Strategy for trapping intermediates in the folding of ribonuclease and for using 1H-nmr to determine their structures

The major unfolded form of ribonuclease A is known to show well-populated structural intermediates transiently during folding at 0°–10°C. We describe here how the exchange reaction between D₂O and peptide NH protons can be used to trap folding intermediates. The protons protected from exchange during folding can be characterized by ¹H-nmr after folding is complete. The feasibility of using ¹H-nmr to resolve a set of protected peptide protons is demonstrated by using a specially prepared sample of ribonuclease S in D₂O in which only the peptide protons of residues 7–14 are in the ¹H-form. All eight of these protected peptide protons are H-bonded. Resonance assignments made on isolated peptides containing these residues have been used to identify the protected protons. Other sets of protected protons trapped in the ¹H-form can also be isolated by differential exchange, using either ribonuclease A or S. Earlier model compound studies have indicated that H-bonded folding intermediates should be unstable in water unless stabilized by additional interactions. Nevertheless, peptides derived from ribonuclease A that contain residues 3–13 do show partial helix formation in water at low temperatures. We discuss the possibility that specific interactions between side chains can stabilize short α-helixes by nucleating the helix, and that specific interactions may also define the helix boundaries at early stages in folding.     

Recognition of riboflavin and the capsular polysaccharide of Haemophilus influenzae type b by antibodies generated to the haptenic epitope D-ribitol

D-Ribitol, a five–carbon sugar alcohol, is an important metabolite in the pentose phosphate pathway; it is an integral part of riboflavin (vitamin B2) and cell wall polysaccharides in most Gram-positive and a few Gram-negative bacteria. Antibodies specific to D-ribitol were generated in New Zealand white rabbits by using reductively aminated D-ribose-BSA conjugate as the immunogen. MALDI-TOF and amino group analyses of ribitol-BSA conjugate following 120 h reaction showed ~27–30 mol of ribitol conjugated per mole BSA. The presence of sugar alcohol in the conjugates was also confirmed by an increase in molecular mass and a positive periodic acid–Schiff staining in SDS-PAGE. Caprylic acid precipitation of rabbit serum followed by hapten affinity chromatography on ribitol–KLH–Sepharose CL-6B resulted in pure ribitol–specific antibodies (~45–50 μg/mL). The affinity constant of ribitol antibodies was found to be 2.9?×?10⁷ M^?1 by non-competitive ELISA. Ribitol antibodies showed 100 % specificity towards ribitol, ~800 % cross–reactivity towards riboflavin, 10–15 % cross–reactivity with sorbitol, xylitol and mannitol, and 5–7 % cross–reactivity with L-arabinitol and meso-erythritol. The specificity of antibody to ribitol was further confirmed by its low cross-reactivity (0.4 %) with lumichrome. Antibodies to D-ribitol recognized the purified capsular polysaccharide of Haemophilus influenzae type b, which could be specifically inhibited by ribitol. In conclusion, antibodies specific to D-ribitol have been generated and characterized, which have potential applications in the detection of free riboflavin and ribitol in biological samples, as well as identification of cell-surface macromolecules containing ribitol.     

Conformational Activation of Antithrombin by Heparin Involves an Altered Exosite Interaction with Protease

Heparin allosterically activates antithrombin as an inhibitor of factors Xa and IXa by enhancing the initial Michaelis complex interaction of inhibitor with protease through exosites. Here, we investigate the mechanism of this enhancement by analyzing the effects of alanine mutations of six putative antithrombin exosite residues and three complementary protease exosite residues on antithrombin reactivity with these proteases in unactivated and heparin-activated states. Mutations of antithrombin Tyr²⁵³ and His³¹⁹ exosite residues produced massive 10–200-fold losses in reactivity with factors Xa and IXa in both unactivated and heparin-activated states, indicating that these residues made critical attractive interactions with protease independent of heparin activation. By contrast, mutations of Asn²³³, Arg²³⁵, Glu²³⁷, and Glu²⁵⁵ exosite residues showed that these residues made both repulsive and attractive interactions with protease that depended on the activation state and whether the critical Tyr²⁵³/His³¹⁹ residues were mutated. Mutation of factor Xa Arg¹⁴³, Lys¹⁴⁸, and Arg¹⁵⁰ residues that interact with the exosite in the x-ray structure of the Michaelis complex confirmed the importance of all residues for heparin-activated antithrombin reactivity and Arg¹⁵⁰ for native serpin reactivity. These results demonstrate that the exosite is a key determinant of antithrombin reactivity with factors Xa and IXa in the native as well as the heparin-activated state and support a new model of allosteric activation we recently proposed in which a balance between attractive and repulsive exosite interactions in the native state is shifted to favor the attractive interactions in the activated state through core conformational changes induced by heparin binding.     

