR5 recognizes a determinant on all species of ZP except the rat, while McPSI does not recognize either the rabbit or rat ZP. Collectively, these studies suggest that the molecules of the pig, dog, and cat ZP are more closely related to each other than to those of the rabbit ZP, while there is little similarity with rat ZP molecules. Immunoblot analysis of ZP glycoproteins separated by two-dimensional polyacrylamide gel electrophoresis was used to identify antigenic relationships among four different species. The polyclonal antisera show that all of the major proteins of pig, rabbit, cat, and dog ZP are antigenically related.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2004

Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots.

The abundance profile of the human urinary proteome is known to change as a result of diseases or drug toxicities, particularly of those affecting the kidney and the urogenital tract. A consequence of such insults is the ability to identify proteins in urine, which may be useful as quantitative biomarkers. To succeed in discovering them, reproducible urine sample preparation methods and good protein resolution in two-dimensional electrophoresis (2-DE) gels for parallel semiquantitative protein measurements are desirable. Here, we describe a protein fractionation strategy enriching proteins of molecular masses (M(r)) lower than 30 kDa in a fraction separate from larger proteins. The fraction containing proteins with M(r)s higher than 30 kDa was subsequently subjected to immunoaffinity subtraction chromatography removing most of the highly abundant albumin and immunoglobulin G. Following 2-DE display, superior protein spot resolution was observed. Subsequent high-throughput mass spectrometry analysis of ca. 1400 distinct spots using matrix-assisted laser desorption/ionization-time of flight peptide mass fingerprinting and liquid chromatography-electrospray ionization tandem mass spectrometry lead to the successful identification of 30% of the proteins. As expected from high levels of post-translational modifications in most urinary proteins and the presence of proteolytic products, ca. 420 identified spots collapsed into 150 unique protein annotations. Only a third of the proteins identified in this study are described as classical plasma proteins in circulation, which are known to be relatively abundant in urine despite their retention to a large extent in the glomerular blood filtration process. As a proof of principle that our urinary proteome display effort holds promise for biomarker discovery, proteins isolated from the urine of a renal cell carcinoma patient were profiled prior to and after nephrectomy. Particularly, the decrease in abundance of the kininogen 2-DE gel spot train in urine after surgery was striking.

Albumins↗

PubMed1983

Binding of thyroid hormone by heme proteins may signal protein age.

Cellular aging is thought to include the accumulation of proteins with post-translational modifications that alter degradation rates or function or both. Protein catabolism has been regarded as a randomly occurring process, but recent observations have suggested mechanisms by which old and young cells may distinguish recently-synthesized protein molecules from "old" proteins. Hemoglobin, myoglobin and other heme proteins bind thyroid hormone progressively with time and in a poorly-dissociable manner. This cumulative acquisition of thyroid hormone is postulated to be an index of molecular aging.

Erythrocytes↗

PubMed2004

Crystallographic analysis of CaaX prenyltransferases complexed with substrates defines rules of protein substrate selectivity.

Post-translational modifications are essential for the proper function of many proteins in the cell. The attachment of an isoprenoid lipid (a process termed prenylation) by protein farnesyltransferase (FTase) or geranylgeranyltransferase type I (GGTase-I) is essential for the function of many signal transduction proteins involved in growth, differentiation, and oncogenesis. FTase and GGTase-I (also called the CaaX prenyltransferases) recognize protein substrates with a C-terminal tetrapeptide recognition motif called the Ca1a2X box. These enzymes possess distinct but overlapping protein substrate specificity that is determined primarily by the sequence identity of the Ca1a2X motif. To determine how the identity of the Ca1a2X motif residues and sequence upstream of this motif affect substrate binding, we have solved crystal structures of FTase and GGTase-I complexed with a total of eight cognate and cross-reactive substrate peptides, including those derived from the C termini of the oncoproteins K-Ras4B, H-Ras and TC21. These structures suggest that all peptide substrates adopt a common binding mode in the FTase and GGTase-I active site. Unexpectedly, while the X residue of the Ca1a2X motif binds in the same location for all GGTase-I substrates, the X residue of FTase substrates can bind in one of two different sites. Together, these structures outline a series of rules that govern substrate peptide selectivity; these rules were utilized to classify known protein substrates of CaaX prenyltransferases and to generate a list of hypothetical substrates within the human genome.

