Elimination of β-mannose glycan structures in Pichia pastoris

The methylotrophic yeast, Pichia pastoris, is an important organism used for the production of therapeutic proteins. However, the presence of fungal-like glycans, such as those containing β-mannose (Man) linkages, can elicit an immune response or bind to Man receptors, thus reducing their efficacy. Recent studies have confirmed that P. pastoris has four genes from the β-mannosyl transferase (BMT) family and that Bmt2p is responsible for the majority of β-Man linkages on glycans. While expressing recombinant human erythropoietin (rhEPO) in a developmental glycoengineered strain devoid of BMT2 gene expression, cross-reactivity was observed with an antibody raised against host cell antigens. Treatment of the rhEPO with protein N-glycosidase F eliminated cross-reactivity, indicating that the antigen was associated with the glycan. Thorough analysis of the glycan profile of rhEPO demonstrated the presence of low amounts of α-1,2-mannosidase resistant high-Man glycoforms. In an attempt to eliminate the α-mannosidase resistant glycoforms, we used a systemic approach to genetically knock-out the remaining members of the BMT family culminating in a quadruple bmt2,4,1,3 knock-out strain. Data presented here conclude that the additive elimination of Bmt2p, Bmt3p and Bmt1p activities are required for total abolition of β-Man-associated glycans and their related antigenicity. Taken together, the elimination of β-Man containing glycoforms represents an important step forward for the Pichia production platform as a suitable system for the production of therapeutic glycoproteins.     

Biodegradation of cellulose by β-glucosidase and cellulase immobilized on a pH-responsive copolymer

Biodegradation of cellulose involves synergistic action of the endoglucanases, exoglucanases and β-glucosidases in cellulase. However, the yield of glucose is limited by the lack of β-glucosidase to hydrolyze cellobiose into glucose. In this study, β-glucosidase as a supplemental enzyme along with cellulase are co-immobilized on a pHresponsive copolymer, poly (MAA-co-DMAEMA-co-BMA) (abbreviated P_MDB, where MAA is α-methacrylic acid, DMAEMA is 2-dimethylaminoethyl methacrylate and BMA is butyl methacrylate). The thermal and storage stabilities of PMDB with immobilized enzymes are improved greatly, compared with those of free cellulase. Biodegradation of cellulose is carried out in a pH-responsive recyclable aqueous two-phase system composed of poly (AA-co- DMAEMA-co-BMA) (abbreviated P_{ADB 3.8}, where AA is acrylic acid) and P_MDB. Insoluble substrate and P_MDB with immobilized cellulase and β-glucosidase (Celluclast 1.5L FG and Novozyme 188, respectively) were biased to the bottom phase, while the product was partitioned to the top phase in the presence of 40 mM (NH₄)₂SO₄. When the degradation reaction of cellulose is carried out with PMDB containing immobilized cellulase and β-glucosidase, the concentration of glucose reaches 4.331 mg/mL after 108 h. The yield of glucose is 50.25% after P_MDB containing the immobilized enzymes is recycled five times.     

Bounded water kinetic model of β-galactosidase in reverse micelles

In the present investigation, -galactosidase was solubilized into Aerosol OT (AOT)/isooctane reverse micelles. Kinetic data for the hydrolysis of o-nitrophenyl--D-galactopyranoside (ONPG) at different pH values and molar ratios of water to AOT (W_o) were collected. It was observed that the usual kinetic model used for -galactosidase catalysis in aqueous systems failed to represent the experimental data. A bounded water model, however, showed a better correlation between enzymatic activity and W_o. In contrast to the aqueous system, controlling the water concentration in the reverse micelles allows the rate constants for the reaction between water molecules and glycosyl-enzyme complexes to be evaluated.     

Recent progress in understanding Alzheimer's β-amyloid structures

The formation of amyloid fibrils, protofibrils and oligomers from the β-amyloid (Aβ) peptide represents a hallmark of Alzheimer's disease. Aβ-peptide-derived assemblies might be crucial for disease onset, but determining their atomic structures has proven to be a major challenge. Progress over the past 5 years has yielded substantial new data obtained with improved methodologies including electron cryo-microscopy and NMR. It is now possible to resolve the global fibril topology and the cross-β sheet organization within protofilaments, and to identify residues that are crucial for stabilizing secondary structural elements and peptide conformations within specific assemblies. These data have significantly enhanced our understanding of the mechanism of Aβ aggregation and have illuminated the possible relevance of specific conformers for neurodegenerative pathologies.     

