RESUMEN

Surface functioned magnetic silica particles are efficient carriers to achieve facilitated separation and recycling of biocatalysts. However, traditional methods of modifying magnetic silica particles required time-costly sequential coating and surface modification steps and toxic solvents. Herein, a green and efficient routine was proposed to prepare the surface modified silica-coated magnetic microspheres (SCEs@SiO2 @Fe3O4) in one-pot. The elastin-like polypeptides (ELPs)-SpyCatcher chimera (SCEs) were purified by inverse transition cycling with high yield (275 mg/L) and incorporated into the magnetic silica spheres based on the biomimetic silicification capability of ELPs as proved by the EDS and SEM mapping. No SCEs leaked was observed within 48 h, indicating excellent stability in buffer. Then, the biofunctionalized carriers were used to purify and immobilize the target dual enzymes (xylanase-linker-SpyTag-linker-lichenase, bienzymes) directly from the crude cell lysis solution by the spontaneous isopeptide bond reaction between SpyCatcher and SpyTag. The immobilized bienzymes were sphere-like magnetic silica particles with uniform size, which had good magnetic responsiveness. The immobilization yield, immobilization efficiency and activity recovery for xylanase were 86%, 84 % and 72 %, while for lichenase was 92 %, 86 % and 79 %, respectively. Besides, the immobilized bienzymes showed good reusability (>60 %, 10 times for xylanase, >95 %, 8 times for lichenase). The SCEs modified silica-coated magnetic microspheres are expected to provide versatile platforms for single-step of purification and immobilization of multienzymes, offering great potentials in the field of biocatalysis.

Asunto(s)

Enzimas Inmovilizadas , Dióxido de Silicio , Enzimas Inmovilizadas/química , Dióxido de Silicio/química , Biomimética , Microesferas , Fenómenos Magnéticos

RESUMEN

Enzyme separation, purification, immobilization, and catalytic performance improvement have been the research hotspots and frontiers as well as the challenges in the field of biocatalysis. Thus, the development of novel methods for enzyme purification, immobilization, and improvement of their catalytic performance and storage are of great significance. Herein, ferritin was fused with the lichenase gene to achieve the purpose. The results showed that the fused gene was highly expressed in the cells of host strains, and that the resulted fusion proteins could self-aggregate into carrier-free active immobilized enzymes in vivo. Through low-speed centrifugation, the purity of the enzymes was up to > 90%, and the activity recovery was 61.1%. The activity of the enzymes after storage for 608 h was higher than the initial activity. After being used for 10 cycles, it still maintained 50.0% of the original activity. The insoluble active lichenase aggregates could spontaneously dissolve back into the buffer and formed the soluble polymeric lichenases with the diameter of about 12 nm. The specific activity of them was 12.09 times that of the free lichenase, while the catalytic efficiency was 7.11 times and the half-life at 50 ℃ was improved 11.09 folds. The results prove that the ferritin can be a versatile tag to trigger target enzyme self-aggregation and oligomerization in vivo, which can simplify the preparation of the target enzymes, improve their catalysis performance, and facilitate their storage.

Asunto(s)

Ferritinas , Glicósido Hidrolasas , Biocatálisis , Enzimas Inmovilizadas/metabolismo , Ferritinas/genética , Ferritinas/metabolismo , Glicósido Hidrolasas/genética , Glicósido Hidrolasas/metabolismo

