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Free and immobilized enzymes for biofuels, biosensing and bioremediation...
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Free and immobilized enzymes for biofuels, biosensing and bioremediation

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (31 January 2020) | Viewed by 22549

Special Issue Editor

Prof. Dr. Andrea Salis

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Guest Editor
Dipartimento di Scienze Chimiche e Geologiche, Università di Cagliari, Cittadella Universitaria, S.S. 554 bivio Sestu, 09042 Monserrato, CA, Italy
Interests: nanostructured materials; ordered mesoporous silica; metal–organic frameworks; nano–bio interfaces and nanobiotechnologies; biocatalysis (enzyme immobilization, enzymatic biofuel production, biosensors); nanomedicine; ion-specific “Hofmeister” effects; biophysical chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biocatalysis is the use of whole living cells or isolated enzymes for biotechnological purposes. To date, enzymes have been used as powerful green biocatalysts in several fields which range from food industry to biosensing. Enzymes drawbacks are related to their high cost and instability. Both issues can be solved by enzyme immobilization on solid supports. This allows the reuse of the enzymes for several reaction cycles and the possibility to run continuous processes and, more importantly, improve their stability. As new nanostructured materials are discovered new immobilized enzymatic biocatalysts are prepared by means of physical adsorption, covalent binding, entrapment or encapsulation. The possibilities are endless. Nonetheless, there are some cases where enzymes must be kept in solution in the “free form” as, for example, when substrates are in the solid phase. Both free and immobilized enzymes can be used for several applications like organic synthesis particularly for the pharmaceutical industry. Since that field has widely been explored the present Special Issue is dedicated to other, likely less investigated, but very important applications of free and immobilized enzymes. In particular, the issue will focus on the immobilization of enzymes on new inorganic (mesoporous silica, metal organic frameworks, etc) and polymeric materials, and on their use for biofuels (biodiesel and bioethanol) production, bioremediation (oxidation of polluting compounds, like dies, phenols, etc.), and for the realization of enzymatic biosensors and biofuel cells.

Prof. Dr. Andrea Salis
Guest Editor

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Keywords

  • Biocatalysis
  • Enzyme immobilization
  • Nanostructured materials as enzyme supports
  • Biofuels (biodiesel and bioethanol)
  • Enzymatic biofuel cells
  • Enzymatic biosensors
  • Enzymatic bioremediation

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Published Papers (5 papers)