Depression of Humoral Antibody Formation in the Chicken by Thymectomy and Antilymphocyte Serum

STUDIES on the chicken¹ established that transplantation immunity and humoral antibody formation were two independent systems of immune reactivity which were under the developmental control of two distinct primary lymphoid organs—the thymus and the bursa of Fabricius. Although a clear distinction of the two primary lymphoid organs has not been made in mammals, a division between thymus-dependent (T cells) and thymus independent (B cells) lymphocyte functions is now well documented^2,3. In the mouse, T cells are involved in cell mediated immune responses and are also necessary for the full expression of the humoral antibody response to many antigens.     

Intra and intermolecular charge effects on the reaction of the superoxide radical anion with semi-oxidized tryptophan in peptides and N-acetyl tryptophan

The reaction of the superoxide radical anion (O^-·₂), with the semi-oxidized tryptophan neutral radical (Trp^·) generated from tryptophan (Trp) by pulse radiolysis has been observed in a variety of functionalized Trp derivatives including peptides. It is found that the reaction proceeds 4–5 times faster in positively charged peptides, such as Lys-Trp-Lys, Lys-Gly-Trp-Lys and Lys-Gly-Trp-Lys-O-tert-butyl, than in solutions of the negatively charged N-acetyl tryptophan (NAT). However, the reactivity of O^-·₂ with the Trp^· radical is totally inhibited upon binding of these peptides to micelles of negatively charged SDS and is reduced upon binding to native DNA. By contrast, no change in reactivity is observed in a medium containing CTAB, where the peptides cannot bind to the positively charged micelles. On the other hand, the reactivity of the Trp^· radical formed from NAT with O^-·₂ is reduced to half that of the free Trp^· in buffer but is markedly increased in CTAB micelles. The models studied here incorporate elements of the complex environment in which Trp^· and O^-·₂ may be concomitantly formed in biological system and demonstrate the magnitude of the influence such elements may have on the kinetics of reactions involving these two species.     

Discrimination between native and non-native disulfides by protein-disulfide isomerase

The folding assistant and chaperone protein-disulfide isomerase (PDI) catalyzes disulfide formation, reduction, and isomerization of misfolded proteins. PDI substrates are not restricted to misfolded proteins; PDI catalyzes the dithiothreitol (DTT)-dependent reduction of native ribonuclease A, microbial ribonuclease, and pancreatic trypsin inhibitor, suggesting that an ongoing surveillance by PDI can test even native disulfides for their ability to rearrange. The mechanism of reduction is consistent with an equilibrium unfolding of the substrate, attack by the nucleophilic cysteine of PDI followed by direct attack of DTT on a covalent intermediate between PDI and the substrate. For native proteins, the rate constants for PDI-catalyzed reduction correlate very well with the rate constants for uncatalyzed reduction by DTT. However, the rate is weakly correlated with disulfide stability, surface exposure, or local disorder in the crystal. Compared with native proteins, scrambled ribonuclease is a much better substrate for PDI than predicted from its reactivity with DTT; however, partially reduced bovine pancreatic trypsin inhibitor (des(14-38)) is not. An extensively unfolded polypeptide may be required by PDI to distinguish native from non-native disulfides.     

