Human pancreatic ribonuclease presents higher endonucleolytic activity than ribonuclease A.

Analyzing the pattern of oligonucleotide formation induced by HP-RNase cleavage shows that the enzyme does not act randomly and follows a more endonucleolytic pattern when compared to RNase A. The enzyme prefers the binding and cleavage of longer substrate molecules, especially when the phosphodiester bond that is broken is 8-11 nucleotides away from at least one of the ends of the substrate molecule. This more endonucleolytic pattern is more appropriate for an enzyme with a regulatory role. Deleting two positive charges on the N-terminus (Arg4 and Lys6) modifies this pattern of external/internal phosphodiester bond cleavage preference, and produces a more exonucleolytic enzyme. These residues may reinforce the strength of a non-catalytic secondary phosphate binding (p2) or, alternatively, constitute a new non-catalytic phosphate binding subsite (p3).

The cytotoxicity of eosinophil cationic protein/ribonuclease 3 on eukaryotic cell lines takes place through its aggregation on the cell membrane.

Human eosinophil cationic protein (ECP)/ ribonuclease 3 (RNase 3) is a protein secreted from the secondary granules of activated eosinophils. Specific properties of ECP contribute to its cytotoxic activities associated with defense mechanisms. In this work the ECP cytotoxic activity on eukaryotic cell lines is analyzed. The ECP effects begin with its binding and aggregation to the cell surface, altering the cell membrane permeability and modifying the cell ionic equilibrium. No internalization of the protein is observed. These signals induce cell-specific morphological and biochemical changes such as chromatin condensation, reversion of membrane asymmetry, reactive oxygen species production and activation of caspase-3-like activity and, eventually, cell death. However, the ribonuclease activity component of ECP is not involved in this process as no RNA degradation is observed. In summary, the cytotoxic effect of ECP is attained through a mechanism different from that of other cytotoxic RNases and may be related with the ECP accumulation associated with the inflammatory processes, in which eosinophils are present.

Identification and characterization of human eosinophil cationic protein by an epitope-specific antibody.

The eosinophil cationic protein (ECP) is a basic secretion protein involved in the immune response system. ECP levels in biological fluids are an indicator of eosinophil-specific activation and degranulation and are currently used for the clinical monitoring and diagnosis of inflammatory disorders. A polyclonal epitope-specific antibody has been obtained by immunizing rabbits with a conjugated synthetic peptide. A sequence corresponding to a large exposed loop in the human ECP three-dimensional structure (D115-Y122) was selected as a putative antigenic epitope. The antibody was purified on an affinity column using recombinant ECP (rECP) as antigen. The antibody (D112-P123 Ab) specifically recognizes rECP and its native glycosylated and nonglycosylated forms in plasma, granulocytes, and sputum. The antibody detects as little as 1 ng of rECP, can be used both in reducing and nonreducing conditions, and does not cross-react with the highly homologous eosinophil-derived neurotoxin or other proteins of the pancreatic ribonuclease superfamily.

[Catalytic properties of recombinant pancreatic ribonuclease A-K7H]. / Kataliticke osobine rekombinantne pankreasne ribonukleaze A-K7H.

Pancreatic ribonuclease A is an enzyme that binds up ribonucleic acid (RNA) along the multiple binding subsites that essentially recognize the negatively charged phosphates of the substrate. It is endoribonuclease that catalyse depolimerization of single-stranded RNA. This work gives additional support to the existence of the phosphate-binding site p2 and confirms the central role of Lys-7 in establishing and electrostatic interraction with a phosphate group of the substrate. In this work catalytic properties of recombinant ribonuclease K7H have been studied. This enzyme is a mutant enzyme which contains histidine instead of lysine in a position 7, amino-acid that participates in the main catalytic center of RNase A, named p1. It was obtained by site-directed mutagenesis. Kinetic parameters of K7H have determined with C > p i poli (C) as substrates at pH 5.5 i 7.5. Kinetic parameters of K7H for C > p and as a substrate at pH 5.5 have not altered, but at pH 7.5 were significantly increased. Value Km was also increased, that indicates decreasing of affinity. Increasing of catalysis was double. Results of kinetic parameters of K7H with poli (C) as a substrate in pH 5.5 have shown slight difference according to kinetic parameters of commercial RNase A with poli (C). Significant decreasing of values of all kinetic parameters for K7H were reaction at pH 7.5.

