Protein disulphide isomerase-assisted functionalization of proteinaceous substrates

Protein disulphide isomerase (PDI) is an enzyme that catalyzes thiol-disulphide exchange reactions among a broad spectrum of substrates, including proteins and low-molecular thiols and disulphides. As the first protein-folding catalyst reported, the study of PDI has mainly involved the correct folding of several cysteine-containing proteins. Its application on the functionalization of protein-based materials has not been extensively reported. Herein, we review the applications of PDI on the modification of proteinaceous substrates and discuss its future potential. The mechanism involved in PDI functionalization of fibrous protein substrates is discussed in detail. These approaches allow innovative applications in textile dyeing and finishing, medical textiles, controlled drug delivery systems and hair or skin care products.     

Protein folding pathways determined using disulphide bonds.

The best-characterized model pathway of protein folding, that of disulphide bond formation in the small protein BPTI, has been questioned recently. A reinvestigation of that pathway, using alternative methods, concluded that the intermediates with non-native disulphide bonds accumulated to lower levels than previously had been observed. On this basis, a revised pathway was proposed that simply omitted those intermediates. Even if totally correct, however, the new observations are not inconsistent with the important characteristics of the original pathway and even confirmed many of them. Certain crucial observations that were the experimental basis for the original pathway were ignored, and these observations invalidate the revised pathway.     

Protein disulphide isomerase-induced refolding of sonochemically prepared Ribonuclease A microspheres

The present communication describes for the first time the development of Ribonuclease A (RNase A) microspheres using the sonochemical method followed by an enzymatic treatment with protein disulphide isomerase (PDI). Ultrasound application induced changes on the protein physicochemical and biological properties: the enzymatic activity of RNase A was decreased in 35% and the free thiol groups content was significantly increased, probably due to the breakage of protein disulphide bonds and assembly of RNase A monomers. The deconvolution of amide I band, from Fourier Transform Infrared Spectroscopy, showed that the secondary structure of RNase A was slightly changed after microspherization. The PDI application on microspheres promoted the recovery of RNase A biological activity and induced the release of active protein into solution in its native state. These results were promoted by different states of PDI active site: oxidized and reduced, respectively. The PDI aptitude to catalyze the refolding of a protein substrate in the form of spheres is here reported.     

Protein disulphide isomerase from human peripheral blood neutrophils.

Protein disulphide isomerase (PDI) is a 56 kDa resident polypeptide of the endoplasmic reticulum of many cell types. We evaluated the ability of human peripheral blood polymorphonuclear neutrophils (PMN) to synthesize both mRNA and proteins. Using in vitro [35S]-methionine labeling of purified PMN, followed by immunoprecipitation of cell lysates with immobilized polyclonal and monoclonal antibodies and analysis by gel electrophoresis, PMN were shown to synthesize many proteins, including actin. In contrast, incorporation of [35S]-methionine into PDI was not detected. Purification of total RNA from PMN and analysis by Northern blots demonstrated the presence in PMN of PDI-RNA. Western immunoblot evaluations of total PMN protein display an immunoreactive-PDI of 56 kDa. Indirect immunofluorescence studies suggest an abundance of immunoreactive-PDI throughout PMN. We therefore conclude that PDI is synthesized in precursor cells of the bone marrow. Phorbol 12-myristate 13-acetate, a reagent known to affect the degranulation of specific granules, causes the release of immunoreactive-PDI into a post-centrifugation supernatant. PDI, a ubiquitous endoplasmic reticulum resident protein, is shown here to be associated with specific granules in a cell type which has lost its intracellular membrane network during terminal differentiation.     

Protein disulphide isomerase is required for signal peptide peptidase-mediated protein degradation

The human cytomegalovirus glycoprotein US2 induces dislocation of MHC class I heavy chains from the endoplasmic reticulum (ER) into the cytosol and targets them for proteasomal degradation. Signal peptide peptidase (SPP) has been shown to be integral for US2-induced dislocation of MHC class I heavy chains although its mechanism of action remains poorly understood. Here, we show that knockdown of protein disulphide isomerase (PDI) by RNA-mediated interference inhibited the degradation of MHC class I molecules catalysed by US2 but not by its functional homolog US11. Overexpression of the substrate-binding mutant of PDI, but not the catalytically inactive mutant, dominant-negatively inhibited US2-mediated dislocation of MHC class I molecules by preventing their release from US2. Furthermore, PDI associated with SPP independently of US2 and knockdown of PDI inhibited SPP-mediated degradation of CD3δ but not Derlin-1-dependent degradation of CFTR DeltaF508. Together, our data suggest that PDI is a component of the SPP-mediated ER-associated degradation machinery.     

Protein disulphide isomerase binds ammodytoxin strongly: possible implications for toxin trafficking

Ammodytoxin, a group IIA secreted phospholipase A(2) from the venom of the long-nosed viper (Vipera ammodytes ammodytes), is a potent presynaptically acting neurotoxin. It blocks the secretion of neurotransmitter from the nerve cell, thus hindering the communication with the neighbouring neuron or muscle cell. To express the neurotoxicity, ammodytoxin should interact with specific receptors in the axon terminal and express phospholipase activity. Our previous results indicate that, following the association with a receptor on the external side of the presynaptic membrane, the toxin penetrates into the cytosol of the nerve cell. Here, we show that the toxin associates specifically with protein disulphide isomerase, a protein in the lumen of endoplasmic reticulum, which may be crucial for the retention and concentration of the toxin in this cellular compartment and for its subsequent transport across the membrane of endoplasmic reticulum into the cytosol of the nerve cell.     

