Complex Formation of Microbial Alkaline Protease Inhibitor (S-SI) with Subtilisin BPN′ and Its Properties

Microbial alkaline protease inhibitor, S–SI, was investigated on the interaction with subtilisin BPN′ Inhibitory equivalent of S–SI to subtilisin BPN′ was determined that one molecule of S–SI (MW = 23,000) inhibited two molecules of subtilisin BPN′ (MW = 27,700). The S–SI-subtilisin BPN′ complex was isolated by gel filtration on Sephadex G–100 and rhombic crystals were obtained. DIP- and ZAGPCK-subtilisin BPN′ did not form such complex with S–SI. Homogeneity of the complex was determined by disc electrophoresis. The isoelectric point of the complex was pH 5.5. Assay of S–SI dissociated and amino acid analysis of the complex indicated that one subunit (a half molecule) of S–SI was combined with one molecule of subtilisin BPN′ From molecular weight determination, it was clarified that the complex was composed of one molecule (consist of 2 subunits) of S–SI and two molecules of subtilisin BPN′.     

Reactive Site of API-2c,an Alkaline Protease Inhibitor,for Subtilisin BPN′

Differences between α- and β-lipovitellin were examined, especially in regard to the polypeptide and carbohydrate composition of apolipoprotein. Both lipoproteins were composed of at least eight polypeptides with similar molecular weights ranging from 35,000 to 140,000 daltons. Polypeptides with 110,000 daltons were common major constituents. The close similarity of component polypeptides in the two lipoproteins was also assumed from similar amino acid compositions and the identical immunological properties of the two lipoproteins. However, some notable differences were found in the composition of the polypeptides. α-Lipovitellin contained much more polypeptide with 85,000 daltons than β-lipovitellin. Both apolipovitellins were found to be glycoprotein containing mannose, galactose, glucosamine and sialic acid. The sialic acid in α-lipovitellin exceeded that in β-lipovitellin by six times, though only slight differences were found in the content of neutral and amino sugars. The relatively acidic nature of a-lipovitellin compared with β-lipovitellin is attributed not only to the relative predominance in protein phosphorus but also to the predominance in the sialic acid.     

Interaction of Subtilisin BPN′ and Recombinant Fungal Protease Inhibitor F from Silkworm with Substituted P1 Site Residues

Fungal protease inhibitor F (FPI-F) from silkworm inhibits subtilisin and fungal proteases. FPI-F mutants P₁ residues of which, Thr²⁹, were replaced with Glu, Phe, Gly, Leu, Met, and Arg, were prepared. The inhibitory activities of mutated FPI-F against subtilisin and other mammalian proteases indicated that FPI-F might be a specific inhibitor toward subtilisin-type protease.     

Formation of Complex of Proteinous Animal α-Amylase Inhibitor (Haim) with Hog Pancreatic α-Amylase

A limited proteolysis of Avicel-adsorbable, Avicel-disintegrating endocellulase I (molecular weight 130,000) from Geotrichum candidum with subtilisin yielded a protein (molecular weight 80,000) which proved fully active toward soluble substrates such as CM-cellulose, but lost both the abilities to be adsorbed onto insoluble substrates and to disintegrate the cellulose fibres. An immunological experiment showed precipitin lines between endocellulase I and subtilisin-modified endocellulase in the pattern of partial identity. N-Bromosuccinimide-oxidized endocellulase I lost cellulase activity, but retained its adsorbability onto Avicel. It is suggested that endocellulase I had both the affinity site for adsorbing onto insoluble substrates and the ordinary active site.     

Properties and Specific Functional Features of Wheat Grain α-Amylase/Subtilisin Inhibitor

A protein bifunctional inhibitor of endogenous α-amylase and subtilisin has been isolated from wheat grain and purified. The inhibitor specifically inactivates α-amylase isozymes with high isoelectric point values (group α-AMY1) and has almost no effect on the α-AMY2 isozymes with low isoelectric point values. This enzyme does not belong to glycoproteins and has a molecular weight of 21 kDa and an isoelectric point of 7.2. The protein displays a relatively high thermostability and pH optimum of 8.0; its inhibitory activity requires the presence of Ca²⁺ cations. The inhibition of excess α-amylase in wheat grain with a low falling number by the purified protein is studied.     