Reactivities of Shark 19S and 7S IgM Antibodies to <Emphasis Type="Italic">Salmonella typhimurium</Emphasis>

LOWER vertebrates such as sharks can synthesize humoral antibodies in response to antigenic stimulation with a wide variety of antigens¹. Physicochemical studies have shown that sharks can synthesize both 19S and 7S immunoglobulins and that these two proteins belong to the same immunoglobulin class, which seems to be structurally homologous to IgM as defined for higher animals. Thus the shark immunoglobulins have been designated 19S IgM and 7S IgM^2–4. Because the predominant immunoglobulin (IgG) of most mammals is absent from sharks, the shark monomeric (7S) IgM might be functionally analogous to IgG. One example of the functional differences between IgM and IgG antibodies is the greater reactivity of the former in agglutination and bactericidal reactions^5,6. We have isolated and characterized functionally the relatively high levels of agglutinating antibodies which the nurse shark, Gingly-mostoma cirratum, synthesizes in response to Salmonella typhimurium “O” antigens.     

Protein prosthesis: β‐peptides as reverse‐turn surrogates

The introduction of non‐natural modules could provide unprecedented control over folding/unfolding behavior, conformational stability, and biological function of proteins. Success requires the interrogation of candidate modules in natural contexts. Here, expressed protein ligation is used to replace a reverse turn in bovine pancreatic ribonuclease (RNase A) with a synthetic β‐dipeptide: β²‐homoalanine–β³‐homoalanine. This segment is known to adopt an unnatural reverse‐turn conformation that contains a 10‐membered ring hydrogen bond, but one with a donor–acceptor pattern opposite to that in the 10‐membered rings of natural reverse turns. The RNase A variant has intact enzymatic activity, but unfolds more quickly and has diminished conformational stability relative to native RNase A. These data indicate that hydrogen‐bonding pattern merits careful consideration in the selection of beneficial reverse‐turn surrogates.     

Cytotoxic effect of structurally modified bull seminal ribonuclease (AS RNase)

Chemical modifications of bull seminal ribonuclease (AS RNase) cause considerable changes in its cytotoxic activity. However, binding of AS RNase on cells has been changed little or not at all. Every modification (oxidation, reduction, carbomethylation, succinylation and maleylation) inhibited ribonuclease and aspermatogenic and embryotoxic activity of AS RNase. The common cytotoxic effect was also changed to some degree. Inhibition of incorporation of ³H-thymidine to BP-8 tumor cells in culture was observed after application of native, oxidized, reduced, and carboxymethylated AS RNase.     

Development and precise characterization of phospho-site-specific antibody of Ser(357) of IRS-1: elimination of cross reactivity with adjacent Ser(358)

Antibodies that recognize specifically phosphorylated sites on proteins are widely utilized for studying the regulation and biological function of phosphoproteins. The proposed strategy is a powerful, analytical tool allowing the generation of phospho-site specific antibodies albeit adjacent phosphorylation sites are present. Here, we demonstrate the assessment and elimination of cross reactivity of phospho-site-specific-Ser³⁵⁷ IRS-1 antibody. While determining the specificity of p-Ser³⁵⁷ antiserum we came across the cross reactivity of the antiserum with adjacent Ser³⁵⁸ which was successfully abolished by an improved immuno-purification method. The specificity of the purified antiserum was then verified by indirect ELISA, results of ELISA were also mirrored in the experiments carried out in BHK-IR cells using different mutants of IRS-1 carrying mutations at either Ser³⁵⁷/Ser³⁵⁸/Ser^357/358. Immuno-purified-p-Ser³⁵⁷ did not react with IRS-1 Ala³⁵⁷ and IRS-1 Ala^357/358. In conclusion, the present study describes generation and characterization of p-Ser³⁵⁷ IRS-1 antibody, which reacts with IRS-1 in site specific and phosphorylation state-dependent manner without showing cross reactivity to adjacent Ser³⁵⁸. This antibody can be effectively used to further clarify the inhibitory role of Ser³⁵⁷ in insulin signal transduction.     

