Characterization of a selective protein kinase C substrate derived from the MARCKS phosphorylation site domain for use in brain tissue homogenates

Protein kinase C (PKC) isozymes play crucial roles in neuronal signal transduction and can regulate transmitter release, ion channels, neural development, and plasticity. In vitro assays of PKC are frequently used to associate PKC activity with cellular function, and the availability of selective PKC substrates can facilitate such studies. We have characterized a commercially available 12 amino acid peptide derived from the myristoylated alanine-rich C kinase substrate (MARCKS-PSD, Calbiochem) for use in crude rat brain homogenates. Assays were performed at 25 degrees C for 10 min (linear up to 12 min) using optimal concentrations of calcium and lipid cofactors. Kinetic analysis of MARCKS-PSD phosphorylation by PKC purified from rat brain gave a K(m) of 2.3 microM, which was similar to the K(m) of 2.8 microM obtained using rat brain cortical homogenates. The selective PKC inhibitor bisindolylmaleimide reduced phosphorylation of MARCKS-PSD in a concentration-dependent manner, with greater than 95% inhibition at 1.0 microM. MARCKS-PSD was more potent than another widely used selective PKC substrate (neurogranin((28-43)) and was a good substrate for human recombinant PKC alpha, delta, and epsilon but not zeta. The ontogeny of PKC activity was examined in the cortex and cerebellum. PKC activity was low at birth and reached adult levels by 21 days of age in both regions. Calcium-independent PKC activity in brain homogenates could be measured with MARCKS-PSD and accounted for approximately 25 and 10% of total activity in 1-day-old and adult rat cortex, respectively. These results suggest that the MARCKS-PSD peptide can be used as a selective PKC substrate in rat brain homogenates.     

NMR resonance assignment of selectively labeled proteins by the use of paramagnetic ligands

Selective isotopic labeling of larger proteins greatly simplifies protein NMR spectra and reduces signal overlap, but selectively labeled proteins cannot be easily assigned since the sequential assignment method is not applicable. Here we describe a strategy for resonance assignment in selectively labeled proteins. Our approach involves a spin-labeled analog of a ligand of which the three-dimensional structure in complex with the target protein is known. Other methods for introduction of the spin label are possible. The paramagnetic center causes faster relaxation of all neighboring nuclei in a distance-dependent manner. Measurement of this effect allows to deduce distances between isotopically labeled residues and the paramagnetic center which can be used for resonance assignment. The method is demonstrated for the catalytic domain of Abl kinase in complex with the inhibitor, STI571.     

Isolation of tissue collagenase from homogenates of embryonic chick bones

An enzyme capable of digesting undenatured collagen in solution and in the solid state as reconstituted collagen fibrils at neutral pH was extracted from demineralized embryonic chick bone homogenates in 1.0M NaCl at neutral pH. The enzyme could be dissociated from the small amount of collagen which was also solubilized in 1.0M NaCl by the serial use of Diaflo XM-300 and PM-10 membranes, which procedures also concentrated the enzyme. The enzymatic activity was inhibited by EDTA, cysteine and horse serum, and was enhanced by the addition of heparin.     

The use of a synthetic DNA-antibody complex as external reference for chromatin immunoprecipitation

Chromatin immunoprecipitation (ChIP) is an analytical method used to investigate the interactions between proteins and DNA in vivo. ChIP is often used as a quantitative tool, and proper quantification relies on the use of adequate references for data normalization. However, many ChIP experiments involve analyses of samples that have been submitted to experimental treatments with unknown effects, and this precludes the choice of suitable internal references. We have developed a normalization method based on the use of a synthetic DNA-antibody complex that can be used as an external reference instead. A fixed amount of this synthetic DNA-antibody complex is spiked into the chromatin extract at the beginning of the ChIP experiment. The DNA-antibody complex is isolated together with the sample of interest, and the amounts of synthetic DNA recovered in each tube are measured at the end of the process. The yield of synthetic DNA recovery in each sample is then used to normalize the results obtained with the antibodies of interest. Using this approach, we could compensate for losses of material, reduce the variability between ChIP replicates, and increase the accuracy and statistical resolution of the data.     

Distribution in tissue homogenates,and the nature of the linkage of injected proteins to subcellular particles

Intravenously injected labeled proteins were recovered mostly in particulate fractions of rat liver homogenate. Distribution showed changes depending on the time elapsed from the injection. ¹³¹I-albumin undergoes an intraparticulate hydrolysis which shows the highest activity in the gradient fractions associated with the highest level of acid phosphatase. The labeled albumin-bearing particles separated at 27,000 g × 10 minutes released their radioactive protein at the same rate as acid phosphatase appeared in the medium, under the effect of such agents as distilled water, salts, homogenization, sonication and pH changes. The substitution of sucrose for distilled water or salts showed that the particles behave as an osmotic system as do lysosomes. These experiments prove that secondary lysosomes involved in the hydrolysis of foreign proteins, whose existence was shown by other authors only at the histochemical level, may survive the distrupting action of conventional homogenization and maintain many properties characteristic of primary lysosomes in addition to the ability of hydrolysing “in vitro” the engulfed material.     

Carbon monoxide generation from tin- and zinc-protoporphyrin by tissue homogenates

Both heme and tin-protoporphyrin (TP), but not zinc-protoporphyrin (ZP), supported significant NADPH-stimulated, concentration-dependent CO production in all tissues. These rates, for 400 microM substrate, ranged: for heme 0.52 (intestine) to 4.18 (spleen); for TP 0.08 (kidney) to 0.71 (liver); and for ZP 0.01 (liver) to 0.25 (kidney) nmoles CO/hr/mg protein. All three metalloporphyrins (400 microM) supported concentration-dependent CO production in the absence of NADPH. The rates ranged: for heme 0.31 (kidney) to 0.80 (spleen); for TP 0.41 (kidney) to 1.04 (intestine); and for ZP 0.12 (kidney) to 0.51 (spleen) nmoles/hr/mg protein. We conclude that both TP and ZP are subject to in vitro degradation by 13,000 x g supernatants of adult rat organs via CO-producing reactions.