RESUMEN

Acidic xylanases possess the unique features necessary for the tolerance of acidic environments, which may have great potentials for industrial purposes. However, factors controlling the pH-dependent stability of xylanases are only partially known. Here we proposed a residue interaction networks based method to analyze the differences of residue interactions between 6 pairs of experimentally verified acidic and neutral xylanases. They had very close numbers of aromatic amino acids, however extremely significant more (p < 0.001) π-π stacking interactions existed in acidic xylanases, which has not been reported before. Whereas the interactions between Tyrosine-Phenylalanine (Tyr-Phe) and Phenylalanine-Phenylalanine (Phe-Phe) were the main contributors. An equation quantitatively described the relationship between the optimal pH and the number of π-π stacking interactions was proposed. The predicted optimal pHs for three xylanases was 4.13, 6.7 and 6.1, while the experimental values of the optimum pHs were 4.6, 6.5 and 6.5, with an absolute error of 0.47, 0.2 and 0.4 pH unit, respectively. By counting the aromatic residue pairs forming π-π stacking in the 3D structure of an acidic (PDB ID: 1BK1, with an optimal pH of 2) and a neutral (PDB ID:1XXN, with an optimal pH of 6.5) xylanase, we found significant differences existed in the positions ranging from 145 to 166 in forming π-π stacking. Two phenylalanines at position 149 and 157 in the acidic xylanase, which involved in 7 π-π stacking interactions, played an important role in the stability of xylanase at low pH environment, which was further proved by a mutation experiment. A mutated xylanase with Phe149 → Ala149 and Phe157 → Ala157 was expressed and purified, resulting the optimal pH shifted from 2 to 4.5. The interaction networks based method paved a new way in underlying and engineering the acid-stability of xylanase, as well as the characteristics of other enzymes.

Asunto(s)

Proteínas Bacterianas/química , Endo-1,4-beta Xilanasas/química , Fenilalanina/química , Tirosina/química , Alanina/química , Alanina/metabolismo , Secuencia de Aminoácidos , Bacillus subtilis/química , Bacillus subtilis/enzimología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Clonación Molecular , Endo-1,4-beta Xilanasas/genética , Endo-1,4-beta Xilanasas/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Concentración de Iones de Hidrógeno , Isoenzimas/química , Isoenzimas/genética , Isoenzimas/metabolismo , Cinética , Modelos Moleculares , Mutación , Fenilalanina/metabolismo , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Alineación de Secuencia , Homología de Secuencia de Aminoácido , Especificidad por Sustrato , Tirosina/metabolismo

RESUMEN

ß-1, 3-Xylanase is one of the most important hydrolytic enzymes to prepare oligosaccharides as functional foods in seaweed industry. However, less than five ß-1, 3-xylanases have been experimentally expressed and characterized; moreover, none of them is psychrophilic and salt tolerant. Here, we mined a novel ß-1, 3-xylanase (Xyl512) from the genome of the deep-sea bacterium Flammeovirga pacifica strain WPAGA1 and biochemically characterized it in detail. The Xyl512 did not contain any carbohydrate-binding module; the catalytic domain of it belonged to the glycoside hydrolase family 26. The optimum temperature and pH of the purified ß-1, 3-xylanase was 20 °C and pH 7.0 in the condition of no NaCl. However, they shifted to 30 °C and 7.5 with 1.5 mol/L NaCl, respectively. In this condition (1.5 mol/L NaCl), the overall activity was 2-fold as high as that without NaCl. Based on the residue interactions and the electrostatic surfaces, we addressed the possible mechanism of its adaption to low temperature and relative high NaCl concentration. The Xyl512 showed significantly reduced numbers of hydrogen bonds leading to a more flexible structure, which is likely to be responsible for its cold adaptation. While the negatively charged surface may contribute to its salt tolerance. The ß-1, 3-xylanase we identified here was the first reported psychrophilic and halophilic one with functionally characterized. It could make new contributions to exploring and studying the ß-1, 3-xylanase for further associated investigations.

Asunto(s)

Bacteroidetes/enzimología , Endo-1,4-beta Xilanasas/metabolismo , Océanos y Mares , Endo-1,4-beta Xilanasas/química , Endo-1,4-beta Xilanasas/aislamiento & purificación , Estabilidad de Enzimas/efectos de los fármacos , Concentración de Iones de Hidrógeno , Hidrólisis , Cinética , Modelos Moleculares , Proteínas Recombinantes/aislamiento & purificación , Análisis de Secuencia de Proteína , Cloruro de Sodio/farmacología , Electricidad Estática , Temperatura