Protein database searches using compositionally adjusted substitution matrices

Almost all protein database search methods use amino acid substitution matrices for scoring, optimizing, and assessing the statistical significance of sequence alignments. Much care and effort has therefore gone into constructing substitution matrices, and the quality of search results can depend strongly upon the choice of the proper matrix. A long-standing problem has been the comparison of sequences with biased amino acid compositions, for which standard substitution matrices are not optimal. To address this problem, we have recently developed a general procedure for transforming a standard matrix into one appropriate for the comparison of two sequences with arbitrary, and possibly differing compositions. Such adjusted matrices yield, on average, improved alignments and alignment scores when applied to the comparison of proteins with markedly biased compositions. Here we review the application of compositionally adjusted matrices and consider whether they may also be applied fruitfully to general purpose protein sequence database searches, in which related sequence pairs do not necessarily have strong compositional biases. Although it is not advisable to apply compositional adjustment indiscriminately, we describe several simple criteria under which invoking such adjustment is on average beneficial. In a typical database search, at least one of these criteria is satisfied by over half the related sequence pairs. Compositional substitution matrix adjustment is now available in NCBI's protein-protein version of blast.     

Protein folding/refolding analysis by mass spectrometry. Scrambling of disulphide bridges in insulin.

In this paper we present a protocol that allows a dynamic analysis of disulphide-bridge formation, based on freezing the intermediates by acid/acetone precipitation, followed by digestion with pepsin and direct fast-atom-bombardment mass-spectrometric analysis. A rapid definition of the exact nature of disulphide bridges formed can be obtained via a definitive assignment of disulphide-linked peptides according to their unique mass values. With the use of an appropriate thiol concentration, scrambling of the native disulphide bonds in bovine insulin occurs, and the process is catalysed by protein disulphide-isomerase (EC 5.3.4.1). The disruption of native and the formation of new disulphide bonds can be monitored as described above, and interestingly B-chain dimers containing Cys-B7-Cys-B7 and Cys-B7-Cys-B19 bonds are detected.     

Protein secondary structure prediction based on position-specific scoring matrices.

A two-stage neural network has been used to predict protein secondary structure based on the position specific scoring matrices generated by PSI-BLAST. Despite the simplicity and convenience of the approach used, the results are found to be superior to those produced by other methods, including the popular PHD method according to our own benchmarking results and the results from the recent Critical Assessment of Techniques for Protein Structure Prediction experiment (CASP3), where the method was evaluated by stringent blind testing. Using a new testing set based on a set of 187 unique folds, and three-way cross-validation based on structural similarity criteria rather than sequence similarity criteria used previously (no similar folds were present in both the testing and training sets) the method presented here (PSIPRED) achieved an average Q3 score of between 76.5% to 78.3% depending on the precise definition of observed secondary structure used, which is the highest published score for any method to date. Given the success of the method in CASP3, it is reasonable to be confident that the evaluation presented here gives a fair indication of the performance of the method in general.     

Protein sequences classification by means of feature extraction with substitution matrices

Background  

This paper deals with the preprocessing of protein sequences for supervised classification. Motif extraction is one way to address that task. It has been largely used to encode biological sequences into feature vectors to enable using well-known machine-learning classifiers which require this format. However, designing a suitable feature space, for a set of proteins, is not a trivial task. For this purpose, we propose a novel encoding method that uses amino-acid substitution matrices to define similarity between motifs during the extraction step.     

Protein disulphide isomerase can predict the clinical prognostic value and contribute to malignant progression in gliomas

Increasing evidence from structural and functional studies has indicated that protein disulphide isomerase (PDI) has a critical role in the proliferation, survival and metastasis of several types of cancer. However, the molecular mechanisms through which PDI contributes to glioma remain unclear. Here, we aimed to investigate whether the differential expression of 17 PDI family members was closely related to the different clinicopathological features in gliomas from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas data sets. Additionally, four subgroups of gliomas (cluster 1/2/3/4) were identified based on consensus clustering of the PDI gene family. These findings not only demonstrated that a poorer prognosis, higher WHO grade, lower frequency of isocitrate dehydrogenase mutation and higher 1p/19q non-codeletion status were significantly correlated with cluster 4 compared with the other clusters, but also indicated that the malignant progression of glioma was closely correlated with the expression of PDI family members. Moreover, we also constructed an independent prognostic marker that can predict the clinicopathological features of gliomas. Overall, the results indicated that PDI family members may serve as possible diagnostic markers in gliomas.     

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.     

Thiol and disulphide contents of hen ovalbumin. C-Terminal sequence and location of disulphide bond

1. The thiol and disulphide contents of hen ovalbumin were investigated by p-chloromercuribenzoate titration, by determination of cysteic acid content after performic acid oxidation, by measurement of uptake of radioactive iodoacetic acid, and by assay of S-aminoethylcysteine after reaction with ethyleneimine. All results showed that ovalbumin had 6 half-cystine residues. Experiments with and without reducing agents demonstrated that there were 4 thiol groups and 1 disulphide bond. 2. A peptide containing equimolar amounts of S-carboxymethyl-cysteine, serine, valine and proline, but no lysine or arginine, was obtained by radioactive labelling of the cysteine residues with iodo[¹⁴C]acetic acid followed by electrophoretic and chromatographic separation of tryptic digests. It was concluded that the C-terminal sequence of ovalbumin is -Cys-Val-Ser-Pro. 3. The location of the disulphide bond was studied by using a double-labelling technique. It was shown that one end of the disulphide was located in this C-terminal peptide.