Biochemical characterization and immobilization of a novel pectate lyase ErPL2 for efficient preparation of pectin oligosaccharides

Pectate lyase (ErPL2) from Echinicola rosea JL3085 showed maximal activity at 45 °C and pH 9.0 with 0.6 mM CaCl₂. The K_m and V_max values of ErPL2 for polygalacturonic sodium were 2.098 mmol/L and 0.955 mmol/s, respectively. ErPL2 endolytically degraded pectic substances into oligosaccharides with degree of polymerization (DP) 1-5. To improve the thermostability and pH operation range, recombinant ErPL2 was immobilized onto mesoporous titanium oxide particles (MTOPs). MTOPs have abundant hydroxyl groups on the surface, which is a non-toxicity and good biocompatibility carrier. The residual enzyme activity of immobilized ErPL2 at 40 °C increased remarkably from 11% to 91% compared with free enzyme. The operable pH range was extended from 8-9 to 9-11. Surprisingly, the catalytic efficiency of immobilized ErPL2 was about 19 times higher than free enzyme. To our knowledge this is the first attempt of pectate lyase immobilized on MTOPs and it provides a new option for improving the catalytic performance.

Biochemical, structural and physical changes in aging human skin, and their relationship

Skin is the largest organ of the human body, having the purpose of regulating temperature, protecting us from microbes or mechanical shocks, and allowing the sensations from touch. It is generally accepted that aging induces profound changes in the skin's biochemical, structural and physical properties, which can lead to impaired biological functions and/or diverse diseases. So far, the effects of aging on these skin properties have been well documented. However, very few studies have focused exclusively on the relationship among these critical properties in the aging process, which is this review's primary focus. Many in vivo, ex vivo, and in vitro techniques have been previously used to characterize these properties of the skin. This review aims to provide a comprehensive overview on the effects of aging on the changes in biochemical, structural, and physical properties, and explore the potential mechanisms of skin with the relation between these properties. First, we review different or contradictory results of aging-related changes in representative parameters of each property, including the interpretations of the findings. Next, we discuss the need for a standardized method to characterize aging-related changes in these properties, to improve the way of defining age-property relationship. Moreover, potential mechanisms based on the previous results are explored by linking the biochemical, structural, and physical properties. Finally, the need to study changes of various functional properties in the separate skin layers is addressed. This review can help understand the underlying mechanism of aging-related alterations, to improve the evaluation of the aging process and guide effective treatment strategies for aging-related diseases.

Opinion: What do rescue experiments with heterologous proteins tell us and what not?

The recent progress in sequencing technology allowed the compilation of gene lists for a large number of organisms, though many of these organisms are hardly experimentally tractable when compared with well-established model organisms. One popular approach to further characterize genes identified in a poorly tractable organism is to express these genes in a model organism, and then ask what the protein does in this system or if the gene is capable of replacing the homologous endogenous one when the latter is mutated. While this is a valid approach for certain questions, I argue that the results of such experiments are frequently wrongly interpreted. If, for example, a gene from a parasitic nematode is capable of replacing its homologous gene in the model nematode Caenorhabditis elegans, it is often concluded that the gene is most likely involved in the same biological process in its own organism as the C. elegans gene is in C. elegans. This conclusion is not valid. All this experiment tells us is that the chemical properties of the parasite protein are similar enough to the ones of the C. elegans protein that it can perform the function of the C. elegans protein in C. elegans. Here I discuss this misconception and illustrate it using the analog of similar electric switches (components) controlling various devices (processes).

An integrated deep learning and dynamic programming method for predicting tumor suppressor genes, oncogenes, and fusion from PDB structures

Mutations in proto-oncogenes (ONGO) and the loss of regulatory function of tumor suppression genes (TSG) are the common underlying mechanism for uncontrolled tumor growth. While cancer is a heterogeneous complex of distinct diseases, finding the potentiality of the genes related functionality to ONGO or TSG through computational studies can help develop drugs that target the disease. This paper proposes a classification method that starts with a preprocessing stage to extract the feature map sets from the input 3D protein structural information. The next stage is a deep convolutional neural network stage (DCNN) that outputs the probability of functional classification of genes. We explored and tested two approaches: in Approach 1, all filtered and cleaned 3D-protein-structures (PDB) are pooled together, whereas in Approach 2, the primary structures and their corresponding PDBs are separated according to the genes' primary structural information. Following the DCNN stage, a dynamic programming-based method is used to determine the final prediction of the primary structures' functionality. We validated our proposed method using the COSMIC online database. For the ONGO vs TSG classification problem the AUROC of the DCNN stage for Approach 1 and Approach 2 DCNN are 0.978 and 0.765, respectively. The AUROCs of the final genes' primary structure functionality classification for Approach 1 and Approach 2 are 0.989, and 0.879, respectively. For comparison, the current state-of-the-art reported AUROC is 0.924. Our results warrant further study to apply the deep learning models to humans' (GRCh38) genes, for predicting their corresponding probabilities of functionality in the cancer drivers.

