Preparation of fluorescence quenched libraries containing interchain disulphide bonds for studies of protein disulphide isomerases

Protein disulphide isomerase is an enzyme that catalyses disulphide redox reactions in proteins. In this paper, fluorogenic and interchain disulphide bond containing peptide libraries and suitable substrates, useful in the study of protein disulphide isomerase, are described. In order to establish the chemistry required for the generation of a split-synthesis library, two substrates containing an interchain disulphide bond, a fluoroescent probe and a quencher were synthesized. The library consists of a Cys residue flanked by randomized amino acid residues at both sides and the fluoroescent Abz group at the amino terminal. All the 20 natural amino acids except Cys were employed. The library was linked to PEGA‒beads via methionine so that the peptides could be selectively removed from the resin by cleavage with CNBr. A disulphide bridge was formed between the bead‒linked library and a peptide containing the quenching chromophore (Tyr(NO₂)) and Cys(pNpys) activated for reaction with a second thiol. The formation and cleavage of the interchain disulphide bonds in the library were monitored under a fluoroescence microscope. Substrates to investigate the properties of protein disulphide isomerase in solution were also synthesized. © 1998 European Peptide Society and John Wiley & Sons, Ltd.     

Studies on the sub-units of triose phosphate isomerase

The sub-unit structure of rabbit muscle triose phosphate isomerase was studied by determination of the number of unique cysteine peptides. Alkylation of the thiol groups with radioactive iodoacetate in the presence of guanidine hydrochloride gave the S-carboxy[¹⁴C]methyl derivative of the protein. This was digested with trypsin, and the radioactive peptides were fractionated by ion-exchange chromatography; four main radioactive peaks were obtained, one of which contained two radioactive peptides. Peptide `maps' of the tryptic digest showed five main spots. The relationship between the members of both sets of five peptides was established. The radioactive peptides were characterized, and the results indicated the presence of five unique cysteine residues in the protein. Since there are approximately ten thiol groups/molecule, there are two closely related or identical sub-units. Studies of the terminal residues bear out this suggestion; only one kind of N-terminal residue (alanine) and one kind of C-terminal residue (glutamine) were detected. These results are in accord with the evidence from crystallography.     

Periplasmic disulphide bond formation is essential for cellulase secretion by the plant pathogen Erwinia chrysanthemi

Secretion to the cell exterior of cellulase EGZ and of at least six pectinases enables the Gram-negative Erwinia chrysanthemi to cause severe plant disease. The C-terminal cellulose-binding domain (CBD) of EGZ was found to contain a disulphide bond which forms, in the periplasm, between residues Cys-325 and Cys-382. Dithiothreitol (DTT)-treatment of native EGZ showed that the disulphide bond was dispensable, both for catalysis and cellulose binding. Adding DTT to E. chrysanthemi cultures led to immediate arrest of secretion of EGZ which accumulated in the periplasm where the CBD was eventually proteolysed. Site-directed mutagenesis that affected Cys residues involved in disulphide bond formation resulted in molecules that were catalytically active and able to bind to cellulose but were no longer secreted, Instead they accumulated in the periplasm. Interestingly, the region around EGZ Cys-325 is conserved in two pectinases secreted by the same pathway as EGZ. We conclude that the conserved Cys, and possibly adjacent residues, bear essential information for EGZ to be secreted and that periplasmic disulphide bond formation is an obligatory step which provides a pre-folded functional form of EGZ with secretion competence.     

NADP-malate dehydrogenase from Zea mays leaves: Amino acid composition and thiol content of active and inactive forms

NADP-malate dehydrogenase (L-malate: NADP⁺ oxidoreductase, E.C. 1.1.1.82) was purified from the leaves of Zea mays L. and its subunit molecular weight, amino acid composition and the changes in number of thiol groups during activation were determined. The amino acid composition we found differed from that reported earlier for the Z. mays enzyme but was very similar to that reported for the enzyme isolated from pea leaves. The maize enzyme contains fewer methionine residues (3 compared to 5 in pea) but a greater total number of cysteine residues (6 compared to 3 in pea). In its inactive form (oxidised) the enzyme contained 2 thiols per subunit of which only 1 reacts with 5,5′-dithiobis(2-nitrobenzoic acid) when the enzyme is in its native form. During activation by dithiothreitol two disulphide bonds are reduced per subunit to give 4 new thiol groups. We conclude that NADP-malate dehydrogenase from leaves of the C₄ plant Z. mays is very similar to the enzyme from the C₃ plant pea. However, apparently two disulphide bonds are reduced during the reductive activation of the Z. mays enzyme in vitro compared with 1 disulphide bond for the pea enzyme.     