Local interactions favor the native 8-residue disulfide loop in the oxidation of a fragment corresponding to the sequence Ser-50-Met-79 derived from bovine pancreatic ribonuclease A

A 30-residue peptide was obtained from ribonuclease A by chemical cleavage with cyanogen bromide, subsequent sulfitolysis with concomitant S-sulfonation, and finally enzymatic cleavage withStaphylococcus aureus protease. The peptide was converted to the free thiol form by reductive cleavage of the S-sulfo-protecting groups withd,l-dithiothreitol. This peptide consisted of residues 50–79 of the native sequence of ribonuclease A, with the exception that methionine-79 had been converted to homoserine. Included in this sequence are residues cysteine-65 and cysteine-72, which form a disulfide bond in the native enzyme, as well as cysteine-58. This molecule may form one of three possible intramolecular disulfide bonds upon thiol oxidation, viz. one loop of 15 and 2 of 8 residues each. These isomeric peptides were prepared by oxidation with cystamine, 2-aminoethanethiolation of residual thiols, and fractionation by reverse-phase high-performance liquid chromatography. Disulfide pairings were established by mapping the tryptic fragments and confirming their composition by amino acid analysis. After protracted incubation under oxidizing conditions at 25.0°C andp H 8.0, the 26-member ring incorporating the native disulfide bond between residues 65 and 72 is the dominant product. Assuming that equilibrium is established, we infer that local interactions in the sequence of ribonuclease A significantly stabilize the native 8-residue disulfide loop with respect to the non-native 8-residue loop (G°=–1.1±0.1 kcal mole^–1). The implications of this observation for the oxidative folding of the intact protein are discussed.     

Changes in Ribonuclease Activity and Content of RNA during Dormancy and Growth of Bird-cherry Buds

Ribonuclease has been extracted from buds of bird-cherry (Prunus padus L.) by a three-step method. In step 1 ribonuclease was extracted from the homogenized tissue at p^H 6. In step 2 the tissue residue from (1) was extracted at p^H 7. In step 3 the tissue residue from (2) was extracted with a buffer of p^H 8.5 and containing 0.7 M KCl. The ribonuclease from step 1 and 2 is named soluble and that from step 3 bound ribonuclease. The activity of the soluble ribonuclease was very low in October and increased slowly until March. When the buds sprouted in April the activity of this fraction rose rapidly. The activity of the bound ribonuclease was rather high in October and increased continuously from autumn to spring. RNA accumulated slowly between autumn and spring. The change in activity of the two ribonuclease fractions is discussed in relation to development.     

Gold Immunochromatography Assay for the Rapid Detection of Spiramycin in Milk and Beef Samples Based on a Monoclonal Antibody

Spiramycin (SP) residues in food do harm to human health. It is necessary to establish rapid detection method for SP. In this work, a monoclonal antibody (mAb)‐based gold immunochromatography assay (GICA) is developed for the rapid detection of SP. Under optimum conditions, the half‐maximal inhibitory concentration of SP‐mAb is 0.43 ng mL^–1. The subtype of SP‐mAb is IgG2b. This antibody has no cross‐reactivity with other analogues and has high affinity (4.52 × 10¹⁰ L mol^–1). Qualitative results can be visualized with the naked eye, with a visual detection limit of 1.0 ng mL^–1 and cut‐off value of 10 ng mL^–1. A hand‐held strip scanner is used for the quantitative analysis, with LOD 0.43 ng mL^–1 in assay buffer. The recoveries of SP ranged from 72.3% to 112% in milk and 98.5% to 115% in beef, with variable coefficient ranging from 9.4% to 11.7% in milk and 8.14% to 15.4% in beef. Besides, the proposed GICA method for SP is confirmed by LC–MS/MS in SP‐spiked milk and beef samples. Overall, the developed GICA can be a useful tool for SP residues on‐site screening in milk and beef samples.     

Atypical incorporation of single amino acids into myelin proteins.