Alkyl and Aryl Transferases↗

PubMed2003

The transcription factor Eyes absent is a protein tyrosine phosphatase.

Post-translational modifications provide sensitive and flexible mechanisms to dynamically modulate protein function in response to specific signalling inputs. In the case of transcription factors, changes in phosphorylation state can influence protein stability, conformation, subcellular localization, cofactor interactions, transactivation potential and transcriptional output. Here we show that the evolutionarily conserved transcription factor Eyes absent (Eya) belongs to the phosphatase subgroup of the haloacid dehalogenase (HAD) superfamily, and propose a function for it as a non-thiol-based protein tyrosine phosphatase. Experiments performed in cultured Drosophila cells and in vitro indicate that Eyes absent has intrinsic protein tyrosine phosphatase activity and can autocatalytically dephosphorylate itself. Confirming the biological significance of this function, mutations that disrupt the phosphatase active site severely compromise the ability of Eyes absent to promote eye specification and development in Drosophila. Given the functional importance of phosphorylation-dependent modulation of transcription factor activity, this evidence for a nuclear transcriptional coactivator with intrinsic phosphatase activity suggests an unanticipated method of fine-tuning transcriptional regulation.

Amino Acid Motifs↗

PubMed2005

The p53 pathway: positive and negative feedback loops.

The p53 pathway responds to stresses that can disrupt the fidelity of DNA replication and cell division. A stress signal is transmitted to the p53 protein by post-translational modifications. This results in the activation of the p53 protein as a transcription factor that initiates a program of cell cycle arrest, cellular senescence or apoptosis. The transcriptional network of p53-responsive genes produces proteins that interact with a large number of other signal transduction pathways in the cell and a number of positive and negative autoregulatory feedback loops act upon the p53 response. There are at least seven negative and three positive feedback loops described here, and of these, six act through the MDM-2 protein to regulate p53 activity. The p53 circuit communicates with the Wnt-beta-catenin, IGF-1-AKT, Rb-E2F, p38 MAP kinase, cyclin-cdk, p14/19 ARF pathways and the cyclin G-PP2A, and p73 gene products. There are at least three different ubiquitin ligases that can regulate p53 in an autoregulatory manner: MDM-2, Cop-1 and Pirh-2. The meaning of this redundancy and the relative activity of each of these feedback loops in different cell types or stages of development remains to be elucidated. The interconnections between signal transduction pathways will play a central role in our understanding of cancer.

Amino Acid Sequence↗

PubMed2005

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

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

Binding Sites↗

PubMed1981

Relative stability of membrane proteins in Escherichia coli.

The relative stability of membrane proteins in Escherichia coli was investigated to determine whether these proteins are degraded at heterogeneous rates and, if so, whether the degradative rates are correlated with the sizes or charges of the proteins. Cells growing in a glucose-limited chemostat with a generation time of 15 h were labeled with [(14)C]leucine. After allowing 24 h for turnover of (14)C-labeled proteins, the cells were labeled for 15 min with [(3)H]leucine. By this protocol, the rapidly degraded proteins have a high ratio of (3)H to (14)C, whereas the stable proteins have a lower ratio. The total cell envelope fraction was collected by differential centrifugation, and the proteins were separated by two-dimensional polyacrylamide gel electrophoresis. The relative ratio for each protein was determined by dividing its (3)H/(14)C ratio by the (3)H/(14)C ratio of the total membrane fraction. Although most of the 125 membrane proteins had relative ratios close to the average for the total membrane fraction, 19 varied significantly from this value. These differences were also observed when the order of addition of [(14)C]leucine and [(3)H]leucine was reversed. In control cultures labeled simultaneously with both isotopes, the relative ratios of these 19 proteins were similar to that of the total membrane fraction. Thirteen of these proteins had low relative ratios, which suggested that they were more stable than the average protein. An experiment in which the normal labeling procedure was followed by a 60-min chase period in the presence of excess unlabeled leucine suggested that the low relative ratios of 3 of these 13 proteins may be due to a slow post-translational modification step. Six membrane proteins had high relative ratios, which indicated that they were degraded rapidly. In contrast to the relationships found for soluble proteins in mammalian cells, there were no strong correlations between the degradative rates and either the isoelectric points or the molecular weights of membrane proteins in E. coli.