Preparation and Irreversible Inhibition Mechanism Insight into a Recombinant Kunitz Trypsin Inhibitor from Glycine max L. Seeds

Soybean Kunitz trypsin inhibitor (SKTI), extracted from soybean (Glycine max L.) seeds, possesses insect resistance and anti-tumor properties. But its specific mechanisms of action are not yet known. This article reports an efficient method to produce recombinant SKTI (rSKTI) in Escherichia coli, reveals some biochemical properties of rSKTI, and discusses the inhibition mechanism of SKTI. The rSKTI was expressed as inclusion body in E. coli BL21 (DE3). After refolding, the active rSKTI was obtained and was further purified with anion-exchange chromatography (DEAE-FF) efficiently. There were similar biochemical properties between SKTI and rSKTI. The optimum pH and the optimum temperature were pH 8.0 and 35 °C, respectively, being stable during pH 7.0-11.0 and below 37 °C. The activity against trypsin was inhibited by Co2+, Mn2+, Fe3+, Al3+, and epoxy chloropropane. Inhibition kinetic assay of SKTI against trypsin as Lineweaver-Burk plots analysis both showed an unchanged Km and a decreased Vmax with N-benzoyl-L-arginine ethyl ester (BAEE) as substrate. Molecular modeling showed Arg63 of SKTI (active residue of SKTI) that interacts with four residues of trypsin, including three catalytic site (His57, Asp102, and Ser195) and one binding site (Asp189), forming five interactions. These provide reference for understanding the inhibition mechanism of such kind of Kunitz trypsin inhibitors.

Purification and biochemical characterization of a novel transglutaminase from Mythimna separata larvae (Noctuidae, Lepidoptera)

A novel transglutaminase (MsTGase) from Mythimna separata larvae was separated and purified; its biochemical property and enzymatic catalytic activities were investigated. MsTGase was obtained chromatographically by the precipitation of Sephadex G-100 gel and DEAE-Cellulose-52 ion-exchange column with 48-fold purification and a reproducible yield of approximately 12%. Molecular weight of the MsTGase was 63.5 KDa and its N-terminal amino acid sequence was GKIEEG-LVI. Michaelis constant of the MsTGase for the substrate N-CBZ-Gln-Gly was 12.83mM with a V_max of 7.99U/mL. Optimum conditions for MsTGase activity were at 42°C and pH7.5. The enzyme didn't possess metal ion at its catalytic active site; its activity could be significantly inhibited by Mg²⁺, but activated by Ca²⁺. Chlorpyrifos and spinosad showed a strong potential to increase MsTGase activity, supporting the view that MsTGase was a novel target. Moreover, the formation of intermolecular cross-links of casein and bovine serum albumin polymerized by MsTGase in the presence of DTT was observed. These findings pave the way for future studies on the physiological role of MsTGase and the potential impact of its regulation on MsTGase-associated pest management.

Data on the effect of hypomyelinating leukodystrophy 6 (HLD6)-associated mutations on the TUBB4A properties

Hypomyelinating leukodystrophy (HLD) is genetic demyelinating or dysmyelinating disease and is associated with at least 13 responsible genes. The mutations seem likely cause the functional deficiency of their gene products. HLD4- and HLD5-associated HSPD1 and FAM126A mutations affect biochemical properties of the gene products (Miyamoto et al. (2015,2014) [[1], [2]]). Herein we provide the data regarding the effects of HLD6-associated tubulin beta 4A (TUBB4A) mutations on the properties.

The effect of the cytoplasmic tail of influenza C virus CM2 protein on its biochemical properties and intracellular processing

CM2 is an integral membrane protein encoded by the influenza C virus M gene. To examine the effects of the cytoplasmic tail of CM2 on its biochemical properties, deletion and substitution mutations were introduced into CM2 cytoplasmic tail at residues 47–115, and the expressed CM2 mutants were investigated. Although the cytoplasmic tail is not essential for the oligomerization of CM2, it may affect the degree of oligomerization. The residues 47–48, 67–69, 73–90 and 113–115 were all required for the proper expression of CM2. Pulse-chase experiments suggest that residues 47–48, 67–69, 73–75 and 79–87 stabilize CM2, thereby affecting CM2 expression. The C-terminal region at residues 61–115 is not essential for CM2 transport to the cell surface, and a 14-amino-acid, but not an 11-amino-acid, cytoplasmic tail is sufficient for the cell surface expression of CM2. These results suggest that either certain amino acid sequences or the length of the CM2 cytoplasmic tail are necessary for the proper conformational maturation, stability, expression level and intracellular transport of CM2.