Amino acid composition and terminal residues of aspartate aminotransferase from ox heart

1. The amino acid composition of highly purified aspartate aminotransferase from ox heart was determined. 2. Alanine is the only N-terminal residue. 3. Leucine was identified as the only C-terminal residue. 4. No disulphide bridges are present in the enzyme molecule. 5. The thiol groups are not equally accessible, the accessibility being comparatively easier in the apoenzyme molecule.     

The sequential synthesis of the polypeptide chain of serum albumin by the microsome fraction of rat liver

1. The isolated microsome fraction of regenerating rat liver was incubated with cell sap, a source of energy and [³⁵S]methionine, [¹⁴C]isoleucine or [¹⁴C]leucine for different periods of time, and microsomal albumin isolated. 2. The distribution of these isotopes in albumin was determined by separation of tryptic peptides from the protein. Radioactivity was measured in peptides either qualitatively by radioautography or quantitatively by labelling with both ³H and ¹⁴C. 3. A gradient of radioactivity existed at all times in albumin isolated after incubating microsomes. 4. The shorter the incubation time the fewer the peptides labelled in albumin, but the peptides with highest specific activity after short incubation times corresponded to those with highest specific activities after long incubation times. 5. Leucine released from the C-terminus of albumin had a higher specific activity than the mean specific activity of the remaining leucine residues in albumin. 6. The peptide with the highest specific activity in albumin is probably derived from the C-terminus of the protein. 7. [¹⁴C]Glutamic acid is incorporated into the N-terminus of albumin after incubating the microsome fraction with this isotopically labelled amino acid, cell sap and a source of energy. The specific activity of the N-terminal glutamic acid under these conditions is less than the mean specific activity of the remaining glutamic acid and glutamine residues in albumin. 8. The results are interpreted as reflecting a sequential synthesis of serum albumin in the isolated microsome fraction of rat liver. The direction of synthesis of albumin is from the N-terminus towards the C-terminus. 9. The bulk of incorporation of radioactive amino acid into albumin in the isolated microsome fraction is due to completion of partially completed, pre-existing peptide and polypeptide chains. A limited synthesis of new chains of albumin does, however, occur.     

Interactions between cysteine residues as probes of protein conformation: the disulphide bond between Cys-14 and Cys-38 of the pancreatic trypsin inhibitor.

The rate constants for the reversible reduction by dithiothreitol of the disulphide bond linking eysteines 14 and 38 of the native pancreatic trypsin inhibitor have been measured. The results are consistent with this disulphide bond being formed as the last step in refolding of the fully reduced inhibitor.The rates of reduction of several model linear disulphides have been measured under the same conditions. A linear relationship was found between the rate of reduction and the ionization tendency of the thiol group generated.The apparent pK value of the thiol groups of cysteines 14 and 38 of the selectively reduced inhibitor were measured by the pH-dependence of their rate of alkylation with iodoacetamide. The rate of reduction of the disulphide bond between these two residues was very close to that predicted from the model compounds.The kinetics and thermodynamics of disulphide bond formation and breakage are shown to be useful for experimental determination of conformational transitions in proteins and model peptides.     

Changes in proportion of thiol to disulphide in acid-soluble nuclear proteins of Echinus during the first cell cycle

1. DNA synthesis in Echinus esculentus eggs kept at 10°C takes place just after fusion, 0.75–1.5h after fertilization, and at telophase at about 2.67–3.33h after fertilization. 2. An increase in the thiol/thiol+disulphide ratio in acid extracts from washed nuclear fractions of the eggs is found at fusion, at early stages of mitosis and at telophase. When DNA is being synthesized, the relative amount of thiol in the extracts increases. 3. There are at least five thiol-containing histones in the acid extract together with a diffusible thiol peptide containing methyl-lysine and 3-methylhistidine and a thiol-containing acidic protein.     