Crystal structure of eosinophil cationic protein at 2.4 A resolution.

Eosinophil cationic protein (ECP) is located in the matrix of the eosinophil's large specific granule and has marked toxicity for a variety of helminth parasites, hemoflagellates, bacteria, single-stranded RNA virus, and mammalian cells and tissues. It belongs to the bovine pancreatic ribonuclease A (RNase A) family and exhibits ribonucleolytic activity which is about 100-fold lower than that of a related eosinophil ribonuclease, the eosinophil-derived neurotoxin (EDN). The crystal structure of human ECP, determined at 2.4 A, is similar to that of RNase A and EDN. It reveals that residues Gln-14, His-15, Lys-38, Thr-42, and His-128 at the active site are conserved as in all other RNase A homologues. Nevertheless, evidence for considerable divergence of ECP is also implicit in the structure. Amino acid residues Arg-7, Trp-10, Asn-39, His-64, and His-82 appear to play a key part in the substrate specificity and low catalytic activity of ECP. The structure also shows how the cationic residues are distributed on the surface of the ECP molecule that may have implications for an understanding of the cytotoxicity of this enzyme.

[Endonuclease activity of recombinant pancreatic nuclease (A-K7H)]. / Endonukleazna aktivnost rekombinantne pankreasne ribonukleaze A-K7H.

Pancreatic ribonuclease A (RNase A) is a endonuclease that catalyzes depolymerization of ribonucleic acid (RNA) releasing oligonucleotides. In the process of binding enzyme with substrate are involved several non-catalytic phosphate binding subsites, one of them is p2, additional to main catalytic site p1. RNaza A prefers binding and cleavage of longer substrate molecules, and 3',5'-phosphodiester bond should be some six-seven residues apart from the end of molecules of the chain of RNA. In this work is analysed endonuclease activity of recombinant pancreatic RNase A (K7H), that in position seven instead of a lysine there is a histidine, amino acid residue that participates in main catalytic site p1. Mutant enzyme is obtained by site-directed mutagenesis by Kunkel. Results of this investigation have shown that substitution of lysine by histidine in position seven of RNase A has produced total deletion of p2 subsite, and K7H has lost endonuclease activity, and has become exonuclease. These results confirm central role of Lys-7 in establishing p2 subsite and endonuclease activity of pancreatic RNase A.

Kinetic and product distribution analysis of human eosinophil cationic protein indicates a subsite arrangement that favors exonuclease-type activity.

With the use of a high yield prokaryotic expression system, large amounts of human eosinophil cationic protein (ECP) have been obtained. This has allowed a thorough kinetic study of the ribonuclease activity of this protein. The catalytic efficiencies for oligouridylic acids of the type (Up)nU>p, mononucleotides U>p and C>p, and dinucleoside monophosphates CpA, UpA, and UpG have been interpreted by the specific subsites distribution in ECP. The distribution of products derived from digestion of high molecular mass substrates, such as poly(U) and poly(C), by ECP was compared with that of RNase A. The characteristic cleavage pattern of polynucleotides by ECP suggests that an exonuclease-like mechanism is predominantly favored in comparison to the endonuclease catalytic mechanism of RNase A. Comparative molecular modeling with bovine pancreatic RNase A-substrate analog crystal complexes revealed important differences in the subsite structure, whereas the secondary phosphate-binding site (p2) is lacking, the secondary base subsite (B2) is severely impaired, and there are new interactions at the po, Bo, and p-1 sites, located upstream of the P-O-5' cleavable phosphodiester bond, that are not found in RNase A. The differences in the multisubsites structure could explain the reduced catalytic efficiency of ECP and the shift from an endonuclease to an exonuclease-type mechanism.

The contribution of noncatalytic phosphate-binding subsites to the mechanism of bovine pancreatic ribonuclease A.

