Nonreducing Research Articles

SAXS reveals highly flexible interdomain linkers of tandem acyl carrier protein-thioesterase domains from a fungal nonreducing polyketide synthase.

Menisporopsin A is a fungal bioactive macrocyclic polylactone, the biosynthesis of which requires only reducing (R) and nonreducing (NR) polyketide synthases (PKSs) to guide a series of esterification and cyclolactonization reactions. There is no structural information pertaining to these PKSs. Here, we report the solution characterization of singlet and doublet acyl carrier protein (ACP2 and ACP1 -ACP2 )-thioesterase (TE) domains from NR-PKS involved in menisporopsin A biosynthesis. Small-angle X-ray scattering (SAXS) studies in combination with homology modelling reveal that these polypeptides adopt a distinctive beads-on-a-string configuration, characterized by the presence of highly flexible interdomain linkers. These models provide a platform for studying domain organization and interdomain interactions in fungal NR-PKSs, which may be of value in directing the design of functionally optimized polyketide scaffolds.

Enhancement of covalent aggregate quantification of protein therapeutics by non-reducing capillary gel electrophoresis using sodium hexadecyl sulfate (CE-SHS)

Capillary gel electrophoresis (CGE) using sodium dodecyl sulfate (CGE-SDS or CE-SDS) is commonly used in the biotechnology industry to assess the purity of a complex therapeutic during manufacturing process optimization and also for commercial release and stability testing. However, for therapeutic proteins mAb-1 and mAb-2, non-reducing (NR) CE-SDS yielded higher than expected % aggregate which considerably lowered its apparent purity relative to the purity reported by other complementary methods, such as Size Exclusion Chromatography (SEC). Furthermore, a strong protein load dependence on aggregate levels was observed which prevented any reasonable assessment of the true purity value. The solution was to supplement SDS with the relatively hydrophobic detergent sodium hexadecyl sulfate (SHS) in the sieving gel buffer matrix which virtually eliminated the protein load-dependence and reduced the % aggregate value to expected levels when compared to SEC. Analytical Ultracentrifugation (AUC) was used to help confirm the accuracy of the SEC results. This work underscored how using detergents other than SDS in CGE applications can be valuable in the commercial biologics space and provided an example of how SEC can be used to confirm the accuracy of CGE data.

Molecular interaction of antifungal compounds with fungal type I Polyketide synthase and preventing hepatocarcinogenesis

Background: The type I fungal iterative Polyketide synthase (PKS) is found in many toxigenic Aspergillus species. PKS is an important biological non- reducing (NR) type enzymes. It possesses highly active Acyl Carrier Protein (ACP) domain that is implicated in thiol ester-bound intermediates in involved in fungal polyketides, fatty acids and other non-ribosomal peptides formation. These natural polyketide and fatty acids are participated in formation of aflatoxin biosynthesis. These aflatoxins are highly responsible for hepatocarcinhgenesis (HCC), one of commonest cancer among humans living in tropical regions. The HCC has also been shown the synergetic effect with viral infections especially hepatitis B. The risk of HCC is drastically increased under episodic exposure of aflatoxin contaminated feed and hepatitis B that can be fatal if delay in diagnosis and proper treatment. Methods & Materials: The ACP domain as 3D coordinates 2KR5.pdb of polyketide synthase of Aspergillus parasiticus is taken from RCSB. The requisite antifungal ligand files for docking purpose i.e. neoeriocitrin (CID: 114627), blasticidin-S (CID: 16380), blasticidin-S hydrochloride (CID: 258) and pipernomaline (CID: 9974595) protein were retrieved from PubChem Database. The protein preparation, ligand library preparation, sites identification and docking (LibDock Score) were performed by using dynamic software Discovery Studio version 3.5. Results: In the three different sites, site 1 (x: -7.589; y: -2.949; z: 4.007) shown the most effective docking results. At this site 1, the highest LibDock score of 160.282 for 2KR5- neoeriocitrin had shown the successful inhibition of polyketide synthase. Lys4, Asp80, Gly84, Gly86, Asp87 and Gly89 are the amino acides of the protein that are interacted with neoeriocitrin. Conclusion: The Computational study and prediction of three different active sites in ACP domain of PKS of Aspergillus parasiticus had shown the successful interaction with proper ligands. The neoeriocitrin and similar other organic compounds are the very effective flavonoid found in grape fruits that can essentially use in treating HCC and Hepatitis patients.