Top surface blade residues and the central channel water molecules are conserved in every repeat of the integrin-like β-propeller structures

An integrin-like β-propeller domain contains seven repeats of a four-stranded antiparallel β-sheet motif (blades). Previously we described a 3D structural motif within each blade of the integrin-type β-propeller. Here, we show unique structural links that join different blades of the β-propeller structure, which together with the structural motif for a single blade are repeated in a β-propeller to provide the functional top face of the barrel, found to be involved in protein-protein interactions and substrate recognition. We compare functional top face diagrams of the integrin-type β-propeller domain and two non-integrin type β-propeller domains of virginiamycin B lyase and WD Repeat-Containing Protein 5.     

Enhancement of enzymatic hydrolysis rate of olive oil in water by dimethyl β-cyclodextrin

Summary The hydrolysis rate of olive oil byCandida cylindracea lipase in an aqueous solution without surfactants can be increased up to 6-fold by the addition of up to 60 mg/ml of dimethyl -cyclodextrin (DMCD).     

Design and characterization of novel β-cyclodextrin based copolymer materials

Reported herein are the systematic design and characterization of several novel polyurethane (PU) copolymers containing a macrocyclic porogen (β-cyclodextrin; β-CD). These copolymers were synthesized from the reaction between β-CD with different types of diisocyanate linker molecules (e.g., 1,6-hexamethylene diisocyanate (HDI), 4,4′-dicyclohexylmethane diisocyanate (CDI), 4,4′-diphenylmethane diisocyanate (MDI), 1,4-phenylene diisocyanate (PDI) and 1,5-naphthalene diisocyanate (NDI)) at variable synthetic conditions. The copolymers were characterized using diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), solid state ¹³C CP-MAS NMR, ¹H/¹³C solution NMR spectroscopy, thermogravimetric analysis (TGA) and elemental analyses (CHN). The PU copolymers were generally insoluble in water and the optimal preparation of copolymer materials for sorption-based applications is for β-CD/linker synthetic mole ratios from 1:1 to 1:3. The practical upper limit of the crosslink density (∼1:7, β-CD/linker) depends on the steric bulk of the cross linker units.     

Colocalization of β1,4galactosyltransferase with mannose 6-phosphate receptor in monensin-induced TGN-derived structures

Previously, we demonstrated that beta 1,4galactosyltransferase (gal-T1) reversibly segregates from alpha 2,6sialyltransferase (ST6Gal) to swollen vesicles after monensin treatment of the cells. To further explore this phenomenon, we investigated the response to monensin of various Golgi proteins. Within 30 min of monensin treatment, gal-T1 moved from the Golgi apparatus, as defined by localization of giantin, to swollen vesicles whereas ST6Gal, alpha 2,3(N)sialyltransferase, mannosidase II, and N-acetylgalactosaminyltransferase 2 remained associated with the Golgi apparatus. Stably transfected CHO cells exhibited a similar phenomenon of monensin-induced displacement of recombinant gal-T1 to swollen vesicles while recombinant ST6Gal remained colocalized with endogenously expressed giantin. Gal-T1 and the cation-insensitive mannose 6-phosphate receptor colocalized in swollen vesicles as observed at both light and electron microscopic levels. When monensin was replaced by chloroquine, gal-T1 remained arrested in swollen vesicles. Brefeldin A treatment known to cause relocation of Golgi-associated gal-T1 to the endoplasmic reticulum had no effect on gal-T1 trapped in swollen vesicles. This evidence suggests that monensin blocks gal-T1 trafficking in post-Golgi structures and argues against swelling of gal-T1-containing trans Golgi cisternae as previously assumed.     