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Research

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27 pages, 8613 KiB  
Article
Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential
by Azat Vadimovich Abdullatypov
Int. J. Mol. Sci. 2020, 21(1), 366; https://doi.org/10.3390/ijms21010366 - 6 Jan 2020
Cited by 4 | Viewed by 4631
Abstract
Three-dimensional structures of six closely related hydrogenases from purple bacteria were modeled by combining the template-based and ab initio modeling approach. The results led to the conclusion that there should be a 4Fe3S cluster in the structure of these enzymes. Thus, these hydrogenases [...] Read more.
Three-dimensional structures of six closely related hydrogenases from purple bacteria were modeled by combining the template-based and ab initio modeling approach. The results led to the conclusion that there should be a 4Fe3S cluster in the structure of these enzymes. Thus, these hydrogenases could draw interest for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of the 4Fe3S cluster’s microenvironment showed intragroup heterogeneity. A possible function of the C-terminal part of the small subunit in membrane binding is discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) was carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in the number of hydrophobic interactions and ionic interactions. Molecular tunnels were mapped in the models and compared with structures from the PDB. Protein–protein docking showed that these enzymes could exchange electrons in an oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E. coli, H. marinus, R. eutropha, and S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvi. gelatinosus. Full article
(This article belongs to the Special Issue Free and immobilized enzymes for biofuels, biosensing and bioremediation )
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13 pages, 2068 KiB  
Article
Construction of a Robust Cofactor Self-Sufficient Bienzyme Biocatalytic System for Dye Decolorization and its Mathematical Modeling
by Haitao Ding, Wei Luo, Yong Yu and Bo Chen
Int. J. Mol. Sci. 2019, 20(23), 6104; https://doi.org/10.3390/ijms20236104 - 3 Dec 2019
Cited by 8 | Viewed by 2657
Abstract
A triphenylmethane reductase derived from Citrobacter sp. KCTC 18061P was coupled with a glucose 1-dehydrogenase from Bacillus sp. ZJ to construct a cofactor self-sufficient bienzyme biocatalytic system for dye decolorization. Fed-batch experiments showed that the system is robust to maintain its activity after [...] Read more.
A triphenylmethane reductase derived from Citrobacter sp. KCTC 18061P was coupled with a glucose 1-dehydrogenase from Bacillus sp. ZJ to construct a cofactor self-sufficient bienzyme biocatalytic system for dye decolorization. Fed-batch experiments showed that the system is robust to maintain its activity after 15 cycles without the addition of any expensive exogenous NADH. Subsequently, three different machine learning approaches, including multiple linear regression (MLR), random forest (RF), and artificial neural network (ANN), were employed to explore the response of decolorization efficiency to the variables of the bienzyme system. Statistical parameters of these models suggested that a three-layered ANN model with six hidden neurons was capable of predicting the dye decolorization efficiency with the best accuracy, compared with the models constructed by MLR and RF. Weights analysis of the ANN model showed that the ratio between two enzymes appeared to be the most influential factor, with a relative importance of 54.99% during the decolorization process. The modeling results confirmed that the neural networks could effectively reproduce experimental data and predict the behavior of the decolorization process, especially for complex systems containing multienzymes. Full article
(This article belongs to the Special Issue Free and immobilized enzymes for biofuels, biosensing and bioremediation )
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12 pages, 1899 KiB  
Article
C1 Compound Biosensors: Design, Functional Study, and Applications
by Jin-Young Lee, Bong Hyun Sung, So-Hyung Oh, Kil Koang Kwon, Hyewon Lee, Haseong Kim, Dae-Hee Lee, Soo-Jin Yeom and Seung-Goo Lee
Int. J. Mol. Sci. 2019, 20(9), 2253; https://doi.org/10.3390/ijms20092253 - 7 May 2019
Cited by 13 | Viewed by 5160
Abstract
The microbial assimilation of one-carbon (C1) gases is a topic of interest, given that products developed using this pathway have the potential to act as promising substrates for the synthesis of valuable chemicals via enzymatic oxidation or C–C bonding. Despite extensive studies on [...] Read more.
The microbial assimilation of one-carbon (C1) gases is a topic of interest, given that products developed using this pathway have the potential to act as promising substrates for the synthesis of valuable chemicals via enzymatic oxidation or C–C bonding. Despite extensive studies on C1 gas assimilation pathways, their key enzymes have yet to be subjected to high-throughput evolution studies on account of the lack of an efficient analytical tool for C1 metabolites. To address this challenging issue, we attempted to establish a fine-tuned single-cell–level biosensor system constituting a combination of transcription factors (TFs) and several C1-converting enzymes that convert target compounds to the ligand of a TF. This enzymatic conversion broadens the detection range of ligands by the genetic biosensor systems. In this study, we presented new genetic enzyme screening systems (GESSs) to detect formate, formaldehyde, and methanol from specific enzyme activities and pathways, named FA-GESS, Frm-GESS, and MeOH-GESS, respectively. All the biosensors displayed linear responses to their respective C1 molecules, namely, formate (1.0–250 mM), formaldehyde (1.0–50 μM), and methanol (5–400 mM), and they did so with high specificity. Consequently, the helper enzymes, including formaldehyde dehydrogenase and methanol dehydrogenase, were successfully combined to constitute new versatile combinations of the C1-biosensors. Full article
(This article belongs to the Special Issue Free and immobilized enzymes for biofuels, biosensing and bioremediation )
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13 pages, 2129 KiB  
Article
Accelerated CO2 Hydration with Thermostable Sulfurihydrogenibium azorense Carbonic Anhydrase-Chitin Binding Domain Fusion Protein Immobilised on Chitin Support
by Juan Hou, Xingkang Li, Michal B. Kaczmarek, Pengyu Chen, Kai Li, Peng Jin, Yuanmei Liang and Maurycy Daroch
Int. J. Mol. Sci. 2019, 20(6), 1494; https://doi.org/10.3390/ijms20061494 - 25 Mar 2019
Cited by 30 | Viewed by 4269
Abstract
Carbonic anhydrases (CAs) represent a group of enzymes that catalyse important reactions of carbon dioxide hydration and dehydration, a reaction crucial to many biological processes and environmental biotechnology. In this study we successfully constructed a thermostable fusion enzyme composed of the Sulfurihydrogenibium azorense [...] Read more.
Carbonic anhydrases (CAs) represent a group of enzymes that catalyse important reactions of carbon dioxide hydration and dehydration, a reaction crucial to many biological processes and environmental biotechnology. In this study we successfully constructed a thermostable fusion enzyme composed of the Sulfurihydrogenibium azorense carbonic anhydrase (Saz_CA), the fastest CA discovered to date, and the chitin binding domain (ChBD) of chitinase from Bacillus circulans. Introduction of ChBD to the Saz_CA had no major impact on the effect of ions or inhibitors on the enzymatic activity. The fusion protein exhibited no negative effects up to 60 °C, whilst the fusion partner appears to protect the enzyme from negative effects of magnesium. The prepared biocatalyst appears to be thermally activated at 60 °C and could be partially purified with heat treatment. Immobilisation attempts on different kinds of chitin-based support results have shown that the fusion enzyme preferentially binds to a cheap, untreated chitin with a large crystallinity index over more processed forms of chitin. It suggests significant potential economic benefits for large-scale deployment of immobilised CA technologies such as CO2 utilisation or mineralisation. Full article
(This article belongs to the Special Issue Free and immobilized enzymes for biofuels, biosensing and bioremediation )
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Review