Dependence of Complex Formation of (1 → 3)-β-d-Glucan with Congo Red on Temperature in Alkaline Solutions

The formation of a complex between (1 → 3)-β-d-glucan and congo red in dilute alkaline solutions (0.1 and 0.15 m sodium hydroxide) where the glucan takes an ordered conformation was studied by measuring visible absorption spectra of the solutions at various temperatures between 15 and 35°C. The average number of the glucose residues forming the binding site to accommodate one dye molecule decreased with increasing temperature or decreasing alkaline concentration, suggesting possible conformational changes of the glucan chain. The complex formation constant, K, increased with increasing temperature, and thermodynamical parameters, ?H° and ?S°, for the complex formation in 0.1 m and 0.15 m aqueous NaOH solutions were obtained at 25°C to be 14 kcal/mol and 77 e.u. (0.1 m), and 12 kcal/mol and 68 e.u. (0.15 m), respectively. These results indicate that the driving force for the complex formation is entropic in nature stemming from the decrease of “iceberg formation”.     

The First and Second Dissociation Constants of Subtilisin BPN′-Plasminostreptin Complex Determined by a Polarographic Method,and the Effects of pH on Them

A polarographic method based on the Brdi?ka current (the polarographic catalytic hydrogen evolution current produced by proteins in the presence of cobalt salts) was applied to direct titration of subtilisin BPN′ (S.BPIST) with plasminostreptin (PS) at a concentration level of 10”⁸ m. The first and second dissociation constants of the S.BPN-PS complex were determined by fitting theoretical curves to the titration data, in which the multiple equilibria involving microscopically distinct forms of S.BPN-PS complex were taken into account. The intrinsic free energy change in the first binding of S.BPN′ to dimeric PS was larger than that in the second binding. The dependence of the microscopic dissociation constants of S.BPN′-PS complex on pH indicates the participation of ionizable groups of pK_a 8.0 and 9.4 in the complex formation. The repulsive effect between negatively charged molecules of S.BPN′ and PS in the complex formation at elevated pH is suggested.     

Isolation and Properties of an α-Amylase Inhibitor (0.53) from Wheat (Triticum aestivum)

A droplet gel-entrapping method used for enzyme immobilization was improved to simplify the procedure and to increase the enzyme stability. This immobilization technique is suitable for coupled enzyme reactions requiring cofactors. Leucine dehydrogenase (LeuDH) and formate dehydrogenase (FDH) were freeze-dried with bovine serum albumin, dextrin and stabilizers. The freeze-dried enzyme powder was suspended in a methylcellosolve solution containing polyethyleneglycol(#4000)diacrylate, N,N′-methylenebisacrylamide and 2-hydroxyethylacrylate, and the suspension was gelled with initiators. The gel was cut up and the pieces were washed in a buffer to remove the methylcellosolve and the dextrin inside. The maximum conversion ratio for a LeuDH-FDH gel column was determined to be 99.8% by means of the recycling reaction. On longterm operation at 30 °C for leucine production, the initial conversion ratio (7.2%) gradually decreased to 6.6% over the first 10 days. However, the conversion ratio remained almost constant after the 10th day. The effects of flow rate, temperature, pH, and the concentrations of formate, α- ketoisocaproate, ammonium and NAD on the leucine productivity with the gel column were also investigated.     

Effect of Cu2+ on Complex Formation Between a Deoxyribozyme and Its Substrates†

Abstract

Effect of metal ions on secondary-structure formation of a deoxyribozyme-two substrates complex has been investigated by using surface plasmon resonance and secondary-structure predicting calculation. The result showed that Cu²⁺ not only acts on the ligation reaction but also plays the role of a promoter which makes an active conformation of the deoxyribozyme-substrate complex.

     

Purification and Some Properties of an α-Amylase Inhibitor (Paim) from Streptomyces corchorushii

Paim, a microbial animal amylase inhibitor, was purified from the culture filtrate of Streptomyces corchorushii by salting out with ammonium sulfate and column chromatography on DEAE-cellulose, TEAE-cellulose, SP-Sephadex C-50, and Octyl Sepharose CL-4B. Paim was separated into 2 fractions (Paim I and II), both homogeneous on disc electrophoresis. The molecular weight of Paim I was 4100 and that of II, 4400 by amino acid analysis. Paim I and II consisted of 39 and 42 amino acid residues, respectively, and contained no lysine, isolecucine, or phenylalanine. Paim contained no carbohydrate moiety, and was stable even after being treated at 100°C for lOmin in the pH range from 5 to 8.     