RESUMEN

BACKGROUND: Effective and simple methods that lead to higher enzymatic efficiencies are highly sough. Here we proposed a foldon-triggered trimerization of the target enzymes with significantly improved catalytic performances by fusing a foldon domain at the C-terminus of the enzymes via elastin-like polypeptides (ELPs). The foldon domain comprises 27 residues and can forms trimers with high stability. RESULTS: Lichenase and xylanase can hydrolyze lichenan and xylan to produce value added products and biofuels, and they have great potentials as biotechnological tools in various industrial applications. We took them as the examples and compared the kinetic parameters of the engineered trimeric enzymes to those of the monomeric and wild type ones. When compared with the monomeric ones, the catalytic efficiency (k cat /K m ) of the trimeric lichenase and xylanase increased 4.2- and 3.9- fold. The catalytic constant (k cat ) of the trimeric lichenase and xylanase increased 1.8- fold and 5.0- fold than their corresponding wild-type counterparts. Also, the specific activities of trimeric lichenase and xylanase increased by 149% and 94% than those of the monomeric ones. Besides, the recovery of the lichenase and xylanase activities increased by 12.4% and 6.1% during the purification process using ELPs as the non-chromatographic tag. The possible reason is the foldon domain can reduce the transition temperature of the ELPs. CONCLUSION: The trimeric lichenase and xylanase induced by foldon have advantages in the catalytic performances. Besides, they were easier to purify with increased purification fold and decreased the loss of activities compared to their corresponding monomeric ones. Trimerizing of the target enzymes triggered by the foldon domain could improve their activities and facilitate the purification, which represents a simple and effective enzyme-engineering tool. It should have exciting potentials both in industrial and laboratory scales.

Asunto(s)

Bacillus subtilis/fisiología , Endo-1,4-beta Xilanasas/química , Escherichia coli/fisiología , Mejoramiento Genético/métodos , Glicósido Hidrolasas/química , Ingeniería de Proteínas/métodos , Catálisis , Endo-1,4-beta Xilanasas/biosíntesis , Endo-1,4-beta Xilanasas/genética , Activación Enzimática , Evolución Molecular , Regulación Bacteriana de la Expresión Génica/genética , Regulación Enzimológica de la Expresión Génica/genética , Glicósido Hidrolasas/biosíntesis , Glicósido Hidrolasas/genética , Dominios Proteicos , Pliegue de Proteína , Multimerización de Proteína/genética , Especificidad por Sustrato

RESUMEN

Many factors influence the elastin-like polypeptides (ELPs) self-assembled into micron-sized particles. However, few efforts were made to investigate these factors. Using the ELPs [KV8F]n as the target, we studied systematically the factors with the dynamic light scattering. Our results show that the particle size increased and the uniform of particles decreased with the increase of the molecular weight. The analysis of size variation in self-assembled ELPs in response to changes in salt concentration indicated that the size increased with increasing the salt concentration, and the opposite response was observed when the concentration was above 0.4 mol/L. Under these conditions, the particles are micron-sized and larger than 1.1 µm. However, when the fusions containing the same ELPs and xylanase or 1,3-propanediol oxidoreductase, the size of the self-assembled ELPs particles decreased dramatically, which was only about 1/10 of that of the free ELPs. We proposed that the solvent accessible charged area of the enzymes could interact with the ELPs, the sterical hindrance of the enzymes prevent the aggregation of the ELPs. This might be the most important parameter in altering the particle size sharply.

Asunto(s)

Elastina/química , Péptidos/química , Peso Molecular , Tamaño de la Partícula , Sales (Química)/química

RESUMEN

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the authors. When using the resampling method to preprocess the raw data of the paper used, some of the types of the proteins (i.e., the HI, HO and NP) were changed; thus, the predicting accuracy cannot reflect the real results. This means the effectiveness of resampling methods in this article gives false results. The Publisher apologizes for any inconvenience this may cause.

RESUMEN

Understanding of proteins adaptive to hypersaline environment and identifying them is a challenging task and would help to design stable proteins. Here, we have systematically analyzed the normalized amino acid compositions of 2121 halophilic and 2400 non-halophilic proteins. The results showed that halophilic protein contained more Asp at the expense of Lys, Ile, Cys and Met, fewer small and hydrophobic residues, and showed a large excess of acidic over basic amino acids. Then, we introduce a support vector machine method to discriminate the halophilic and non-halophilic proteins, by using a novel Pearson VII universal function based kernel. In the three validation check methods, it achieved an overall accuracy of 97.7%, 91.7% and 86.9% and outperformed other machine learning algorithms. We also address the influence of protein size on prediction accuracy and found the worse performance for small size proteins might be some significant residues (Cys and Lys) were missing in the proteins.

