Spectrophotometric ribonuclease assays using dinucleoside monophosphate substrates

Posttranslational incorporation of noncanonical amino acids in the RNase S system by semisynthetic protein assembly

The unique ribonuclease S (RNase S) system, derived from proteolytic cleavage of bovine ribonuclease A (RNase A), consists of a tight complex formed by a peptide (amino acids 1-20) and a protein (21-124) part. These fragments, designated as S-peptide and S-protein, can be separated by two purification steps. By addition of synthetic S-peptide derivatives to the S-protein, semisynthetic RNase S is reassembled with high efficiency. Based on this peptide-protein complementation noncanonical amino acids can be easily introduced into a protein host. Here we describe the preparation of the S-protein from RNase A as well as the characterization of the reassembled semisynthetic RNase S complex. Complex formation can be monitored by RNase activity, circular dichroism, or fluorescence polarization. Structure-based enzyme design of the RNase S scaffold is possible based on high-resolution crystal structures of RNase S and its semisynthetic variants.

Protein metabolism in alcoholism: effects on specific tissues and the whole body

Ethanol is one of the few nutrients that is profoundly toxic. Alcohol causes both whole-body and tissue-specific changes in protein metabolism. Chronic ethanol missuse increases nitrogen excretion with concomitant loss of lean tissue mass. Even acute doses of alcohol elicit increased nitrogen excretion. The loss of skeletal muscle protein (i.e., chronic alcoholic myopathy) is one of several adverse reactions to alcohol and occurs in up to two-thirds of all ethanol misusers. There are a variety of other diseases and tissue abnormalities that are entirely due to ethanol-induced changes in the amounts of individual proteins or groups of tissue proteins; for example, increased hepatic collagen in cirrhosis, reduction in myosin in cardiomyopathy, and loss of skeletal collagen in osteoporosis. Ethanol induces changes in protein metabolism in probably all organ or tissue systems. Clinical studies in alcoholic patients without overt liver disease show reduced rates of skeletal muscle protein synthesis though whole-body protein turnover does not appear to be significantly affected. Protein turnover studies in alcohol misusers are, however, subject to artifactual misinterpretations due to non-abstinence, dual substance misuse (e.g., cocaine or tobacco), specific nutritional deficiencies, or the presence of overt organ dysfunction. As a consequence, the most reliable data examining the effects of alcohol on protein metabolism is derived from animal studies, where nutritional elements of the dosing regimen can be strictly controlled. These studies indicate that, both chronically and acutely, alcohol causes reductions in skeletal muscle protein synthesis, as well as of skin, bone, and the small intestine. Chronically, animal studies also show increased urinary nitrogen excretion and loss of skeletal muscle protein. With respect to skeletal muscle, the reductions in protein synthesis do not appear to be due to the generation of reactive oxygen species, are not prevented with nitric oxide synthase inhibitors, and may be indirectly mediated by the reactive metabolite acetaldehyde. Changes in skeletal muscle protein metabolism have profound implications for whole body physiology, while protein turnover changes in organs such as the heart (exemplified by complex alterations in protein profiles) have important implications for cardiovascular function and morbidity.

A fluorescence-based assay for ribonuclease A activity

A sensitive assay for ribonuclease A activity based on the relief of fluorescence quenching within a defined oligomeric substrate (5' fluorescein-AAAArUAAAA-3'-rhodamine) is described. The substrate can be produced using an automated nucleic acid synthesizer and commercially available reagents. Together with a nonfluorescent cosubstrate (5'-dimethoxytrityl-AAAArUAAAA), the compound can be used to determine kinetic constants for the first step (transphosphorylation) of the ribonuclease-catalyzed reaction. These measurements should be useful for structure-based analyses of ribonuclease activity since a crystal structure has been determined for a closely analogous enzyme-inhibitor complex.