Hyaluronan synthase assembles hyaluronan on a [GlcNAc(β1,4)]n-GlcNAc(α1→)UDP primer and hyaluronan retains this residual chitin oligomer as a cap at the nonreducing end.

Class I hyaluronan synthases (HAS) assemble [GlcNAc(β1,4)GlcUA(β1,3)]n-UDP at the reducing end and also make chitin. Streptococcus equisimilis HAS (SeHAS) also synthesizes chitin-UDP oligosaccharides, (GlcNAc-β1,4)n-GlcNAc(α1→)UDP (Weigel et al. 2015). Here we determined if HAS uses chitin-UDPs as primers to initiate HA synthesis, leaving the non-HA primer at the nonreducing (NR) end. HA made by SeHAS membranes was purified, digested with streptomyces lyase, and hydrophobic oligomers were enriched by solid phase extraction and analyzed by MALDI-TOF MS. Jack bean hexosaminidase (JBH) and MS/MS were used to analyze 19 m/z species of possible GnHn ions with clustered GlcNAc (G) residues attached to disaccharide units (H): (GlcNAcβ1,4)2-5[GlcUA(β1,3)GlcNAc]2-6. JBH digestion sequentially removed GlcNAc from the NR-end of GnHn oligomers, producing successively smaller GnH2-3 series members. Since lyase releases dehydro-oligos (dHn; M-18), only the unique NR-end oligo lacks dehydro-GlcUA. Hn oligomers were undetectable in lyase digests, whereas JBH treatment created new H2-6m/z peaks (i.e. HA tetra- through dodeca-oligomers). MS/MS of larger GnHn species produced chitin (2-5 GlcNAcs), HA oligomers and multiple smaller series members with fewer GlcNAcs. All NR-ends (97%) started with GlcNAc, as a chitin trimer (three GlcNAcs), indicating that GlcNAc(β1,4)2GlcNAc(α1→)-UDP may be optimal for initiation of HA synthesis. Also, HA made by live S. pyogenes cells had G4Hn chitin-oligo NR-ends. We conclude that chitin-UDP functions in vitro and in live cells as a primer to initiate synthesis of all HA chains and these primers remain at the NR-ends of HA chains as residual chitin caps [(GlcNAc-β1,4)3-4].

Phylogenetic and Structural Analysis of Polyketide Synthases inAspergilli

Polyketide synthases (PKSs) of Aspergillus species are multidomain and multifunctional megaenzymes that play an important role in the synthesis of diverse polyketide compounds. Putative PKS protein sequences from Aspergillus species representing medically, agriculturally, and industrially important Aspergillus species were chosen and screened for in silico studies. Six candidate Aspergillus species, Aspergillus fumigatus Af293, Aspergillus flavus NRRL3357, Aspergillus niger CBS 513.88, Aspergillus terreus NIH2624, Aspergillus oryzae RIB40, and Aspergillus clavatus NRRL1, were selected to study the PKS phylogeny. Full-length PKS proteins and only ketosynthase (KS) domain sequence were retrieved for independent phylogenetic analysis from the aforementioned species, and phylogenetic analysis was performed with characterized fungal PKS. This resulted into grouping of Aspergilli PKSs into nonreducing (NR), partially reducing (PR), and highly reducing (HR) PKS enzymes. Eight distinct clades with unique domain arrangements were classified based on homology with functionally characterized PKS enzymes. Conserved motif signatures corresponding to each type of PKS were observed. Three proteins from Protein Data Bank corresponding to NR, PR, and HR type of PKS (XP_002384329.1, XP_753141.2, and XP_001402408.2, respectively) were selected for mapping of conserved motifs on three-dimensional structures of KS domain. Structural variations were found at the active sites on modeled NR, PR, and HR enzymes of Aspergillus. It was observed that the number of iteration cycles was dependent on the size of the cavity in the active site of the PKS enzyme correlating with a type with reducing or NR products, such as pigment, 6MSA, and lovastatin. The current study reports the grouping and classification of PKS proteins of Aspergilli for possible exploration of novel polyketides based on sequence homology; this information can be useful for selection of PKS for polyketide exploration and specific detection of Aspergilli.

