The biology of the post-genomic era: the proteomics.

The complete identification of coding sequences in a number of species has led to announce the beginning of the post-genomic era, new tools have become available to study complex phenomena in biological systems. Rapid advances in genomic sequencing and bioinformatics have established the field of genomics to investigate thousands genes' activity through mRNA display. However, recent studies have demonstrated a lack of correlation between the transcriptional profiles and the actual protein levels in cells, so investigation of the expressed part of the genome is also required to link genomic data to biological function.

Identification of protein substrates for transglutaminase in Caenorhabditis elegans.

Transglutaminase-dependent cross-linking of proteins leads to protein polymerisation that confers stability as well as resistance to mechanical disruption and chemical attack. Various transglutaminases have been implicated in a wide range of biological phenomena occurring in both extracellular and intracellular compartments, but further clarification of the physiological role of these enzymes requires identification of possible substrate molecules. Here we report the detection, purification, and identification of two proteins, enolase and ATP synthase alpha subunit as glutamine donor protein substrates for the transglutaminase of the nematode Caenorhabditis elegans.

Heat shock and apoptosis. The two defense systems of the organism may have overlapping molecular elements.

Stress response and apoptosis are two interrelated end points of the defense systems of living organisms. The molecular elements of the two have strong influences on each other. Ceramide formation and signal-induced phosphorylation cascades may be critical in determining the final fate of cells exposed to environmental changes.

Biochemical characterization and localization of transglutaminase in wild-type and cell-death mutants of the nematode Caenorhabditis elegans.

Transglutaminase activity was characterized in extracts of the nematode Caenorhabditis elegans using a microtiter plate method, and found to be Ca2+-dependent, optimal at pH 8.0, and to be inhibited by EGTA, ammonia, iodoacetamide and GTP. Monoclonal and polyclonal antibodies raised against human tissue transglutaminase also inhibited the activity and detected a 61-kDa protein from the worm lysate.

Lessons to learn from the cell death and heat shock genes of Caenorhabditis elegans.

The nematode Caenorrhabditis elegans is an applicable experimental system for simulation of complex biochemical processes of mammalian cells and tissues. The genetic pathway of programmed cell death (PCD) has been partially clarified in the nematode. Analysis of cell death genes of C.

Coupling between external viscosity and the intramolecular dynamics of ribonuclease T1: a two-phase model for the quenching of protein fluorescence.

Our recent equilibrium dialysis studies showed that proteins are able to interact preferentially with acrylamide (Punyiczki et al. (1993) Biophys. Chem.

Viscosity dependence of acrylamide quenching of ribonuclease T1 fluorescence. The gating mechanism.

The structural regulation of the access of acrylamide molecules, as quenchers, to the buried tryptophans of a protein can be modelled by a simple gate concept. Such a gate, when open, allows transient exposure of the fluorophore to the quencher molecule in solution. We have previously shown that the observed viscosity dependence of acrylamide quenching process in ribonuclease T1 (RNAse T1) is not reconcilable with the gating mechanism.

The effect of viscosity on the accessibility of the single tryptophan in human serum albumin.

When reactions take place with one of the reactants tied to protein matrix, movements along the reaction coordinate towards the transition state can become coupled to structural fluctuations of the protein matrix. This investigation aims to test the assumptions underlying the arguments supporting such a coupling. A coupling is allowed only if the activation barrier is high and broad enough as shown to be the case for the proton catalyzed isotope exchange at Trp-63 of lysozyme.

The enzyme capable to cleave trypsin active site titrant as substrate is a carboxylesterase with electrophoretic mobility similar to albumin.

An enzyme isolated from Ehrlich ascites plasma and capable of cleaving trypsin active site titrant 4-nitrophenyl-p-guanidinobenzoate (Steven, F.S. and Al-Achmad, R.

Plasminogen activator activity and plasminogen independent amidolytic activity in tear fluid from healthy persons and patients with anterior segment inflammation.

Plasminogen activator activity and plasminogen independent amidolytic activity were measured in human tears by a spectrophotometric method using human plasminogen and chromogenic peptide substrate S-2251. This assay is sensitive predominantly to urokinase-like plasminogen activator. Tears were collected with glass capillaries.