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The cytoplasmic tail modulates the efficiency of CM2 oligomerization.

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The residues 47–48, 67–69, 73–90 and 113–115 are required for the proper expression of CM2.

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The residues 47–48, 67–69, 73–75 and 79–87 stabilize CM2.

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Cytoplasmic 14 amino acids are sufficient for the cell surface expression of CM2.

Expression optimization and biochemical properties of two glycosyl hydrolase family 3 beta-glucosidases

The β-glucosidases from Saccharomycopsis fibuligera (SfBGL1) and Trichoderma reesei (TrBGL1) were cloned and expressed in Pichia pastoris. Methanol concentration and pH significantly affected the production. The combined effects of the two factors were optimized by using the response surface method, resulting in a 137% and 84% increase in rTrBGL1 and rSfBGL1 yield compared to single-factor experiment. Structure and biochemical properties of the two enzyme were investigated and compared. They belong to glycosyl hydrolase family 3 and exhibit significant hydrolysis activity and low-level transglycosylation activity. The two enzymes show similar substrate affinity and ion-tolerance, and both of them can be activated by Cr(6+), Mn(2+) and Fe(2+). The rSfBGL1 has greater catalytic speed, higher specific activity and acid-tolerance than rTrBGL1, but rTrBGL1 is more thermostable and has higher optimal temperature than rSfBGL1. This study provides a useful and quick optimal method for recombinant enzyme production and makes a valuable comparison of biochemical properties, which opens important avenues of exploration for relationship between structure and function and further practical applications.

Purification and characterization of a phenoloxidase in the hemocytes of Ephestia kuehniella Zeller (Lepidoptera: Pyralidae): effects of insect growth regulators and endogenous inhibitors

A phenoloxidase was extracted and purified from hemocytes of Ephestia kuehniella by using ammonium sulfate, Sepharyl G-100 and DEAE-Cellulose fast flow chromatographies. At the final stage of purification, a protein was purified by molecular mass of 78.5 kDa, specific activity of 1.17 U/mg protein, recovery of 20.48% and purification fold of 16.71. The purified PO showed the highest activity at pH 4-5 and temperatures of 35-40 °C. Na(+), K(+), Mn(+), Zn(2+) and Mg(2+) decreased activity of the purified PO but Ca(2+) and Cu(2+) increased the enzymatic activity. EDTA (General chelating agent), DTC (Copper chelating agent) and EGTA (Calcium chelating agent) significantly decreased PO activity but TTHA (Magnesium chelating agent) showed no statistically significant effects. Kinetic parameters of the purified enzyme showed the highest Vmax when L-DOPA was used as substrate but no significant differences were observed in case of Km for used L-DOPA, pyrocatechol and hydroquinone. In vitro inhibition of the purified PO by using two insect growth regulators, Hexaflumuron and Pyriproxyfen, revealed IC50 of 96.41 and 38.59 µg/ml for these compounds, respectively. Kinetic studies using different concentrations of L-DOPA and IC50 concentrations of the two IGRs revealed the increase of Km value versus control and competitive inhibition. Finally, column chromatography of hemolymph revealed peak III showing endogenous inhibitors of phenoloxidase by molecular weight of 27.3 that showed competitive inhibition on the PO.

Biosynthesis, structural architecture and biotechnological potential of bacterial tannase: a molecular advancement

Tannin-rich materials are abundantly generated as wastes from several agroindustrial activities. Therefore, tannase is an interesting hydrolase, for bioconversion of tannin-rich materials into value added products by catalyzing the hydrolysis of ester and depside bonds and unlocked a new prospect in different industrial sectors like food, beverages, pharmaceuticals, etc. Microorganisms, particularly bacteria are one of the major sources of tannase. In the last decade, cloning and heterologous expression of novel tannase genes and structural study has gained momentum. In this article, we have emphasized critically on bacterial tannase that have gained worldwide research interest for their diverse properties. The present paper delineate the developments that have taken place in understanding the role of tannase action, microbial sources, various cultivation aspects, downstream processing, salient biochemical properties, structure and active sites, immobilization, efforts in cloning and overexpression and with special emphasis on recent molecular and biotechnological achievements.