Production of New Cladosporin Analogues by Reconstitution of the Polyketide Synthases Responsible for the Biosynthesis of this Antimalarial Agent.

The antimalarial agent cladosporin is a nanomolar inhibitor of the Plasmodium falciparum lysyl-tRNA synthetase, and exhibits activity against both blood- and liver-stage infection. Cladosporin can be isolated from the fungus Cladosporium cladosporioides, where it is biosynthesized by a highly reducing (HR) and a non-reducing (NR) iterative type I polyketide synthase (PKS) pair. Genome sequencing of the host organism and subsequent heterologous expression of these enzymes in Saccharomyces cerevisiae produced cladosporin, confirming the identity of the putative gene cluster. Incorporation of a pentaketide intermediate analogue indicated a 5+3 assembly by the HR PKS Cla2 and the NR PKS Cla3 during cladosporin biosynthesis. Advanced-intermediate analogues were synthesized and incorporated by Cla3 to furnish new cladosporin analogues. A putative lysyl-tRNA synthetase resistance gene was identified in the cladosporin gene cluster. Analysis of the active site emphasizes key structural features thought to be important in resistance to cladosporin.

Production of New Cladosporin Analogues by Reconstitution of the Polyketide Synthases Responsible for the Biosynthesis of this Antimalarial Agent

AbstractThe antimalarial agent cladosporin is a nanomolar inhibitor of the Plasmodium falciparum lysyl‐tRNA synthetase, and exhibits activity against both blood‐ and liver‐stage infection. Cladosporin can be isolated from the fungus Cladosporium cladosporioides, where it is biosynthesized by a highly reducing (HR) and a non‐reducing (NR) iterative type I polyketide synthase (PKS) pair. Genome sequencing of the host organism and subsequent heterologous expression of these enzymes in Saccharomyces cerevisiae produced cladosporin, confirming the identity of the putative gene cluster. Incorporation of a pentaketide intermediate analogue indicated a 5+3 assembly by the HR PKS Cla2 and the NR PKS Cla3 during cladosporin biosynthesis. Advanced‐intermediate analogues were synthesized and incorporated by Cla3 to furnish new cladosporin analogues. A putative lysyl‐tRNA synthetase resistance gene was identified in the cladosporin gene cluster. Analysis of the active site emphasizes key structural features thought to be important in resistance to cladosporin.

Identification of the binding of β-lactoglobulin (β-Lg) with sulfhydryl (–SH) blocking reagents by polyacrylamide gel electrophoresis (PAGE) and electrospray ionisation/time of flight-mass spectrometry (ESI/TOF-MS)

β-Lactoglobulin (β-Lg) is relatively unstable during thermal processes used in the dairy industry. One of many ways to improve the heat stability of β-Lg is by chemical modification by protein–reagent binding. Potential reagents, such as 5,5'-dithiobis-2-nitrobenzoic acid (DTNB) and N-ethylmaleimide (NEM), bind to the exposed free sulfhydryl (–SH) group of denatured β-Lg and prevent it from being involved in protein aggregation reactions. However, no study has shown the specific binding of these reagents to β-Lg. Furthermore, the question of how many molecules of these reagents bind to β-Lg remains unanswered. In this research, the reactions of DTNB or NEM with the reactive monomers of β-Lg were identified by the presence of bands for 5-thio-2-nitrobenzoyl (TNB)- or NEM-modified monomers on Native-PAGE and Non-Reducing (NR) sodium deodecyl sulphate (SDS)-PAGE gels, and by an additional mass of β-Lg monomers corresponding to a molecule of TNB or NEM in mass spectra.