—Purified myelin incorporated l -[¹⁴C]leucine and l -[¹⁴C]lysine into myelin proteins in an enzymatic process similar to that of renal brush border membranes. The system was not inhibited by cycloheximide or puromycin or by pretreatment with ribonuclease; the reaction was inhibited by cetophenicol. ATP was an effector, shifting the optimal pH from 7.2 to 8.3. In the presence of ATP, myelin was less dense in a sucrose gradient. Ammonia was released from the membrane during the incorporation of amino acids. Myelin preloaded with cold leucine did not incorporate [¹⁴C]leucine but did incorporate [¹⁴C]lysine; there was no cross inhibition between the two amino acids. The incorporation was into or onto proteins of the Wolfgram proteolipid fraction of myelin. The incorporation was of the high affinity type with a K_m of 10^?7m and was restricted to the natural amino acids.     

A thermally induced alteration in lysosome membranes: Salt permeability at 0 and 37 °C

Preparations of radioactive lysosomes were obtained from mouse kidney after injection of radioactive iodine-labeled bovine ribonuclease. Stability of these lysosomes in various media was estimated from measurements of proteolytic activity towards the ribonuclease, and of ribonuclease retention in particles. The lysosomes were stable at 37 °C in isotonic, sucrose-free solutions of KCl, NaCl and potassium acetate, and in mixtures of these with MgCl₂, showing that these salts are relatively impermeant through the lysosomal membranes. The membranes were less permeable to Na⁺ than to K⁺. Both KCl and NaCl exerted their optimal protective effects over a broad concentration range above 0.125 M in 0.025 M acetate buffer. Mg²⁺ enhanced the protective effect of both K⁺ and Na⁺; the osmotic effect of 0.075 M NaCl-0.05 M MgCl₂ was indistinguishable during the entire course of ribonuclease digestion from that of isotonic sucrose. Osmotic protection by KCl-MgCl₂ was demonstrated over the pH range 5.5–7.0. A marked alteration in membrane properties occurs at lower temperatures in 0.11 M KCl-0.01 M MgCl₂ such that, at 0 °C, K⁺ permeability is much higher than at 37 °C, as shown by a several-fold decrease in stability at the lower temperature.     

Partial denaturation of macromolecules by chemical agents

The denaturation of a macromolecule such as a polypeptide is considered in the case where the total number of noncovalent internal bonds broken in the binding process of the chemical agent is only a fraction, α_s, of the total number of noncovalent internal bonds involved in its helical native conformation. Starting from a two-parameter (s, σ) model of the helix–random coil transition of polypeptides, the transition temperature is derived as a function of the fraction α_s, and of the concentration and the binding constant of the chemical agent. The lower limit of the transition temperature and the corresponding slope of the transition curve are shown to depend on α_s. As an illustration, existing data on the partial acid denaturation of the enzymes ribonuclease A and muromidase are analyzed. The resulting average enthalpies of a noncovalent bond in the native ribonuclease A and muromidase are found to be 1.81 kcal/mole and 1.54 kcal/mole, respectively; the corresponding entropies are 5.4 and 4.4 cal/deg./mole, respectively. As a further example, existing data on a partially methylated enzyme ribonuclease A are also considered.     

Phytochrome Control of the Level of Extractable Ribonuclease Activity in Etiolated Hypocotyls

AN increase in RNA degrading activity of hypocotyl homo-genates can be detected 6–10 h after transferring 5 day old, dark-grown seedlings of Lupinus albus L. to continuous white light¹. This increase is concomitant with the onset of inhibition of hypocotyl extension^{1, 2}. The ribonuclease component whose level of activity is affected by light treatment (tentatively identified as a ribonucleate nucleotido-2′-transferase (cyclizing) (EC 2.7.7.17)) is associated with the ribosomes (and polysomes)¹ in hypocotyl homogenates. This is in contrast to the bulk of RNA degrading activity in homogenates which is associated with the soluble fraction¹. Isolation of the ribosomal fraction therefore makes it possible to follow changes in the level of activity of this ribonuclease which would be too small to detect in unfractionated cell homogenates. The results reported here indicate that the photoconversion of the red-absorbing form of phytochrome (P_r) to the physiologically-active far-red-absorbing form (P_fr) leads to a specific increase in ribosome-bound ribonuclease activity.     