Cloning, Functional Expression and Characterization of an Alkaline Protease from Bacillus licheniformis

A gene (apr 46) encoding a protease was cloned from Bacillus licheniformis RSP-09-37. It had an ORF of 1725 bp, encoding a pre-protein of 575 amino acids (63.2 kDa), which was functionally expressed and processed in E. coli JM 109. The mature protein, Apr 46, consists of 500 amino acids with a calculated molecular mass of 55 kDa. This protease shows 29-50% homology to known serine proteases and conserved domains. N-terminal sequencing suggests that Apr 46 protease is identical to a B. licheniformis RSP-09-37 protease, which is further supported by a similar stability in acetonitrile.     

Rice Bifunctional α-Amylase/Subtilisin Inhibitor: Cloning and Characterization of the Recombinant Inhibitor Expressed in Escherichia coli

The complete nucleotide sequences of the cDNA and its gene that encode a bifunctional α-amylase/subtilisin inhibitor of rice (Oryza sativa L.) (RASI) were analyzed. RASI cDNA (939 bp) encoded a 200-residue polypeptide with a molecular mass of 21,417 Da, including a signal peptide of 22 amino acids. Sequence comparison and phylogenetic analysis showed that RASI is closely related to α-amylase/subtilisin inhibitors from barley and wheat. RASI was found to be expressed only in seeds, suggesting that it has a seed-specific function. A coding region of RASI cDNA without the signal peptide was introduced into Escherichia coli and was expressed as a His-tagged protein. Recombinant RASI was purified to homogeneity in a single step by Ni-chelating affinity column chromatography and characterized to elucidate the target enzyme. The recombinant inhibitor had strong inhibitory activity toward subtilisin, with an equimolar relationship, comparable with that of native RASI, and weak inhibitory activity toward some microbial α-amylases, but not toward animal or insect α-amylases. These results suggest that RASI might function in the defense of the seed against microorganisms.     

Physiological Changes of Rhodotorula glutinis Induced by an Acid Protease Inhibitor (S–PI)

An acid protease inhibitor (S–PI) accelerated the growth of Rhodotorula glutinis. This acceleration of the growth was observed only when the pH of the culture fluid lowered during the cultivation, but was not observed when the pH of the culture fluid was adjusted to 2.8 with NaOH. The increase in number of cells was closely related to cell deaths. The cell deaths were observed in an active growing state but not in a resting state. S–PI increased the DNA, RNA and protein content in the cell and decreased the lipid, especially the phospholipid content. When the yeast was cultured in an acidic medium having an initial pH of 1.8 in the presence of S–PI, the decrease of the phospholipid in the cell preceded, followed by the leakage of potassium ion, UV absorbing materials and free pool amino acid from the cell which were accompanied with the cell death. On the basis of these results, physiological changes occuring in the yeast cell are discussed.     

Purification of a Protease Inhibitor from Hevea brasiliensis cell suspension and it’s effect on the growth of Phytophthora palmivora

Protease inhibitors (PIs) are one family of pathogenesis-related proteins (PR-proteins) that play essential roles in defense mechanisms against an attack by a pathogenic microorganism or insect. Cell suspension derived from a seed integument of rubber tree (Hevea brasiliensis) treated for 48 h with 20 μM copper sulphate, an abiotic elicitor, had an increased production of PIs. The intracellular PIs were detected in an extract of treated cells; however, much higher levels of PIs were found in the medium (extracellular). Using azocasein as substrate, these PIs possessed strong inhibitory activity against subtilisin A but not against trypsin, chymotrysin and papain. These extracellular PIs were purified by anion exchange chromatography, DEAE-Sepharose (CL-6B), eluted with 0.06 M NaCl in 20 mM Tris-HCl (pH 7.0). The active fractions were then subjected to native and SDS preparative gel electrophoresis, respectively. A single band of a purified PI with a molecular weight of 25 kDa was revealed after a tricine SDS-PAGE and stained with silver nitrate. The yield of this purified protein was 3.14 ng.g^?1. The activity of the purified PI was stable up to 70 °C, and its activity was retained in the buffer pH values of 2–10. The biological activity of the obtained PI was investigated. It was found that the PI at 5 μg.mL^?1 (0.2 μM) inhibited the mycelium growth of Phytophthora palmivora, a rubber tree pathogen.     