Bacterial Proteins↗

PubMed2005

Thermodynamic stability of a kappaI immunoglobulin light chain: relevance to multiple myeloma.

Immunoglobulin light chains have two similar domains, each with a hydrophobic core surrounded by beta-sheet layers, and a highly conserved disulfide bond. Differential scanning calorimetry and circular dichroism were used to study the folding and stability of MM-kappaI, an Ig LC of kappaI subtype purified from the urine of a multiple myeloma patient. The complete primary structure of MM-kappaI was determined by Edman sequence analysis and mass spectrometry. The protein was found to contain a cysteinyl post-translational modification at Cys(214). Protein stability and conformation of MM-kappaI as a function of temperature or denaturant conditions at pH 7.4 and 4.8 were investigated. At pH 4.8, calorimetry demonstrated that MM-kappaI undergoes an incomplete, cooperative, partially reversible thermal unfolding with increased unfolding temperature and calorimetric enthalpy as compared to pH 7.4. Secondary and tertiary structural analyses provided evidence to support the presence of unfolding intermediates. Chemical denaturation resulted in more extensive protein unfolding. The stability of MM-kappaI was reduced and protein unfolding was irreversible at pH 4.8, thus suggesting that different pathways are utilized in thermal and chemical unfolding.

Amino Acid Sequence↗

PubMed1999

Characterization of prenylated protein methyltransferase in Leishmania.

Prenylated protein methyltransferase, an enzyme involved in the post-translational modification of many signalling proteins, has been characterized in a parasitic flagellated protozoan, Leishmania donovani. The activity of this enzyme was monitored by the methylation of an artificial substrate, an S-prenylated cysteine analogue, with S-adenosyl-l-[methyl-(3)H]methionine as methyl donor. More than 85% of the methyltransferase activity was associated with membranes. The enzyme methylates N-acetyl-S-trans, trans-farnesyl-l-cysteine and N-acetyl-S-all-trans-geranylgeranyl-l-cysteine, but N-acetyl-S-trans, trans-geranyl-l-cysteine only very weakly. In contrast with the enzyme from mammals, the leishmanial enzyme had a greater affinity for the farnesylated substrate than for the geranylgeranylated one. Activity in vitro was not modulated by cAMP, protein kinase C activator or guanosine 5'-[gamma-thio]triphosphate. An analysis of the endogenous substrates showed that the carboxymethylated proteins were also isoprenylated. The main carboxymethylated proteins have molecular masses of 95, 68, 55, 46, 34-23, 18 and less than 14 kDa. Treatment of cells with N-acetyl-S-trans,trans-farnesyl-l-cysteine decreased the carboxymethylation level, whereas treatment with guanosine 5'-[gamma-thio]triphosphate increased the carboxymethylation of various proteins, particularly those of molecular masses 30-20 kDa.

Animals↗

PubMed2001

Secondary structure and post-translational modifications of the leucine-rich repeat protein PGIP (polygalacturonase-inhibiting protein) from Phaseolus vulgaris.

A detailed analysis of the secondary structure has been carried out on the polygalacturonase-inhibiting protein (PGIP) from Phaseolus vulgaris, a leucine-rich repeat (LRR) protein present in the cell wall of many plants. Far-UV CD and infrared spectroscopies coupled to constrained secondary structure prediction methods indicated the presence of 12 alpha- and 12 beta-segments, thus allowing a schematic representation of three domains of the protein, namely, the central LRR region and the two cysteine-rich flanking domains. Peptides from endoproteinase-degraded PGIP were analyzed by mass spectrometry, and four disulfide bonds were identified. Mass spectrometric analysis in combination with glycosidase treatments revealed two N-linked oligosaccharides located on Asn 64 and Asn 141. The main structure resembled the typical complex plant N-glycan consisting of a core pentasaccharide beta1,2-xylosylated, carrying an alpha1,3-fucose linked to the innermost N-acetylglucosamine and one outer arm N-acetylglucosamine residue. The schematic representation of PGIP structural domains is discussed in the framework of the structure and function of LRR proteins.

Amino Acid Sequence↗