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17 pages, 1835 KiB  
Review
Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization
by Ying Wang, Ling Leng, Md Khairul Islam, Fanghua Liu, Carol Sze Ki Lin and Shao-Yuan Leu
Int. J. Mol. Sci. 2019, 20(13), 3354; https://doi.org/10.3390/ijms20133354 - 8 Jul 2019
Cited by 24 | Viewed by 5189
Abstract
Cellulosomes are an extracellular supramolecular multienzyme complex that can efficiently degrade cellulose and hemicelluloses in plant cell walls. The structural and unique subunit arrangement of cellulosomes can promote its adhesion to the insoluble substrates, thus providing individual microbial cells with a direct competence [...] Read more.
Cellulosomes are an extracellular supramolecular multienzyme complex that can efficiently degrade cellulose and hemicelluloses in plant cell walls. The structural and unique subunit arrangement of cellulosomes can promote its adhesion to the insoluble substrates, thus providing individual microbial cells with a direct competence in the utilization of cellulosic biomass. Significant progress has been achieved in revealing the structures and functions of cellulosomes, but a knowledge gap still exists in understanding the interaction between cellulosome and lignocellulosic substrate for those derived from biorefinery pretreatment of agricultural crops. The cellulosomic saccharification of lignocellulose is affected by various substrate-related physical and chemical factors, including native (untreated) wood lignin content, the extent of lignin and xylan removal by pretreatment, lignin structure, substrate size, and of course substrate pore surface area or substrate accessibility to cellulose. Herein, we summarize the cellulosome structure, substrate-related factors, and regulatory mechanisms in the host cells. We discuss the latest advances in specific strategies of cellulosome-induced hydrolysis, which can function in the reaction kinetics and the overall progress of biorefineries based on lignocellulosic feedstocks. Full article
(This article belongs to the Special Issue Free and immobilized enzymes for biofuels, biosensing and bioremediation )
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