Characterization of lamprey fibrinopeptides

1. Lamprey fibrinopeptide B is a relatively large peptide made up of about 40 amino acid residues. The peptide is highly electronegative, containing a large number of aspartic acid residues and a tyrosine O-sulphate residue. 2. The amino acid sequence of the first 18 residues from the N-terminal end of fibrinopeptide B has been established. The C-terminal ends with the sequence Val-Arg. Fibrino-peptide B is released by both lamprey and bovine thrombins. 3. Lamprey fibrino-peptide A is a short peptide containing only eight residues. The proposed amino acid sequence is: Asp-Asp-Ser-Ile/Leu-Asp-Ser-Leu/Ile-ArgThis peptide is released by lamprey thrombin but not by bovine thrombin.     

The disulphide bonds of the heavy chain of rabbit immunoglobulin G

Six peptides containing eight half-cystine residues were isolated in good yield, after either oxidation or reduction and carboxymethylation of fragment C-1, which contains the N-terminal half of the heavy chain of rabbit immunoglobulin G. The sequences of five of these peptides had been reported previously (Cebra, Steiner & Porter, 1968b; Wilkinson, 1969) and that of the sixth was established. Other peptides containing half-cystine residues were isolated in much lower yield and are presumed to be derived from minor sequence variants. The cystine-containing peptides from enzymic digests of whole immunoglobulin G and Fc fraction were studied by several techniques and the results obtained enable us to put forward a scheme of the arrangement of the inter- and intra-chain disulphide bonds.     

Initiation of ovalbumin synthesis in chicken oviduct magnum: Transient labeling of the NH2-terminus by methionine

The incorporation of [³⁵S]methionine into ovalbumin, a protein containing NH₂-terminal N-acetylglycine, has been studied in chicken oviduct magnum cells. The purification of [³⁵S]methionine-labeled ovalbumin from total oviduct proteins was accomplished by dialysis of a crude extract at pH 3.6 followed by chromatography on carboxymethyl cellulose. The radioactive ovalbumin eluted from the column in three peaks (P₀, P₁, and P₂-containing 0, 1, and 2 moles of phosphate, respectively, per mole of ovalbumin). The kinetics of labeling of peaks P₀ and P₁ showed that the ratio of radioactivity in NH₂-terminal methionine to total incorporation was greater at 2 min of labeling than at later times. The transient labeling of the NH₂-terminus of ovalbumin with methionine indicates that methionine is the initiator amino acid for the synthesis of this protein, which in its mature form contains NH₂-terminal N-acetylglycine.     

Conformational aspects of N-glycosylation of proteins. Studies with linear and cyclic peptides as probes

Conformational aspects of N-glycosylation of glycoproteins have been studied by using a series of peptides which contained, in addition to the `marker sequence' Asn-Gly-Thr, two cysteine residues in various positions of the peptide chain. The presence of two cysteines permitted a partial fixation of the above triplet sequence in cyclic structures of various size by intramolecular disulphide bond formation. Comparison of the glycosyl acceptor properties of the linear peptides and their corresponding cyclic analogues allows the following statements. The considerably lower acceptor capabilities of the cyclic derivatives indicate that the restriction of rotational degrees of freedom imposed by disulphide bonding results in a conformation which hinders a favourable interaction of the peptide substrate with the N-glycosyltransferase. On the other hand, the glycosylation rate of linear peptides increases with increasing chain length, suggesting that the amino acids on both the N- and C-terminal side of the `marker sequence' may contribute to a considerable extent to the induction of an `active' conformation. Realization of a potential sugar attachment site requires a hydrogen bond interaction within the `marker sequence' between the oxygen of threonine (serine) as the hydrogen bond acceptor and the β-amide of asparagine as the donor [Bause & Legler (1981) Biochem. J. 195, 639–644]. This interaction is obviously facilitated when the peptide chain can adopt a conformation which resembles a β-turn or other loop structure. The available experimental and statistical data are discussed in terms of possible structural features for N-glycosylation, with the aid of space-filling models.     

