Initiation lysates

Rau, M., Ohlmann, T., Morley, S. J., and Pain, V. M. (1996). A reevaluation of the capbinding protein, eIF4E, as a rate-limiting factor for initiation of translation in reticulocyte lysate. J. Biol. Chem. 271, 8983—8990. 

In the initial experiments, we resolved reticulocyte lysates on DEAE-cellulose into two crude fractions Fraction 1, which contained proteins not adsorbed to the resin, and Fraction 2, which contained all proteins adsorbed to the resin and eluted with high salt. The original aim of this fractionation was to get rid of hemoglobin, which was known to be in Fraction 1, while most non-hemoglobin proteins of reticulocytes were known to be in Fraction 2. We found that neither fraction was active by itself, but ATP-dependent protein degradation could be reconstituted by combination of the two fractions [13]. The active component in Fraction 1 was a small, heat-stable protein we have exploited its stability to heat treatment for its purification to near homogeneity. We termed this protein at that time APF-1, for ATP-dependent Proteolysis Factor 1 [13]. The identity of APF-1 with ubiquitin was established later by Wilkinson et al. [14], subsequent to the discovery in my laboratory of its covalent ligation to protein substrates, as described below. 

The suppressor tRNA developed by the Chamberlin lab for use in a rabbit reticulocyte lysate is based on an E. coli glycyl tRNA, which was initially chosen because glycyl-tRNA synthetases do not rely on a double-sieve editing mechanism for enzymatic hydrolysis of misacylated tRNAs [26]. Two base pair changes were made to the acceptor stem to allow incorporation of the optimal T7 RNA polymerase promoter into the DNA template for tRNA y-Con [27,28],... 

When the C-terminal domain is expressed as a separate polypeptide, IN213-288 can be purified from the initial soluble fraction from cell lysates [33]. This small protein fragment, therefore, was an attractive target for structure determination. 

The test is performed for diagnosis of all clinical forms of SASD. This analysis is usually done after an initial TLC screening test that is positive for free sialic acid, and an increased free sialic acid value in the quantitative urine determination test. The test is like the quantitative urine test performed with the periodate-TBA assay [5, 22]. However, in this case interference is decreased by prepurification of the sample using ion-exchange chromatography [12]. Fibroblasts are cultured under standardized conditions. Cell lysates are prepared by tip sonification in distilled water and the cleared lysates are applied to small Dowex columns. NeuAc is eluted, freeze dried,... 

The uPAR protein was initially purified from lysates of phorbol ester-stimulated U937 cells by affinity chromatography using diisopropyl fluoro-phosphates (DFP)-inactivated uPA [53, 54]. uPAR is anchored in the plasma membrane by a glycosylphosphatidylinositol (GPI) moiety and it consists of 283 amino acids in its processed form [55, 56]. The protein is composed of three domains and each domain contains 90 amino acids. The domains are connected by linker regions with a length of 15-20 amino acids [57, 58]. The disulfide bonds in the N-terminal domain I have been experimentally determined and the pattern of cysteine residues in the sequence has revealed... 

Antibody arrays immobilized on glass surfaces mimic DNA microarrays in format and spot size. The biggest challenge in protein profiling using antibody microarrays is selection of validated antibodies that are useful in the desired sample environment. Many of the initial reports used antibody arrays assayed for cytokines because serum presents a relatively simple sample assay environment compared to tissue and also because there are numerous validated antibodies available for this clinically important set of proteins. Tissue and cell lysates present more complex assay environments with more opportunities for antibody cross-reactivity and other interferences which erode the biological meaningfulness of the data. 

INITIAL PURIFICATION AND ASSAY OF ACTIVITIES IN CEU--FREE LYSATES 105... 

The standard assay mixture contained 50 mM Tris-HCl (pH 7.5), 1 mM MgCl2, 1 mM dithiothreitol, 0.1 to 10 mM substrate, and the appropriate amount of enzyme in a final volume of 500 nL. Cytidine monophosphate (CMP) at an initial concentration of 0.2 mM was used to assay red blood cell lysates. Incubations were carried out at 37°C for either 30 or 60 minutes before the reaction was stopped by adding 100 /u.L of assay mixture to 50 fiL of ice-cold 1.2 M perchloric acid. After the tubes had cooled for 10 minutes in an ice bath, proteins were removed by centrifugation and 130 /u.L of the supernate was neutralized by the addition of 35 /u,L of 1 M K2C03. Potassium perchlorate was removed by centrifugation before analysis by HPLC. 

Enzyme assays were conducted in a 10 mL screw-neck glass test tube containing 100 fiL of lysate, 90 fiL of a 250 /ng/mL solution of 6-mercaptopurine in 0.01 M HC1, and 15 /uL of 250 mM sodium phosphate buffer (pH 9.2). Reactions were initiated by the addition of 32 fiL of a 3 1 mixture of 250 fiM S-adenosyl-L-methionine and 30 mM dithiothreitol. The final pH was 7.5. After a 1-hour incubation at 37°C, the reaction was stopped by the addition of 850 fjL of ice-cold 3.5 mM dithiothreitol and 50 fih of 1.5 M H2S04. The tubes were then heated at 100°C for 2 hours. To each tube, 500 fiL of 3.4 M NaOH was added, immediately followed by 8 mL of toluene-amyl alcohol-phenyl mercuric acetate. The tubes were shaken for 10 minutes and centrifuged. Then 6 mL of the toluene layer was transferred to a glass-stoppered conical test tube and 0.2 mL of 0.1 M HC1 added. After vortex-mixing and centrifuging, the toluene layer was discarded. Samples (50 fiL in 0.1 M HC1) were used for HPLC analysis. Product formation was linear for up to 120 minutes and 150 /u,L of lysate. 

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