Disulfide proteomics for identification of extracellular or secreted proteins

The combination of SDS-PAGE and MS is one of the most powerful and perhaps most frequently used gel-based proteomics approaches in protein identification. However, one drawback of this method is that separation takes place under denaturing and reducing (R) conditions and as a consequence, all proteins with identical apparent molecular mass (Mr) will run together. Therefore, low-abundant proteins may not be easily identified. Another way of investigating proteins by proteomics is by analyzing subproteomes from a total proteome such as phosphoproteomics, glycoproteomics, or disulfide proteomics. Here, we took advantage of the property of secreted proteins to form disulfide bridges and investigated disulfide-linked proteins, using SDS-PAGE under nonreducing (NR) conditions. We separated sera from normal subjects and from patients with various diseases by SDS-PAGE (NR) and (R) conditions, followed by LC-MS/MS analysis. Although we did not see any detectable difference between the sera separated by SDS-PAGE(R), we could easily identify the disulfide-linked proteins separated by SDS-PAGE (NR). LC-MS/MS analysis of the disulfide-linked proteins correctly identified haptoglobin (Hp), a disulfide-linked protein usually found as a heterotetramer or as a disulfide-linked heteropolymer. Western blotting under NR and R conditions using anti-Hp antibodies confirmed the LC-MS/MS experiments and further confirmed that upon reduction, the disulfide-linked Hp heterotetramers and polymers were no longer disulfide-linked polymers. These data suggest that simply by separating samples on SDS-PAGEunder NR conditions, a different, new proteomics subset can be revealed and then identified.

A potential generic downstream process using Cibracon Blue resin at very high loading capacity produces a highly purified monoclonal antibody preparation from cell culture harvest

The use of a dye-ligand chromatography for the purification of monoclonal antibody (MAb) from cell culture and other feed streams has been largely overlooked in large scale production. Cibracon Blue dye (CB), a polycyclic anionic ligand, interacts with protein through a specific interaction between the dye, acting as a mimic of NAD + and NADP +, or through non-specific electrostatic, hydrophobic, and other forces. In this paper, a CB resin was used to effectively and efficiently separate an IgG 4 MAb from host and process impurities following the capture of the MAb on a Protein-A (PA) column. The CB unit operation, challenged at ≤180 g MAb/L of resin with the PA eluate, reduced BSA (1–2 log), host cell protein (HCP; 2–3 log), MAb oligomer (31–85%), fragment (from ∼0.8% to <0.1%), and other undesired MAb species. Purity, as measured by non-reducing (NR) SDS-PAGE, was improved 33–85%, to 92–99.5% overall (>99% by reducing SDS-PAGE). A facile three column scalable production scheme, employing CB as the second column in the process was used to generate highly purified MAb from cell culture harvest derived from two media of very different compositions. Free CB dye was ≤1 ng/mg in MAb preparations purified through the three column process and then concentrated and buffer exchanged into the appropriate buffer using tangential flow filtration (TFF).

Minimal Heparin/Heparan Sulfate Sequences for Binding to Fibroblast Growth Factor-1

The glycosaminoglycans heparin and heparan sulfate (HS) bind to fibroblast growth factor FGF1 and promote its dimerization, a proposed prerequisite for binding to a cellular receptor and triggering mitogenic signals. The problem of minimal structural requirements for heparin/HS sequences to bind FGF1 was approached by surface plasmon resonance (SPR), NMR spectroscopy, and MALDI mass spectrometry studies using the three synthetic tetrasaccharides GlcNSO36OR-IdoA2SO3-GlcNSO36OR′-IdoA2SO3OPr (AA, R = R′ = SO3; BA, R = H, R′ = SO3; BB, R = R′ = H; Pr, propyl). AA and BA significantly interact with the protein, whereas BB is practically inactive. The NMR spectra show that, whereas the interaction of AA primarily involves the GlcNSO36SO3IdoA2SO3 disaccharide moiety at its nonreducing end, residues at both the nonreducing (NR) and reducing side (R) appear to be involved in the weaker complex of BA. Furthermore, MALDI experiments show that, in addition to 1:1 protein:tetrasaccharide complexes, AA and BA are able to form 2:1 complexes, indicating that heparin/HS-induced dimerization of FGF1 requires only one 6-OSO3 group per tetrasaccharide.

Differential expression and regulation of CD6 on T-cell subsets revealed by monoclonal antibody (MAb) CH11.

