Biomedical subjects

György Babnigg

Publications and source records attributed to György Babnigg.

6 recordsLinked to original sources

PubMed2006

Tyrosine phosphatase and cytochrome P450 activity are critical in regulating store-operated calcium channels in human fibroblasts.

Diverse signaling pathways have been proposed to regulate store-operated calcium entry (SOCE) in a wide variety of cell types. However, it still needs to be determined if all of these known pathways operate in a single cell type. In this study, we examined involvement of various signaling molecules in SOCE using human fibroblast cells (HSWP). Bradykinin (BK)-stimulated Ca2+ entry, previously shown to be via SOCE, is enhanced by the addition of vanadate, an inhibitor of tyrosine phosphatases. Furthermore, SOCE is regulated by cytochrome P-450, as demonstrated by the fact that the products of cytochrome P-450 activity (14,15 EET) stimulated SOCE while econazole, an inhibitor of cytochrome P450, suppressed BK-stimulated Ca2+ entry. In contrast, Ca2+ entry was unaffected by the guanylate cyclase inhibitor LY83583, or the membrane permeant cyclic GMP analog 8-bromo-cyclic GMP (8-Br-cGMP). Neither nitric oxide donors nor phorbol esters affected BK-stimulated Ca2+ entry. SOCE in HSWP cells is primarily regulated by tyrosine phosphorylation and the cytochrome P-450 pathway, but not by cyclic GMP, nitric oxide, or protein kinase C. Thus, multiple pathways do operate in a single cell type leading to the activation of Ca2+ entry and some of these signaling pathways are more prominently involved in regulating calcium entry in different cell types.

Bradykinin↗

PubMed2006

A database of unique protein sequence identifiers for proteome studies.

In proteome studies, identification of proteins requires searching protein sequence databases. The public protein sequence databases (e.g., NCBInr, UniProt) each contain millions of entries, and private databases add thousands more. Although much of the sequence information in these databases is redundant, each database uses distinct identifiers for the identical protein sequence and often contains unique annotation information. Users of one database obtain a database-specific sequence identifier that is often difficult to reconcile with the identifiers from a different database. When multiple databases are used for searches or the databases being searched are updated frequently, interpreting the protein identifications and associated annotations can be problematic. We have developed a database of unique protein sequence identifiers called Sequence Globally Unique Identifiers (SEGUID) derived from primary protein sequences. These identifiers serve as a common link between multiple sequence databases and are resilient to annotation changes in either public or private databases throughout the lifetime of a given protein sequence. The SEGUID Database can be downloaded (http://bioinformatics.anl.gov/SEGUID/) or easily generated at any site with access to primary protein sequence databases. Since SEGUIDs are stable, predictions based on the primary sequence information (e.g., pI, Mr) can be calculated just once; we have generated approximately 500 different calculations for more than 2.5 million sequences. SEGUIDs are used to integrate MS and 2-DE data with bioinformatics information and provide the opportunity to search multiple protein sequence databases, thereby providing a higher probability of finding the most valid protein identifications.

Amino Acid Sequence↗

PubMed2004

GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes.

GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel patterns of proteomes from organisms with known genome information (available at http://gelbank.anl.gov and ftp://bioinformatics.anl.gov/gelbank/). Currently it includes 131 completed, mostly microbial proteomes available from the National Center for Biotechnology Information. A web interface allows the upload of 2D gel patterns and their annotation for registered users. The images are organized by species, tissue type, separation method, sample type and staining method. The database can be queried based on protein or 2DE-pattern attributes. A web interface allows registered users to assign molecular weight and pH gradient profiles to their own 2D gel patterns as well as to link protein identifications to a given spot on the pattern. The website presents all of the submitted 2D gel patterns where the end-user can dynamically display the images or parts of images along with molecular weight, pH profile information and linked protein identification. A collection of images can be selected for the creation of animations from which the user can select sub-regions of interest and unlimited 2D gel patterns for visualization. The website currently presents 233 identifications for 81 gel patterns for Homo sapiens, Methanococcus jannaschii, Pyro coccus furiosus, Shewanella oneidensis, Escherichia coli and Deinococcus radiodurans.

Databases, Factual↗

PubMed2003

Differential tyrosine phosphorylation of plasma membrane Ca2+-ATPase and regulation of calcium pump activity by carbachol and bradykinin.