Structure of the Thiostrepton Resistance Methyltransferase��S-Adenosyl-l-methionine Complex and Its Interaction with Ribosomal RNA

The x-ray crystal structure of the thiostrepton resistance RNA methyltransferase (Tsr)·S-adenosyl-l-methionine (AdoMet) complex was determined at 2.45-Å resolution. Tsr is definitively confirmed as a Class IV methyltransferase of the SpoU family with an N-terminal “L30-like” putative target recognition domain. The structure and our in vitro analysis of the interaction of Tsr with its target domain from 23 S ribosomal RNA (rRNA) demonstrate that the active biological unit is a Tsr homodimer. In vitro methylation assays show that Tsr activity is optimal against a 29-nucleotide hairpin rRNA though the full 58-nucleotide L11-binding domain and intact 23 S rRNA are also effective substrates. Molecular docking experiments predict that Tsr·rRNA binding is dictated entirely by the sequence and structure of the rRNA hairpin containing the A1067 target nucleotide and is most likely driven primarily by large complementary electrostatic surfaces. One L30-like domain is predicted to bind the target loop and the other is near an internal loop more distant from the target site where a nucleotide change (U1061 to A) also decreases methylation by Tsr. Furthermore, a predicted interaction with this internal loop by Tsr amino acid Phe-88 was confirmed by mutagenesis and RNA binding experiments. We therefore propose that Tsr achieves its absolute target specificity using the N-terminal domains of each monomer in combination to recognize the two distinct structural elements of the target rRNA hairpin such that both Tsr subunits contribute directly to the positioning of the target nucleotide on the enzyme.RNA modifications and the enzymes that catalyze their formation are critical for cellular viability. Certain RNA modifications are extremely well characterized, such as CCA addition and amino acylation of the 3′-ends of tRNA, and the contributions of some nucleotide modifications to the creation of specific functional tRNA structures (1–3). Although the single most common nucleotide modification is pseudouridine, by far the most abundant type of RNA chemical modification is methylation (4). A vast array of unique mono-, di-, and trimethylations of each RNA base and/or ribose sugar 2′-OH is possible, and important new functions for these modifications continue to emerge. In ribosomal RNA (rRNA),² for example, modifications cluster in functionally critical regions where methylation may act as a checkpoint in ribosome subunit assembly (5), influence the process of translation (6), and alter resistance to certain antibiotics (7, 8).RNA methylation is catalyzed by members of two classes (I and IV) of S-adenosyl-l-methionine (AdoMet)-dependent RNA methyltransferase (MTase) enzymes (9). In bacteria, rRNA methylations are incorporated by both “housekeeping” MTases and those that confer resistance to antibiotics. Although members of the former group are often highly conserved, the latter are generally only found in the antibiotic-producing strain as one mechanism of defense against self-intoxication (10). However, several instances of antibiotic resistance MTase genes in non-producer strains, including pathogenic bacteria, have been identified, and it is clear that these genes are mobile resistance determinants, usually obtained by lateral gene transfer.Several classes of antibiotics target the conserved centers on the ribosome, altering or blocking critical steps in translation such as decoding and peptidyl transfer, to exert their bactericidal effect (11). RNA MTases have been identified as clinically significant resistance determinants to a number of these, including the aminoglycoside (Arm MTase) and erythromycin (Erm MTase) antibiotics (12, 13). Another functionally critical ribosome domain, the factor binding site (or “GTPase” center), is also the target for a family of thiazole-containing peptide antibiotics (14), which includes thiostrepton. These antibiotics have been important biochemical tools for studies of ribosome function but are of limited clinical use due to their poor aqueous solubility. Thiostrepton is, however, used in veterinary medicine, and recent studies suggest it may have application in development of novel antimalarial and anticancer strategies (15, 16). The minimal rRNA sequence for interaction of thiostrepton is a highly conserved, independently folded 58-nucleotide rRNA domain that is also bound by ribosomal protein L11. Resistance to thiostrepton can result from mutations in the N-terminal domain of L11 or its entire absence, whereas mutation of the target nucleoside (A1067) confers far greater resistance (17–19). In the thiostrepton producer Streptomyces azureus the thiostrepton resistance MTase (Tsr) catalyzes the 2′-O-methylation of A1067 resulting in specific and total resistance to thiostrepton (20).Here we present the crystal structure of Tsr in complex with AdoMet. The structure definitively places Tsr into the SpoU/TrmD (SPOUT) family of enzymes and provides the basis for modeling the Tsr·rRNA recognition process.     

Properties of a Trypsin Inhibitor from Job’s-tears (Coix lacryma-jobi L. var. Ma-yuen Stapf)

A heat stable trypsin inhibitor was found in the bran of soft-shelled job’s-tears (Coix lacryma-jobi L. var. Ma-yuen Stapf) seeds. This inhibitor seemed to be a simple protein, and the molecular weight was about 12,000. Similar to other heat stable trypsin inhibitors, this inhibitor also contained many cysteine or cystine residues in the molecule. This inhibitor inhibited bovine trypsin at the molar ratio of 1 to 2, showing that it was double-headed. Its activity was stable against the change of pH at the range of 3 to 11 and high temperature of 100°C under certain conditions. However, the degree of heat stability of the inhibitory activity depended highly upon the kind of the solution in which this inhibitor was dissolved.     