Unusual hepatic mitochondrial arginase in an Indian air-breathing teleost,Heteropneustes fossilis: Purification and characterization

A functional urea cycle with both cytosolic (ARG I) and mitochondrial (ARG II) arginase activity is present in the liver of an ureogenic air-breathing teleost, Heteropneustes fossilis. Antibodies against mammalian ARG II showed no cross-reactivity with the H. fossilis ARG II. ARG II was purified to homogeneity from H. fossilis liver. Purified ARG II showed a native molecular mass of 96 kDa. SDS–PAGE showed a major band at 48 kDa. The native enzyme, therefore, appears to be a homodimer. The pI value of the enzyme was 7.5. The purified enzyme showed maximum activity at pH 10.5 and 55 °C. The K_m of purified ARG II for l-arginine was 5.25 ± 1.12 mM. l-Ornithine and N^ω-hydroxy-l-arginine showed mixed inhibition with K_i values 2.16 ± 0.08 and 0.02 ± 0.004 mM respectively. Mn^+ 2 and Co^+ 2 were effective activators of arginase activity. Antibody raised against purified H. fossilis ARG II did not cross-react with fish ARG I, and mammalian ARG I and ARG II. Western blot with the antibodies against purified H. fossilis hepatic ARG II showed cross reactivity with a 96 kDa band on native PAGE and a 48 kDa band on SDS–PAGE. The molecular, immunological and kinetic properties suggest uniqueness of the hepatic mitochondrial ARG II in H. fossilis.     

Variant specific glycoproteins of Trypanosoma equiperdum: cross reacting determinants and chemical studies

Two variant specific surface antigens (VSSA) (BoTat-1 and BoTat-28) were purified from clones of $\text{Trypanosoma equiperdum}$ and tested for immunological cross reactivity. Competitive radioimmunoassay revealed the presence of cross reacting determinants. Limited tryptic cleavage of BoTat-28 resulted in the purification of two fragments F₁ and F₂ with respectively 38,000 and 28,000 apparent molecular weight. F₁ represents a large N-terminal fragment containing 30 % of the total sugar content. F₂ is characterized by an N-terminal amino acid sequence different from that of the native glycoprotein and contains all the carbohydrate. Inhibition of the heterologous precipitation reaction was only achieved with F₂ and reaches 100 % as with the native glycoproteins. These results demonstrate the presence of cross reacting determinants located in the C-terminal part of the molecule.     

Incorporation of cytokinin N-benzyladenine into tobacco callus transfer ribonucleic Acid and ribosomal ribonucleic Acid preparations

The incorporation of the cytokinin N⁶-benzyladenine into tobacco (Nicotiana tabacum) callus tRNA and rRNA preparations isolated from tissue grown on medium containing either N⁶-benzyladenine-8-¹⁴C or N⁶-benzyladenine-8-¹⁴C: benzene-³H(G) has been examined. N⁶-benzyladenine was incorporated into both the tRNA and rRNA preparations as the intact base. Over 90% of the radioactive N⁶-benzyladenosine recovered from the RNA preparations was associated with the rRNA. Purification of the crude rRNA by either MAK chromatography or Sephadex G-200 gel filtration had no effect on the N⁶-benzyladenosine content of the RNA preparation. The distribution of N⁶-benzyladenosine moieties in tobacco callus tRNA fractionated by BD-cellulose chromatography did not correspond to the distribution of ribosylzeatin activity. N⁶-benzyladenosine was released from the rRNA preparation by treatment with venom phosphodiesterase and phosphatase, ribonuclease T₂ and phosphatase, or ribonuclease T₂ and a 3′-nucleotidase. N⁶-benzyladenosine was not released from the RNA preparation by treatment with either ribonuclease T₂ or phosphatase alone or by successive treatment with ribonuclease T₂ and a 5′-nucleotidase. Brief treatment of the rRNA preparation with ribonuclease T₁ and pancreatic ribonuclease converted the N⁶-benzyladenosine moieties into an ethyl alcohol soluble form. On the basis of these and earlier results, the N⁶-benzyladenosine recovered from the tobacco callus RNA preparations appears to be present as a constituent of RNA and not as a nonpolynucleotide contaminant.