The enzymatic catalysis of polymeric substrates such as proteins, polysaccharides or nucleic acids requires precise alignment between the enzyme and the substrate regions flanking the region occupying the active site. In the case of ribonucleases, enzyme-substrate binding may be directed by electrostatic interactions between the phosphate groups of the RNA molecule and basic amino acid residues on the enzyme. Specific interactions between the nitrogenated bases and particular amino acids in the active site or adjacent positions may also take place. The substrate-binding subsites of ribonuclease A have been characterized by structural and kinetic studies. In addition to the active site (p1), the role of other noncatalytic phosphate-binding subsites in the correct alignment of the polymeric substrate has been proposed. p2 and p0 have been described as phosphate-binding subsites that bind the phosphate group adjacent to the 3' side and 5' side, respectively, of the phosphate in the active site. In both cases, basic amino acids (Lys-7 and Arg-10 in p2, and Lys-66 in p0) are involved in binding. However, these binding sites play different roles in the catalytic process of ribonuclease A. The electrostatic interactions in p2 are important both in catalysis and in the endonuclease activity of the enzyme, whilst the p0 electrostatic interaction contributes only to binding of the RNA.

The subsites structure of bovine pancreatic ribonuclease A accounts for the abnormal kinetic behavior with cytidine 2',3'-cyclic phosphate.

The kinetics of the hydrolysis of cytidine 2',3'-cyclic phosphate (C>p) to 3'-CMP by ribonuclease A are multiphasic at high substrate concentrations. We have investigated these kinetics by determining 3'-CMP formation both spectrophotometrically and by a highly specific and quantitative chemical sampling method. With the use of RNase A derivatives that lack a functional p2 binding subsite, evidence is presented that the abnormal kinetics with the native enzyme are caused by the sequential binding of the substrate to the several subsites that make up the active site of ribonuclease. The evidence is based on the following points. 1) Some of the unusual features found with native RNase A and C>p as substrate disappear when the derivatives lacking a functional p2 binding subsite are used. 2) The kcat/Km values with oligocytidylic acids of increasing lengths (ending in C>p) show a behavior that parallels the specific velocity with C>p at high concentrations: increase in going from the monomer to the trimer, a decrease from tetramer to hexamer, and then an increase in going to poly(C). 3) Adenosine increases the kcat obtained with a fixed concentration of C>p as substrate. 4) High concentrations of C>p protect the enzyme from digestion with subtilisin, which results in a more compact molecule, implying large substrate concentration-induced conformational changes. The data for the hydrolysis of C>p by RNase A can be fitted to a fifth order polynomial that has been derived from a kinetic scheme based on the sequential binding of several monomeric substrate molecules.

Production of human pancreatic ribonuclease in Saccharomyces cerevisiae and Escherichia coli.

Human pancreatic ribonuclease (HP-RNase) has considerable promise as a therapeutic agent. Structure-function analyses of HP-RNase have been impeded by the difficulty of obtaining the enzyme from its host. Here, a gene encoding HP-RNase was designed, synthesized, and inserted into two expression vectors that then direct the production of HP-RNase in Saccharomyces cerevisiae (fused to either an unmodified or a modified a-factor pre-pro segment) or Escherichia coli (fused to the pelB signal sequence). HP-RNase produced in S. cerevisiae was secreted into the medium as an active enzyme, isolable at 0.1-0.2 mg/liter of culture. This isolate was heterogeneous due to extensive glycosylation and incomplete maturation of the pre-pro segment. HP-RNase produced in E. coli with the pET expression system was purified from the insoluble fraction of the cell lysate. Renaturation of the reduced and denatured protein produced active, homogeneous enzyme recoverable at 1 mg/liter of culture. The N terminus of the HP-RNase produced from the bacterial expression system was processed fully in vivo. The yeast system, combined with techniques that allow detection of picograms of ribonuclease activity, offers a sensitive probe for studies of post-translational modification and secretory targeting in eukaryotic cells. The bacterial system enables studies both to reveal new structure-function relationships in ribonucleases and to evaluate the use of HP-RNase as a cytotoxin that is tolerated by the human immune system.

Bovine pancreatic ribonuclease A as a model of an enzyme with multiple substrate binding sites.

Bovine pancreatic ribonuclease A is an enzyme that catalyses the depolymerization of RNA. This process involves the interaction of the enzyme with the polymeric substrate in the active site and its correct alignment on the surface of the enzyme through multiple binding subsites that essentially recognize the negatively charged phosphate groups of the substrate. The enzyme shows a strong specificity for pyrimidine bases at the 3'-position of the phosphodiester bond that is cleaved and a preference for purine bases at the 5'-position and, probably, for guanine at the next position. On the other hand, the enzyme shows a clear preference for polynucleotide substrates over oligonucleotides. In this review the contributions to the catalytic mechanism of some amino-acid residues that are located at non catalytic binding subsites are analysed.