Crystal structures of Trichoderma reesei β-galactosidase reveal conformational changes in the active site

We have determined the crystal structure of Trichoderma reesei (Hypocrea jecorina) β-galactosidase (Tr-β-gal) at a 1.2? resolution and its complex structures with galactose, IPTG and PETG at 1.5, 1.75 and 1.4? resolutions, respectively. Tr-β-gal is a potential enzyme for lactose hydrolysis in the dairy industry and belongs to family 35 of the glycoside hydrolases (GH-35). The high resolution crystal structures of this six-domain enzyme revealed interesting features about the structure of Tr-β-gal. We discovered conformational changes in the two loop regions in the active site, implicating a conformational selection-mechanism for the enzyme. In addition, the Glu200, an acid/base catalyst showed two different conformations which undoubtedly affect the pK(a) value of this residue and the catalytic mechanism. The electron density showed extensive glycosylation, suggesting a structure stabilizing role for glycans. The longest glycan showed an electron density that extends to the eighth monosaccharide unit in the extended chain. The Tr-β-gal structure also showed a well-ordered structure for a unique octaserine motif on the surface loop of the fifth domain.     

Bioremediation of naphthalene in water by Sphingomonas paucimobilis using new biodegradable surfactants based on poly (ɛ-caprolactone)

New amphiphilic block surfactants ABA based on a central segment of polycaprolactone with different molecular composition were evaluated in the bioremediation of naphthalene in water by Sphingomonas paucimobilis and compared with sodium dodecyl sulphate as reference surfactant (SDS). Also the biodegradation of the new surfactants by bacteria, S. paucimobilis and a mixture of bacteria (Pseudomonas aureginosa, Bacillus subtilis, Bacillus amyloliquefaciens and Bacillus megaterium) was studied by indirect impedance technique and carbon dioxide determination. All the bacteria biodegraded in solution and micellar phase the central segment of PCL with mineralization rates in the range of 0.024–0.036 mg of CO₂ per day.S. paucimobilis biodegraded naphthalene in the presence of the new surfactants and GC analysis demonstrated that conversion to products started immediately after inoculum. In all the experiments, except for SDS, at 140 h of incubation time, the remaining naphthalene concentration was about 10% of the initial concentration. In contrast, the production of CO₂ was delayed 4–7 days and values around 75% of naphthalene mineralization degree were achieved in three weeks. The addition of PCL-surfactants, in solution and in micellar phase, not interfered in the naphthalene mineralization. These results have shown promising potential of these biodegradable PCL-surfactants in surfactant-enhanced remediation (SER) technology for removing residual organics from contaminated groundwater and soils.     

The use of β-galactosidase as a tracer in immunocytochemistry

Summary A new immunocytochemical method using -galactosidase as a tracer is described. The positive staining appears blue on an unstained background. The present method has the high sensitivity and specificity of the immunoperoxidase method and appears to be a practical alternative. The substrate has no carcinogenic activity. Staining is permanent and the sections can be dehydrated and mounted in synthetic media. Enzyme and substrate solutions are stable for several months.     

Studies on the rules of β-strand alignment in a protein β-sheet structure

To further disclose the underlying mechanisms of protein β-sheet formation, studies were made on the rules of β-strands alignment forming β-sheet structure using statistical and machine learning approaches. Firstly, statistical analysis was performed on the sum of β-strands between each β-strand pairs in protein sequences. The results showed a propensity of near-neighbor pairing (or called “first come first pair”) in the β-strand pairs. Secondly, based on the same dataset, the pairwise cross-combinations of real β-strand pairs and four pseudo-β-strand contained pairs were classified by support vector machine (SVM). A novel feature extracting approach was designed for classification using the average amino acid pairing encoding matrix (APEM). Analytical results of the classification indicated that a segment of β-strand had the ability to distinguish β-strands from segments of α-helix and coil. However, the result also showed that a β-strand was not strongly conserved to choose its real partner from all the alternative β-strand partners, which was corresponding with the ordination results of the statistical analysis each other. Thus, the rules of “first come first pair” propensity and the non-conservative ability to choose real partner, were possible important factors affecting the β-strands alignment forming β-sheet structures.     

1H NMR study of rehydration/dehydration and water mobility in β-cyclodextrin

The processes of dehydration and rehydration of β-cyclodextrin were studied by analysis of the (1)H NMR (nuclear magnetic resonance) line shape. Dehydration was carried in an open ampoule as a function of temperature and above 400 K total dehydration of β-cyclodextrin was observed. This result was confirmed by the thermogravimetry (TG) measurements. Rehydration was studied as a function of time at room temperature. After 40 days, β-cyclodextrin was found to absorb eight water molecules. The analysis of temperature changes in the shape of the (1)H NMR line of β-cyclodextrin kept in a closed ampoule and its dielectric measurements provided information on the mobility of water molecules. The water molecules were found to perform complex molecular motions, that is, reorientational jumps below 200K and additionally, translational motion (diffusion) above 200K.     