Role of a disulphide bond in Helicobacter pylori arginase

Arginase is a binuclear Mn²⁺-metalloenzyme of urea cycle that hydrolyses arginine to ornithine and urea. Unlike other arginases, the Helicobacter pylori enzyme is selective for Co²⁺. Previous study reported that DTT strongly inhibits the H. pylori enzyme activity suggesting that a disulphide bond is critical for the catalysis. In this study, we have undertaken steady-state kinetics, circular dichroism and mutational analysis to examine the role of a disulphide bond in this protein. By mutational analysis, we show that the disulphide bond is not important for catalytic activity; rather it plays an important role for the stability of the protein as observed from thermal denaturation studies. The loss of catalytic activity in the wild-type protein with DTT is due to the interaction with Co²⁺. This is verified with the Mn²⁺-reconstituted proteins which showed a marginal loss in the activity with DTT.     

Conformational characteristics of polypeptides containing isolated L-proline residues with cis peptide bonds

The conformational characteristics of the peptide sequence X-l-Pro, where X  Gly or l-Ala and the peptide bond joining X and l-Pro is cis, are evaluated. Semi-empirical potential functions are used to estimate the contributions to the conformational energy made by the non-bonded van der Waals' and electrostatic interactions and the intrinsic torsional potentials about the NC^a and C^aC′ bonds. Rotations φ₁ and ψ₁ about the NC^a and C^aC′ bonds in residue X and rotation ψ₂ about the C^aC′ bond in l-Pro are permitted, while the angle of rotation φ₂ about the NC^a bond in l-Pro is fixed at 120 ° by the pyrrolidine ring. The presence of the cis peptide bond connecting X and l-Pro renders the backbone rotations φ₁, ψ₁ in X dependent upon the rotation ψ₂ about the C^aC′ bond in l-Pro. (Interdependence of rotations in neighboring residues joined by a cis peptide bond was previously observed in l-alanine oligomers.) The number of energetically allowed conformations for the Gly and l-Ala residues preceding a cis peptide bond l-Pro residue are found to be substantially reduced from those permitted when the peptide bond is trans or when l-Pro is replaced by an amino acid residue. On the other hand, ψ₂ = 100 to 160 ° (cis′) and 300 to 0 ° (trans′) are found to be the lowest energy conformations of the l-Pro residue irrespective of the cis or trans conformation of the X-l-Pro peptide bond.     

Vibrational and electronic optical activity of the chiral disulphide group: Implications for disulphide bridge conformation

Using dihydrogendisulphide (H₂S₂), dimethyl‐ ((CH₃)₂S₂), and diethyldisulphide ((CH₃CH₂)₂S₂)as model molecules, theoretical ECD, VCD, and ROA spectra of nonplanar disulphides were calculated by DFT methods. Most of the calculated electronic and vibrational chiroptical features suffer an equivocal relation between calculatedsigns of ECD, VCD, or ROA and the sense of disulphide nonplanarity as noted earlier for low‐lying ECD bands. This is a consequence of local C₂ symmetry of a disulphide group causing most electronic and vibrational transitions to occur as pairs falling to alternative A, B symmetry species, which become degenerate and switch their succession (and consequently the observed chiroptical sign pattern) at the energetically most favorable perpendicular conformation. According to present calculations, the key to resolving this ambiguity may involve the S? S stretching vibrational mode at ～500 cm^?1. The relation of signs of the relevant VCD and ROA features to sense of disulphide chirality seems simpler and less ambiguous. The right‐handed arrangement of the S? S group (0 < χ_{S? S} < 180°) results in mostly negative VCD signals. Although relation to ROA still suffers some ambiguity, it gets clearer along the series H₂S₂–(CH₃)₂S₂–(CH₃CH₂)₂S₂. ROA is also attractive for the analysis of disulphide‐containing peptides and proteins, because applying it to aqueous solutions is not problematic. Chirality, 2010. © 2009 Wiley‐Liss, Inc.     