A monoclonal antibody (MAb), CH11, was developed by immunizing mice with CD4+ gammadelta T-cell receptor (TCR)+ cells. It recognized an antigen expressed in the surface membrane of T-cell lines, but not of U937, lymphoblastoid B cells (LBC), K562, Raji or Daudi cells, indicating selectivity for the T-cell lineage. In addition, it labelled 70-80% of normal peripheral blood mononuclear cells (PBMC), with high expression on the erythrocyte rosetting (E+) fraction, and low/absent expression on E- cells. However, CD4+ T cells expressed higher levels of reactivity than CD8+ or gammadelta+ T-cell receptor (TCR)+ lymphocytes in PB. Furthermore, in 7 of 10 individuals tested, 7.34+/-3.88% of unselected PBMC were CH11- CD3+ and were relatively enriched in CD8+ and in gammadelta TCR+-cells. In addition, thymic gammadelta T cells, and gammadelta lymphoproliferations from two patients were nonreactive or weakly reactive with the MAb. Activation of E+ cells with phorbol-12-myristate-13-acetate (PMA) enhanced CH11 expression uniformly, whereas activation with phytohemagglutinin (PHA) selectively down-regulated expression of the antigen on the CD8+ subset. In Western blots performed in nonreducing (NR) conditions, MAb CH11 detected a 100 kDa molecule in PBMC and Jurkat T-cell lysates. Preincubation of T cells with MAb CH11 specifically abrogated their subsequent reactivity with MAb to CD6, suggesting that MAb CH11 is recognizing an epitope of CD6. Given its function as a receptor for ligands on thymic epithelium, activated leukocytes and synoviocytes, this newly defined heterogeneity of expression and regulation of the CD6 molecule on subsets of T cells may help determine their functional repertoire in vivo.

Detection of reduced acetaldehyde protein adducts using a unique monoclonal antibody.

Acetaldehyde (AA), the major product of alcohol metabolism, has been shown to bind to proteins in vivo and form chemical adducts. These AA-protein adducts have been shown to alter protein structure and function and may result in tissue damage. Recent reports have shown that polyclonal antibodies can be produced that recognize proteins modified in vitro with AA in the presence of sodium cyanoborohydride (NaCNBH3), a strong reducing (R) agent. Antibodies prepared in this way have been shown to recognize proteins in the livers of rats fed alcohol chronically. Because multiple AA-protein adducts can be recognized by polyclonal antisera, and a variety of adducts may be formed in vitro or in vivo, this study was designed to develop monoclonal antibodies specific for proteins modified by AA. In addition, adducts formed under R conditions are probably chemically different than those formed under nonreducing (NR) conditions, and monoclonal antibodies may provide the specificity required to distinguish these chemical differences. Balb/c mice were immunized with bovine brain tubulin that was modified by treatment with 5 mM AA for 7 days under NR conditions. Sera from immunized animals were tested for antibody activity to the immunogen (protein-NR) and for cross-reactivity to protein-R and unmodified protein. Although the highest serum antibody titers were seen toward the NR adduct, antibodies to the R adduct were also detected. This activity difference was independent of the carrier protein, because NR and R bovine serum albumin, keyhole limpet hemocyanin, and actin also gave similar results when used as the adducted protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Changes in molecular variants during in vitro transformation and release of prolactin by the pituitary gland of the lactating rat.