An algorithm for smoothly tessellating β-sheet structures in proteins

An algorithm is presented for tiling the surface of β-sheet structures, smoothed both along the strands and perpendicular to them. The algorithm is intended for creating graphical representations of β structure within the three-dimensional context of proteins. This article presents sufficient detail to allow a programmer with some knowledge of protein structure to implement the tiling algorithm. Several examples of its use are illustrated.     

A native disulfide stabilizes non-native helical structures in partially folded states of equine β-lactoglobulin

Equine β-lactoglobulin (ELG) assumes non-native helices during refolding and in partially folded states. Previously, circular dichroism (CD) combined with site-directed mutagenesis identified helical regions in the acid- and cold-denatured states of ELG. It is also known that a fragment of ELG, CHIBL (residues 88-142), has a structure similar to that of the cold-denatured state. For the study reported herein, the structure of a shorter fragment, CHIBLΔF (residues 97-142), was investigated by CD and nuclear magnetic resonance spectroscopy. The secondary chemical shifts clearly showed that non-native α-helices are present in two different regions, residues 98-107 and 114-135, and are connected by a native disulfide bond. The CD spectra of two peptides that correspond to the helical regions are characterized by weak helical signatures, and the sum of their CD spectra is nearly the same as the spectrum of disulfide-reduced CHIBLΔF. Therefore, the non-native helices are stabilized by the disulfide, and non-native helix formation may occur only during the refolding of the disulfide-intact protein. Supporting this conclusion is the observation that tear lipocalin, a homologue of ELG that lacks the disulfide, does not form non-native helices during folding.     

Phenols in reproductive and somatic structures of lichens: a case of optimal defence?

Optimal defence theory (ODT) attempts to explain variation in plant secondary compounds between different species, different growth conditions and different parts of individual plants. The theory is widely applied to vascular plants and more recently also to seaweeds. Surprisingly, ODT has gained little attention as potential explanation on the distribution of lichen secondary metabolites. In the present study, we analysed intrathalline variation in total phenol content and phenol spectra between reproductive and somatic structures of three foliose lichens, Xanthoria parietina , Vulpicida pinastri and Hypogymnia physodes . The results showed that the concentration of phenolic compounds is higher in sorediate than in non-sorediate lobe ends of V. pinastri and H. physodes as well as in apothecia of X. parietina compared to other parts of the thallus. These results were in accordance with ODT predicting higher allocation of phenols in structures that are most important for the fitness of an individual genet or ramet. This pattern was parallel in all species regardless whether the compounds originate from either acetate-mevalonate or shikimic acid pathways. Moreover, both sexual ( X. parietina apothecia) and asexual (soralia of V. pinastri and H. physodes ) reproductive structures were higher in phenols compared to somatic tissue.     

Evaluation of GFP Tag as a Screening Reporter in Directed Evolution of a Hyperthermophilic β-Glucosidase

By applying a directed evolution methodology specific enzymatic characteristics can be enhanced, but to select mutants of interest from a large mutant bank, this approach requires high throughput screening and facile selection. To facilitate such primary screening of enhanced clones, an expression system was tested that uses a green fluorescent protein (GFP) tag from Aequorea victoria linked to the enzyme of interest. As GFP’s fluorescence is readily measured, and as there is a 1:1 molar correlation between the target protein and GFP, the concept proposed was to determine whether GFP could facilitate primary screening of error-prone PCR (EPP) clones. For this purpose a thermostable β-glucosidase (BglA) from Fervidobacterium sp. was used as a model enzyme. A vector expressing the chimeric protein BglA-GFP-6XHis was constructed and the fusion protein purified and characterized. When compared to the native proteins, the components of the fusion displayed modified characteristics, such as enhanced GFP thermostability and a higher BglA optimum temperature. Clones carrying mutant BglA proteins obtained by EPP, were screened based on the BglA/GFP activity ratio. Purified tagged enzymes from selected clones resulted in modified substrate specificity.