Asunto(s)

Técnicas de Química Analítica/métodos , Proteínas/química , Cloruro de Sodio/química , Máquina de Vectores de Soporte , Aminoácidos/química , Interacciones Hidrofóbicas e Hidrofílicas , Modelos Biológicos , Tamaño de la Partícula

RESUMEN

Traditional bioinformatics methods performed systematic comparison between the halophilic proteins and their non-halophilic homologues, to investigate the features related to hypersaline adaptation. Therefore, proposing some quantitative models to explain the sequence-characteristic relationship of halophilic proteins might shed new light on haloadaptation and help to design new biocatalysts adapt to high salt concentration. Five machine learning algorithm, including three linear and two non-linear methods were used to discriminate halophilic and their non-halophilic counterparts and the prediction accuracy was encouraging. The best prediction reliability for halophilic proteins was achieved by artificial neural network and support vector machine and reached 80 %, for non-halophilic proteins, it was achieved by linear regression and reached 100 %. Besides, the linear models have captured some clues for protein halo-stability. Among them, lower frequency of Ser in halophilic protein has not been report before.

Asunto(s)

Algoritmos , Aminoácidos/química , Inteligencia Artificial , Proteínas/química , Cloruro de Sodio/química , Biología Computacional , Análisis de Componente Principal , Análisis de Regresión

RESUMEN

Background: Support vector machine (SVM), a novel powerful machine learning technology, was used to develop the non-linear quantitative structure-property relationship (QSPR) model of the G/11 xylanase based on the amino acid composition. The uniform design (UD) method was applied to optimize the running parameters of SVM for the first time. Results: Results showed that the predicted optimum temperature of leave-one-out (LOO) cross-validation fitted the experimental optimum temperature very well, when the running parameter C, ξ, and γ was 50, 0.001 and 1.5, respectively. The average root-mean-square errors (RMSE) of the LOO cross-validation were 9.53ºC, while the RMSE of the back propagation neural network (BPNN), was 11.55ºC. The predictive ability of SVM is a minor improvement over BPNN, but it is superior to the reported method based on stepwise regression. Two experimental examples proved the validation of the model for predicting the optimal temperature of xylanase. Conclusion: The results indicated that UD might be an effective method to optimize the parameters of SVM, which could be used as an alternative powerful modeling tool for QSPR studies of xylanase.

Asunto(s)

Biología Computacional/métodos , /química , Redes Neurales de la Computación , Temperatura , Modelos Logísticos

RESUMEN

Elastin-like polypeptides (ELPs) are temperature sensitive biopolymers composed of a Val-Pro-Gly-Xaa-Gly pentapeptide repeat that derived from a structural motif found in mammalian elastin. It was a promising tag for recombinant protein purification. Here, we de novo designed a novel ELPs gene and cloned it into the modified expression vector pET-22b(+). Then, we transformed the recombinant expression vector pET-22b-ELPs into Escherichia coli BL21(DE3). Upon induction by Isopropyl beta-D-Thiogalactoside (IPTG), ELPs was expressed and purified by a non-chromatographic purification method named inverse temperature cycling. The influences of salts types and concentrations on ELPs were also determined. The results showed that the transition temperature of the [KV8F-20] decreased to 19 degrees C by 0.4 mmol/L Na2CO3. Due to its small molecular weight and sensitivity to salt, the ELPs might be a useful purification tag, which can provide a reliable and simple non-chromatographic method for purification of the recombinant protein by inverse transition cycling.

Asunto(s)

Elastina/aislamiento & purificación , Péptidos/aislamiento & purificación , Proteínas Recombinantes/aislamiento & purificación , Cloruro de Sodio/farmacología , Cromatografía , Elastina/biosíntesis , Elastina/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Vectores Genéticos/genética , Péptidos/genética , Péptidos/metabolismo , Proteínas Recombinantes/biosíntesis , Proteínas Recombinantes/genética