A novel fluorogenic substrate for ribonucleases. Synthesis and enzymatic characterization

The synthesis and enzymatic characterization of DUPAAA, a novel fluorogenic substrate for RNases of the pancreatic type is described. It consists of the dinucleotide uridylyl-3',5'-deoxyadenosine to which a fluorophore, o-aminobenzoic acid, and a quencher, 2,4-dinitroaniline, have been attached by means of phosphodiester linkages. Due to intramolecular quenching the intact substrate displayed very little fluorescence. Cleavage of the phosphodiester bond at the 3'-side of the uridylyl residue by RNase caused a 60-fold increase in fluorescence. This allowed the continuous and highly sensitive monitoring of enzyme activity. The substrate was turned over efficiently by RNases of the pancreatic type, but no cleavage was observed with the microbial RNase T1. Compared to the dinucleotide substrate UpA, the specificity constant with RNase A, RNase PL3 and RNase U(s) increased 6-, 18-, and 29-fold, respectively. These differences in increased catalytic efficiency most likely reflect differences in the importance of subsites on the enzyme in the binding of elongated substrates. Studies on the interactions of RNase inhibitor with RNase A using DUPAAA as a reporter substrate showed that it was well suited for monitoring this very tight protein-protein interaction using pre-steady-state kinetic methods.

Two distinct secretory ribonucleases from human cerebrum: purification, characterization and relationships to other ribonucleases

Two RNAases from human cerebrum were purified to an electrophoretically homogeneous state and their molecular masses were 22.0 kDa (tentatively called RNAase HB-1) and 19.0 kDa (RNAase HB-2). Analyses of the amino acid compositions, N-terminal amino acid sequences and catalytic properties of these enzymes provided strong evidence that they were strictly related to the secretory (sec) RNAases, such as the pancreatic enzyme, very similar immunologically to urinary sec RNAase, but clearly distinguishable from urinary non-secretory (nonsec) RNAase. There were several differences between HB-1 and HB-2, namely their immunological reactivities with specific antibodies, heat-stabilities, attached carbohydrate moieties and molecular masses. In particular, HB-2 appeared to be nonglycosylated, in view of its lack of affinity for several conjugated lectins, the absence of hexosamine and no change in electrophoretic mobility before and after peptide:N-glycosidase F digestion, whereas HB-1 and human sec RNAases purified from kidney, pancreas and urine all appeared to be glycosylated, as they moved to the same position as HB-2 when electrophoresed after glycosidase digestion. An antibody against urinary sec RNAase inhibited 75% and 20% of the total activity of the crude cerebral extract against RNA at pH 8.0 and 6.0 respectively, whereas an antibody against urinary nonsec RNAase had no such inhibitory effect. These findings suggest that yet another type(s) of cerebral RNAase, which is unable to cross-react immunologically with sec and nonsec RNAases, may exist. Two RNAases corresponding to HB-1 and HB-2 were identified in fresh cerebrospinal fluid.

Relatedness of a periplasmic, broad-specificity RNase from Aeromonas hydrophila to RNase I of Escherichia coli and to a family of eukaryotic RNases

The isolation, sequencing, and characterization of a periplasmic RNase gene from Aeromonas hydrophila AH1133 is described. Following subcloning of the gene on a 2.7-kb PstI fragment, its direction of transcription and approximate location were determined. Analysis of the nucleotide sequence reveals that the gene is 645 bp long, coding for 215 amino acid residues with a total molecular weight of 24,215. A typical leader sequence is present at the beginning of the corresponding protein. Computer analysis revealed strong local similarities to Escherichia coli RNase I and to the active site of a family of eukaryotic RNases. Expression studies indicate that the RNase natural promoter functions poorly in E. coli. In this organism, the enzyme is mainly localized in the cytoplasm and periplasm, although high levels of expression lead to significant release into the extracellular medium. Functional and physical characterizations further indicate that the periplasmic and cytoplasmic enzymes of A. hydrophila are likely to be the counterparts of E. coli RNase I and its cytoplasmic form RNase I*: as for the E. coli enzymes, the A. hydrophila RNase forms have similar sizes and show broad specificity, and the periplasmic form is more active towards natural polymer RNA than its cytoplasmic counterpart. Both forms are relatively thermosensitive and are reversibly inactivated by up to 0.6% sodium dodecyl sulfate. Southern hybridization revealed homology to E. coli K-12 and Shigella sp. genomic DNA, a finding which correlates with the presence of secreted RNases in these organisms. In contrast, species of phylogenetically closer genera, such as Vibrio and Plesiomonas, did not hybridize to the A. hydrophila RNase gene.