PRL transformation involves a dopamine (DA)-controlled, thiol-mediated decrease in pituitary PRL detectability that precedes and may determine increased PRL release. The present studies were designed to determine 1) whether structural changes occur to adenohypophyseal (AP) PRL during in vitro transformation and may account for decreased PRL detectability; 2) whether such changes occur within AP PRL granules; 3) the type and proportion of secreted PRL variants; and 4) the influence of DA and/or thiol reducing agents upon AP PRL molecular changes. Quartered APs of 8 h nonsuckled lactating rats, injected or not with [3H]leucine (5 mCi/g body wt, 8 h before death) were incubated for 30-240 min. The effects of DA (50 microM) with or without reduced glutathione (10 mM), and the alkylant N-ethylmaleimide (1 mM) were compared to the changes in PRL molecular variants occurring in control incubated AP fragments. Polyacrylamide gel electrophoresis (PAGE) under native conditions and sodium dodecyl sulfate (SDS)-PAGE under reducing (R) or nonreducing (NR) conditions were used to resolve molecular variants of PRL and [3H]PRL, followed by Western blotting and densitometric/liquid scintillation techniques, respectively. Up to 5 and 10 major forms of immunoreactive PRL were resolved by PAGE and SDS-PAGE, respectively. The spontaneous transformation after 30 min incubation was correlated with a decrease of 23K PRL and 23K [3H]PRL bands and an increase in high mol wt (80 to greater than 100K) PRL forms. These changes were reversible upon reduction of the proteins before electrophoresis or after extraction of preparative gels. DA and N-ethylmaleimide prevented, whereas reduced glutathione induced these changes. Similar changes were observed in isolated granules from nonincubated and incubated pituitary fragments. Secreted PRL was also polymorphic, with a high predominance of 23K PRL and 23K [3H]PRL. In addition, a polymeric PRL variant, which in reducing gels showed an apparent mol wt of 27K, was secreted in high proportion, similar to that of 23K PRL. The nature of this polymeric variant of PRL is unclear at present. Altogether, these results suggest that a dynamic interconversion of PRL molecular variants occur during transformation. The decreased detectability associated with PRL transformation appears to involve the association of 23K PRL molecules into a 80 to greater than 100K disulfide-linked oligomer. This association is reversible upon reduction and takes place within secretory granules. DA appears to inhibit PRL transformation by preventing thiol-disulfide interchange.

Membrane glycoproteins involved in hepatocyte adhesion to collagen type I

Liver membrane glycoproteins with affinity for immobilized collagen type I were subjected to preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by electroelution of the separated proteins. Electroeluted glycoproteins with ability to neutralize the inhibitory effect of anti-CollCAM antibodies on hepatocyte adhesion to collagen were collected from several consecutive runs and used to raise a high titer antiserum, denoted anti-CollCAM II. IgG from this antiserum inhibited the attachment of hepatocytes to dishes coated with collagen type I, but not to fibronectin- or collagen type IV-coated dishes. When the antibodies were immobilized to Sepharose CL-4B they bound three sets of glycoproteins with apparent M r's of 105,000, 115,000, and 130,000 as analyzed by SDS-PAGE under nonreducing (NR) conditions. Upon reduction (R) the glycoproteins migrated with apparent M r's of 115,000, 130,000, and 160,000, respectively. The M r 105,000-115,000 (NR) glycoproteins effectively neutralized the inhibitory effect exerted by both anti-CollCAM and anti-CollCAM II antibodies, on hepatocyte spreading and attachment to collagen type I substrates. Peptide mapping suggested the M r 160,000 (R) species to be different from the M r 115,000 (R).

Cellulose Studies

In an attempt to establish unambiguously the presence of the nonreducing end group in cellulose when treated under nondegrading conditions, different celluloses were sub jected to exhaustive methylation, using sodium hydroxide and dimethyl sulfate in toluene. Other methods of methylation were also investigated. Samples with 43.8% methoxyl content were obtained which were found suitable for this investigation. Identification and quantitative estimation of tetramethyl glucose, which originates from the nonre ducing end of the cellulose chain, involved hydrolysis, extraction of the tetramethyl glucose from the main component, trimethyl glucose, and chromatographic analysis. Paper, thin-layer, and gas chromatography were used in the analysis and special techniques were developed for each method. Identification and quantitative estimation by gas chromatography were accomplished for the methyl glucosides and the trimethyl silyl derivatives of the methylated glucoses. Isolation of crystalline tetramethyl glucose and the preparation of its anilide derivative provided unambiguous proof of the presence of nonreducing end groups in cellulose when treated under nondegrading conditions. It was observed that methyl tetramethyl glucoside is volatile at room temperature and atmospheric pressure. This is advanced as a probable reason for the previously reported absence of nonreducing end groups in cellulose. The quantitative method of tetramethyl glucose estimation, in relation to the tri methyl glucose content, was used for the determination of the number average degree of polymerization of cellulose. For methyl celluloses of different origins, these were found to be: 908% ± 18% for cotton cellulose, 465% ± 21% for a commercial methyl cellulose, and 197% ± 20% for viscose rayon cellulose.