We investigated the effects of thapsigargin (TG), bradykinin (BK), and carbachol (CCh) on Ca(2+) entry via endogenous channels in human embryonic kidney BKR21 cells. After depletion of Ca(2+) stores by either TG, BK, or CCh, the addition of Ca(2+) gave a much larger rise in Ca(2+) levels in CCh-treated and TG-treated cells than in cells treated with BK. However, in experiments performed with Ba(2+), a cation not pumped by Ca(2+)-ATPases, only a modest difference between CCh- and BK-stimulated Ba(2+) entry levels was observed, suggesting that the large difference in the Ca(2+) response is mediated by a differential regulation of Ca(2+) pump activity by CCh and BK. This hypothesis is supported by the finding that when Ca(2+) is removed during the stable, CCh-induced Ca(2+) plateau phase, the decline of cytosolic Ca(2+) is much faster in the absence of CCh than in its presence. In addition, if Ca(2+) is released from a caged Ca(2+) compound after a UV pulse, the resulting Ca(2+) peak is much larger in the presence of CCh than in its absence. Thus, the large increase in Ca(2+) levels observed with CCh results from both the activation of Ca(2+) entry pathways and the inhibition of Ca(2+) pump activity. In contrast, BK has the opposite effect on Ca(2+) pump activity. If Ca(2+) is released from a caged Ca(2+) compound, the resulting Ca(2+) peak is much smaller in the presence of BK than in its absence. An investigation of tyrosine phosphorylation levels of the plasma membrane Ca(2+)-ATPase (PMCA) demonstrated that CCh stimulates an increase in tyrosine phosphorylation levels, which has been reported to inhibit Ca(2+) pump activity, whereas in contrast, BK stimulates a reduction of PMCA tyrosine phosphorylation levels. Thus, BK and CCh have a differential effect both on Ca(2+) pump activity and on tyrosine phosphorylation levels of the PMCA.

Bradykinin↗

PubMed2003

ProteomeWeb: a web-based interface for the display and interrogation of proteomes.

The analysis of proteomes, i.e., the proteins expressed by biological organisms under a given set of conditions at a given time, requires separating complex protein mixtures into discrete protein components, measuring their relative abundances, and identifying the individual protein components. Many types of data are generated during the course of proteome analysis, including graphic images of the protein profiles, flat files containing numeric data, spreadsheets for assimilating numeric data, and relational database tables for integrating data from multiple experiments. As part of a project to describe the proteomes of microbes of interest to the U.S. Department of Energy, a World-Wide Web-based interface has been developed for the display of protein profiles generated by two-dimensional gel electrophoresis. The web interface is capable of obtaining protein identifications on the fly, interrogating the quantitative data in the context of available genome sequence information, and relating the proteome data to existing metabolic pathway databases. Analysis of protein expression profiles is expedited, providing the capability to efficiently determine the gene locations for proteins modulated in abundance in response to different growth conditions and to locate the positions of the proteins within specific metabolic pathways. The proteome of the archaeon Methanococcus jannaschii, a microbe for which the complete genome sequence is available, is used to demonstrate the capabilities of this evolving web interface (http://proteomeweb.anl.gov).

Amino Acid Sequence↗

PubMed2002

The role of endogenous human Trp4 in regulating carbachol-induced calcium oscillations in HEK-293 cells.

We utilized 2-aminoethyoxydiphenyl borane, an agent that blocks store-operated Ca(2+) entry, as well as an antisense approach to characterize endogenous Ca(2+) entry pathways in HEK-293 cells. The thapsigargin- and carbachol-induced, but not the 1-oleolyl-2-acytyl-sn-glycerol (OAG)-induced, entry was blocked by 2-aminoethyoxydiphenyl borane. Both reverse transcriptase-PCR and Western blot analyses demonstrated endogenous expression for HTRP1, HTRP3, and HTRP4 and specific suppression of mRNA levels and Trp protein levels in cells stably expressing antisense constructs. Expression of HTRP4 antisense inhibited 35% of the carbachol (CCh)-stimulated Ba(2+) entry and 46% of the OAG-stimulated Sr(2+) entry but in contrast had no effect on the thapsigargin-stimulated Ba(2+) or Sr(2+) entry. HTRP3 antisense reduced, while HTRP1 antisense had no effect on, OAG-induced Sr(2+) entry. Of greater importance, HTRP4 antisense expression, but not HTRP3 antisense expression, blocked the sustained Ca(2+) oscillations produced by low doses of CCh (15 microm), arguing that receptor-stimulated rather than store-operated channels are involved in these sustained oscillations. HTRP4 antisense also inhibited 75% of the arachidonic acid-induced Ca(2+) entry. In summary, these data suggest that HTRP4 proteins in HEK-293 cells, differing from HTRP3 and HTRP1 proteins, do not serve as functional subunits of store-operated channels but do function as subunits for CCh- and OAG-stimulated channels. Furthermore, evidence is provided for the first time for the involvement of a Trp isoform (HTRP4) in the formation of the channel responsible for both arachidonic acid-induced Ca(2+) entry and the Ca(2+) entry needed to sustain long term Ca(2+) oscillations induced by low doses of carbachol.

Arachidonic Acid↗