Structure and Properties of a Complex of α-Synuclein and a Single-Domain Camelid Antibody

The aggregation of the intrinsically disordered protein α-synuclein to form fibrillar amyloid structures is intimately associated with a variety of neurological disorders, most notably Parkinson's disease. The molecular mechanism of α-synuclein aggregation and toxicity is not yet understood in any detail, not least because of the paucity of structural probes through which to study the behavior of such a disordered system. Here, we describe an investigation involving a single-domain camelid antibody, NbSyn2, selected by phage display techniques to bind to α-synuclein, including the exploration of its effects on the in vitro aggregation of the protein under a variety of conditions. We show using isothermal calorimetric methods that NbSyn2 binds specifically to monomeric α-synuclein with nanomolar affinity and by means of NMR spectroscopy that it interacts with the four C-terminal residues of the protein. This latter finding is confirmed by the determination of a crystal structure of NbSyn2 bound to a peptide encompassing the nine C-terminal residues of α-synuclein. The NbSyn2:α-synuclein interaction is mediated mainly by side-chain interactions while water molecules cross-link the main-chain atoms of α-synuclein to atoms of NbSyn2, a feature we believe could be important in intrinsically disordered protein interactions more generally. The aggregation behavior of α-synuclein at physiological pH, including the morphology of the resulting fibrillar structures, is remarkably unaffected by the presence of NbSyn2 and indeed we show that NbSyn2 binds strongly to the aggregated as well as to the soluble forms of α-synuclein. These results give strong support to the conjecture that the C-terminal region of the protein is not directly involved in the mechanism of aggregation and suggest that binding of NbSyn2 could be a useful probe for the identification of α-synuclein aggregation in vitro and possibly in vivo.     

Two Binding Modes of Netropsin are Involved in the Complex Formation with Poly(dA-dT)·Poly(dA-dT) and other Alternating DNA Duplex Polymers

Abstract

Using CD measurements we show that the interaction of netropsin to poly(dA-dT)·poly(dA-dT) involves two binding modes at low ionic strength. The first and second binding modes are distinguished by a defined shift of the CD maximum and the presence of characteristic isodichroic points in the long wavelength range from 313 nm to 325 nm. The first binding mode is independent of ionic strength and is primarily determined by specific interaction to dA·dT base pairs. Employing a netropsin derivative and different salt conditions it is demonstrated that ionic contacts are essential for the second binding mode. Other alternating duplexes and natural DNA also exhibit more or less a second step in the interaction with netropsin observable at high ratio of ligand per nucleotide. The second binding mode is absent for poly(dA)·poly(dT). The presence of a two-step binding mechanism is also demonstrated in the complex formation of poly(dA-dT)·poly(dA-dT) with the distamycin analog consisting of pentamethylpyrrolecarboxamide. While the binding mode I of netropsin is identical with its localization in the minor groove, for binding mode II we consider two alternative interpretations.     

Complex of Amyloid β Peptides with 24-Hydroxycholesterol and Its Effect on Hemicholinium-3 Sensitive Carriers

Brains of Alzheimer disease patients in early stages of dementia contain an increased 24(S)-hydroxycholesterol (cerebrosterol)/cholesterol ratio when compared to controls. In this study, effects of amyloid β peptides and of racemic 24-hydroxycholesterol were evaluated in vitro on undepleted or cholesterol-depleted hippocampal synaptosomes of young and old rats via a high-affinity choline transport and membrane anisotropy measurements. Depletion of membrane cholesterol decreased the transport of [3H]choline, increased the specific binding of [3H]hemicholinium-3 and decreased membrane anisotropy. However, less alterations were found in old when compared to young brains. 500 nM nonaggregated peptides were ineffective but aggregated fragment 1–42 evoked marked drops in the transport and anisotropy values on depleted synaptosomes. 50 μM 24-hydroxycholesterol inhibited choline transport on depleted synaptosomes but it did not influence membrane anisotropy. Peptides eliminated the actions of oxysterol on choline carriers in young but not in old rats. On the other hand, oxysterol eliminated the effects of peptides on membrane anisotropy. Our study suggests a possible role of membrane cholesterol in the regulation of choline carriers and supports data reporting a protective role of membrane cholesterol against toxic effects of amyloid β peptides. Moreover, via Raman spectroscopy we demonstrate for the first time that peptides form a complex with 24-hydroxycholesterol.