Identification of human nonpancreatic-type ribonuclease by antibodies obtained against a synthetic peptide.

An antibody that recognizes human nonpancreatic-type ribonuclease was obtained by immunizing a rabbit with a 14-residue synthetic peptide corresponding to the N-terminal sequence of eosinophil-derived neurotoxin which is identical to human liver ribonuclease. This amino acid sequence is unique to this protein. The anti N-peptide antibody was purified by protein A-Sepharose and by using ELISA and SDS-PAGE immunoblot techniques, the antibody reactivity against EDN and partially purified nonpancreatic-type ribonucleases from human plasma and urine was observed. Cross-reactivity with bovine pancreatic ribonuclease A and other proteins was not detected. In addition, the activity of the nonpancreatic-type ribonuclease was not affected by the antibody. The immune response was elicited without the need for a carrier protein showing that the N-terminal sequence of nonpancreatic ribonuclease contains a specific epitope. This antibody can be used for the immunological identification of both the native and denatured forms of this type of enzyme.

Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition.

The crystal structure of the complex between ribonuclease A and d(ApTpApApG) has been solved by x-ray crystallography using the molecular replacement method. The model includes, besides the enzyme, the d(ApTpApA) 5'-segment (A1T2A3A4) and 68 solvent molecules. The R-factor for the strongest 87% of the measured data that partially extends to 2.3-A resolution is 0.207. The A1 position is well defined; the 5'-O of the deoxyribose establishes a hydrogen bond with a solvent molecule that is, in turn, bonded to the epsilon-amino group of Lys66. The base (B0 site) is well ordered; it interacts with a symmetry-related enzyme molecule. In the crystal, the phosphate group at the p0 site has no direct charge compensation. However, Lys66 is not too far, and, in solution, it could bind to it. The T2 (R1B1p1) site is occupied as in other complex structures, and it is defined by very good electron density. The A3 site shows that the adenine moiety interacts with Asn71 and Gln69 and that the phosphate at p2 forms a salt bridge with Lys7. The most consistent model for the base of A4 (B3), both in terms of electron density and stereochemistry, shows that it forms a hydrogen bond with Gln69 and a g-g- array with the base at B2. The stacking of B2 and B3 may be a general feature of the binding of polyribonucleotides to ribonuclease A. The side chains of Gln69, Asn71, and Glu111 may thus constitute a malleable binding site capable of establishing various hydrogen bonds depending on the nature of the stacked bases. There is no evidence for the 3' G5 site in the electron density map.

Structure of ribonuclease A derivative II at 2.1-A resolution.

The crystal structure of bovine pancreatic ribonuclease A derivative II, a covalent derivative obtained by reaction of 6-chloropurine 9-beta-D-ribofuranosyl 5'-monophosphate with the alpha-amino group of Lys-1, has been determined and refined at 2.1-A resolution with an agreement factor R = 0.166 for 6254 reflections in the resolution shell 8.0 to 2.1 A. Crystals are orthorhombic and belong to space group C222(1) with unit cell parameters a = 75.73 A, b = 57.85 A, and c = 53.26 A. This crystal packing had never been reported before for pancreatic ribonuclease nor its complexes. The structure found is in accordance with the location of p2, B3, and R3 subsites at the N-terminal region of the protein and provides an explanation of the catalytic behavior observed for this derivative. In particular, differences in kinetic parameters and in the pKa value of His-119 between derivative II and native ribonuclease A can be interpreted on the basis of the position of the phosphate moiety within the derivative structure. Some uncertainty remains on the nucleotide sugar conformation determined.

Heterogeneity in the glycosylation pattern of human pancreatic ribonuclease.

Different molecular forms of ribonuclease were isolated from fresh human pancreas obtained from healthy transplant donors. The purification procedure consists of the preparation of an acetone powder, followed by (NH4)2SO4 precipitation and two chromatography steps (cationic exchange and reversed-phase). Protein bands in gel electrophoresis with RNAase activity were monitored using a negative-staining zymogram technique. Several glycosylated enzyme forms with apparent molecular masses ranging from 14 to 40 kDa were separated. Peptides containing the three Asn-Xaa-Thr/Ser acceptor sites for glycosylation were isolated and analysed. The site with Asn-34 was almost completely glycosylated, while the sites with Asn-76 and Asn-88 had carbohydrate in about half and a minor part of the molecules, respectively. The carbohydrate compositions of the glycopeptides are different from those of the same gene product isolated from human urine. C-Terminal threonine was present in part of the molecules, indicating partial degradation by carboxypeptidase.