Immunization with a synthetic robustoxin derivative lacking disulphide bridges protects against a potentially lethal challenge with funnel-web spider (<Emphasis Type="Italic">Atrax robustus</Emphasis>) venom

The venom of male Atrax robustus spiders is potentially lethal to primates. These spiders have been responsible for a number of human deaths. Robustoxin is the lethal toxin in the venom. It is a highly cross-linked polypeptide that has 42 amino acid residues and four disulphide bridges. If these bridges are broken, the resulting polypeptide is nontoxic. Robustoxin was chemically synthesized with all of its eight cysteine residues protected with acetamidomethyl groups in order to avoid formation of disulphide bridges. The resulting derivative was co-polymerized with keyhole limpet haemocyanin. Two Macaca fascicularis monkeys were immunized with this conjugate. The monkeys were challenged, under anaesthesia, with a potentially lethal dose of male A. robustus crude venom. Both monkeys showed some minor symptoms of intoxication but recovered fully with no adverse after-effects. Immunization with the same immunogen, in the absence of keyhole limpet haemocyanin, did not protect a third monkey. The N-terminal 23 amino acid peptide derived from the sequence of robustoxin was synthesized and conjugated with ovalbumin. A fourth monkey was immunized with this conjugate. However, it was not protected against challenge. The implications of these results for the preparation of synthetic peptide vaccines are discussed.     

Thiols attached to rat liver non-histone nuclear proteins.

Up to 88% of the total thiol present in isolated rat liver nuclei can be extracted with 8 M urea 50 mM phosphate pH 7.6. There is approx. 5–10% disulphide material present in this extract. When the thiols were labelled with ¹⁴C-N-ethyl maleimide (¹⁴C-NEM) the thiol material co-electrophoresed with the protein material. If a mixed disulphide was formed with ³⁵S-labelled 5-thio-2-nitrobenzoic acid (Ellman's reagent) the thiol compounds could be removed from the protein by isoelectric focusing in polyacrylamide gel. The mixed disulphides obtained could be resolved into at least 10 components on DEAE cellulose. One of the major components had an estimated molecular weight of 3 000 and did not contain peptide material.     

Role of AIP56 disulphide bond and its reduction by cytosolic redox systems for efficient intoxication

Apoptosis‐inducing protein of 56 kDa (AIP56) is a major virulence factor of Photobacterium damselae subsp. piscicida, a gram‐negative pathogen that infects warm water fish species worldwide and causes serious economic losses in aquacultures. AIP56 is a single‐chain AB toxin composed by two domains connected by an unstructured linker peptide flanked by two cysteine residues that form a disulphide bond. The A domain comprises a zinc‐metalloprotease moiety that cleaves the NF‐kB p65, and the B domain is involved in binding and internalisation of the toxin into susceptible cells. Previous experiments suggested that disruption of AIP56 disulphide bond partially compromised toxicity, but conclusive evidences supporting the importance of that bond in intoxication were lacking. Here, we show that although the disulphide bond of AIP56 is dispensable for receptor recognition, endocytosis, and membrane interaction, it needs to be intact for efficient translocation of the toxin into the cytosol. We also show that the host cell thioredoxin reductase‐thioredoxin system is involved in AIP56 intoxication by reducing the disulphide bond of the toxin at the cytosol. The present study contributes to a better understanding of the molecular mechanisms operating during AIP56 intoxication and reveals common features shared with other AB toxins.     

The site at which 4-iodoacetamidosalicylate reacts with glutamate dehydrogenases

1. Bovine, porcine and chicken liver glutamate dehydrogenases were irreversibly inhibited by a tenfold excess of radioactive 4-iodoacetamidosalicylic acid at pH7.5. 2. Inhibition was accompanied by the covalent incorporation of 1.1 mol of labelled inhibitor/mol of polypeptide chain. Acid hydrolysis yielded N^ε-carboxymethyl-lysine as the sole labelled amino acid. No labelled S-carboxymethylcysteine was recovered from the bovine or porcine enzymes. 3. The labelled bovine enzyme was hydrolysed with trypsin. The radioactivity was found at lysine-126 in a peptide comprising residues 119–130 of the sequence. 4. The amino acid compositions of the tryptic peptides containing labelled lysine from the porcine and chicken enzymes were similar to that of the bovine peptide.