A versatile negative-staining ribonuclease zymogram.

A versatile negative-staining ribonuclease zymogram is described. The method has several advantages as it combines, by means of different staining procedures, high resolving power, sensitivity, and specificity with a rapid, reproducible, and simultaneous analysis of purity of ribonuclease samples on the same polyacrylamide gel. Activity bands can be visualized at any time during the incubation process without staining of the gel. This allows the choice of different staining procedures after incubation. Using poly(C) as substrate less than 1 pg of bovine pancreatic ribonuclease A was detected in less than 2 h after the electrophoretic run. An additional advantage with respect to other methods is that no refrigeration is needed during electrophoresis.

Expression of acinar and ductal products in Capan-1 cells growing in synthetic serum and serum-free media.

BACKGROUND: Capan-1 is a human pancreatic adenocarcinoma cell line of presumed ductal origin. This is based on the histologic appearance of the tumor from which it arose. Yet considerable controversy exists regarding the actual cell of origin for these exocrine carcinomas. Two acinar antigens, ribonuclease and trypsin, were analyzed in cells growing in synthetic serum. METHODS: Capan-1 cells were adapted to grow in basal medium supplemented with synthetic serum, because fetal bovine serum (FBS) normally used to culture cells contains bovine ribonuclease, which can interfere with measurements of the ribonuclease secretion. These cells were also adapted to grow in different serum-free media, allowing us to determine its minimal growth requirements. The presence of ribonuclease in Capan-1 and PANC-1 conditioned media was monitored by activity. Other acinar and ductal markers were monitored using Northern blot analysis. RESULTS: Capan-1, PANC-1, IBF-CP3, and MDAAmp-7 cell lines were successfully adapted to grow in synthetic serum by means of the adaptation protocol reported here. The adaptation of Capan-1 to serum-free media showed that the cells are capable of growing in a medium containing insulin, transferrin, selenium, a nonprotein carrier, and lipoic and linoleic acids. Northern blot analysis showed the expression of carbonic anhydrase II, cytokeratin 18, ribonuclease, and trypsin in Capan-1 cells growing in FBS and synthetic serum. No changes in morphology, karyotype, or gene expression were observed in these cells as a result of the adaptation process. CONCLUSION: The cell line Capan-1 is expressing some ductal as well as acinar products despite its supposed ductal origin. The expression of trypsin at the mRNA level and ribonuclease at mRNA and protein levels is shown in Capan-1 cells. The protein expression will be further investigated as the cell line has been adapted to grow in synthetic serum and serum-free media with no apparent changes with respect to their growth in FBS.

Reverse transphosphorylation by ribonuclease A needs an intact p2-binding site. Point mutations at Lys-7 and Arg-10 alter the catalytic properties of the enzyme.

Bovine pancreatic ribonuclease A interacts with RNA along multiple binding subsites that essentially recognize the negatively charged phosphates of the substrate. This work gives additional strong support to the existence of the postulated phosphate-binding subsite p2 (Parés, X., Llorens, R., Arús, C., and Cuchillo, C. M. (1980) Eur. J. Biochem. 105, 571-579) and confirms the central role of Lys-7 and Arg-10 in establishing an electrostatic interaction with a phosphate group of the substrate. The effects of charge elimination by Lys-7-->Gln (K7Q) and/or Arg-10-->Gln (R10Q) substitutions in catalytic and ligand-binding properties of ribonuclease A have been studied. The values of Km for cytidine 2',3'-cyclic phosphate and cytidylyl-3',5'-adenosine are not altered but are significantly increased for poly(C). In all cases, kcat values are lower. Synthetic activity, i.e. the reversion of the transphosphorylation reaction, is reduced for K7Q and R10Q mutants and is practically abolished in the double mutant. Finally, the extent of the reaction of the mutants with 6-chloropurine-9-beta-D-ribofuranosyl 5'-monophosphate indicates that the phosphate ionic interaction in p2 is weakened. Thus, p2 modification alters both the catalytic efficiency and the extent of the processes in which an interaction of the phosphate group of the substrate or ligand with the p2-binding subsite is involved.