Special Issue "Enzymes and Their Biotechnological Applications"

Quicklinks

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (30 June 2013)

Special Issue Editor

Guest Editor
Prof. Pabulo H. Rampelotto

Center of Biotechnology and PPGBCM, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
Interests: biotechnology; next generation sequencing; metagenomics; molecular biology and biochemistry of microorganisms; extremophiles; grand challenges

Special Issue Information

Dear Colleagues,

The development of new enzymes is one of the most thriving branches of biotechnology. Although the applications of enzymes are already well established in some areas, recent advances in modern biotechnology have revolutionized the development of new enzymes. The use of genetic engineering has further improved manufacturing processes and enabled the commercialization of enzymes that could previously not be produced. Protein engineering and the possibility of introducing small changes to proteins are bringing ever more powerful means of analysis to the study of enzyme structure and its biochemical and biophysical properties, which have leading to the rational modification of enzymes to match specific requirements and also the design of new enzymes with novel properties. The developments in bioinformatics and the availability of sequence data have significantly increased the efficiency of identifying genes with biotech potential from nature. Complementary to chemical synthesis, biosynthesis of drug metabolites with mammalian or microbial bioreactors offers certain advantages, and sometime is the only practical route to the desired metabolite. At the same time, new technological developments are stimulating the chemical and pharmaceutical industry to embrace enzyme technology. Altogether, these advances have made it possible to provide tailor-made enzymes displaying new activities and adapted to new process conditions, enabling a further expansion of their use in several branches of biotechnology. This Special Issue focuses on the discovery and development of new enzymes and their applications in different areas of biotechnology. The Special Issue will contain a collection of papers written by authors who are leading experts in the field including selected papers from the 4th International Symposium on Enzymes & Biocatalysis (SEB-2013). We cordially welcome you to join us in this endeavor. The submission of comprehensive reviews or original research articles is most welcome. It is an opportunity to take part in and to influence future trends in one of the fastest growing fields of research.

Professor Pabulo Henrique Rampelotto
Guest Editor

Submission

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are refereed through a peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed Open Access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 600 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Print Edition available!
A Print Edition of this Special Issue is available here.

Name Pice* Download or order
Enzymes and Their Biotechnological Applications 57.50 CHF here
For contributing authors or bulk orders special prices may apply.
Prices include shipping.

Keywords

  • biocatalysis polymerization and polymer synthesis
  • biocatalysis synthesis of chiral molecules
  • biocatalytic technologies
  • enzyme biosensor
  • enzyme inhibitors
  • environmental enzymology
  • enzymatic protein engineering technology
  • extremophilic enzymes
  • functional genomics and bioinformatics for novel enzymes
  • industrial biotechnology
  • new enzyme development
  • pharmaceutical biotechnology
  • structural and functional characterization of enzymes

Published Papers (21 papers)

View options order results:
result details:
Displaying articles 1-21
Export citation of selected articles as:

Research

Jump to: Review

Open AccessArticle Production of Fungal Glucoamylase for Glucose Production from Food Waste
Biomolecules 2013, 3(3), 651-661; doi:10.3390/biom3030651
Received: 6 August 2013 / Revised: 15 September 2013 / Accepted: 17 September 2013 / Published: 19 September 2013
Cited by 13 | PDF Full-text (398 KB) | HTML Full-text | XML Full-text
Abstract
The feasibility of using pastry waste as resource for glucoamylase (GA) production via solid state fermentation (SSF) was studied. The crude GA extract obtained was used for glucose production from mixed food waste. Our results showed that pastry waste could be used [...] Read more.
The feasibility of using pastry waste as resource for glucoamylase (GA) production via solid state fermentation (SSF) was studied. The crude GA extract obtained was used for glucose production from mixed food waste. Our results showed that pastry waste could be used as a sole substrate for GA production. A maximal GA activity of 76.1 ± 6.1 U/mL was obtained at Day 10. The optimal pH and reaction temperature for the crude GA extract for hydrolysis were pH 5.5 and 55 °C, respectively. Under this condition, the half-life of the GA extract was 315.0 minutes with a deactivation constant (kd) 2.20 × 10−3minutes−1. The application of the crude GA extract for mixed food waste hydrolysis and glucose production was successfully demonstrated. Approximately 53 g glucose was recovered from 100 g of mixed food waste in 1 h under the optimal digestion conditions, highlighting the potential of this approach as an alternative strategy for waste management and sustainable production of glucose applicable as carbon source in many biotechnological processes. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Open AccessArticle A Sensitive DNA Enzyme-Based Fluorescent Assay for Bacterial Detection
Biomolecules 2013, 3(3), 563-577; doi:10.3390/biom3030563
Received: 25 July 2013 / Revised: 9 August 2013 / Accepted: 11 August 2013 / Published: 20 August 2013
Cited by 7 | PDF Full-text (606 KB) | HTML Full-text | XML Full-text
Abstract
Bacterial detection plays an important role in protecting public health and safety, and thus, substantial research efforts have been directed at developing bacterial sensing methods that are sensitive, specific, inexpensive, and easy to use. We have recently reported a novel “mix-and-read” assay [...] Read more.
Bacterial detection plays an important role in protecting public health and safety, and thus, substantial research efforts have been directed at developing bacterial sensing methods that are sensitive, specific, inexpensive, and easy to use. We have recently reported a novel “mix-and-read” assay where a fluorogenic DNAzyme probe was used to detect model bacterium E. coli. In this work, we carried out a series of optimization experiments in order to improve the performance of this assay. The optimized assay can achieve a detection limit of 1000 colony-forming units (CFU) without a culturing step and is able to detect 1 CFU following as short as 4 h of bacterial culturing in a growth medium. Overall, our effort has led to the development of a highly sensitive and easy-to-use fluorescent bacterial detection assay that employs a catalytic DNA. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Open AccessArticle Pyranose Dehydrogenase from Agaricus campestris and Agaricus xanthoderma: Characterization and Applications in Carbohydrate Conversions
Biomolecules 2013, 3(3), 535-552; doi:10.3390/biom3030535
Received: 28 June 2013 / Revised: 9 August 2013 / Accepted: 11 August 2013 / Published: 16 August 2013
Cited by 3 | PDF Full-text (511 KB) | HTML Full-text | XML Full-text
Abstract
Pyranose dehydrogenase (PDH) is a flavin-dependent sugar oxidoreductase that is limited to a rather small group of litter-degrading basidiomycetes. The enzyme is unable to utilize oxygen as an electron acceptor, using substituted benzoquinones and (organo) metal ions instead. PDH displays a broad [...] Read more.
Pyranose dehydrogenase (PDH) is a flavin-dependent sugar oxidoreductase that is limited to a rather small group of litter-degrading basidiomycetes. The enzyme is unable to utilize oxygen as an electron acceptor, using substituted benzoquinones and (organo) metal ions instead. PDH displays a broad substrate specificity and intriguing variations in regioselectivity, depending on substrate, enzyme source and reaction conditions. In contrast to the related enzyme pyranose 2-oxidase (POx), PDHs from several sources are capable of oxidizing α- or β-1→4-linked di- and oligosaccharides, including lactose. PDH from A. xanthoderma is able to perform C-1 and C-2 oxidation, producing, in addition to lactobionic acid, 2-dehydrolactose, an intermediate for the production of lactulose, whereas PDH from A. campestris oxidizes lactose nearly exclusively at the C-1 position. In this work, we present the isolation of PDH-encoding genes from A. campestris (Ac) and A. xanthoderma (Ax) and a comparison of other so far isolated PDH-sequences. Secretory overexpression of both enzymes in Pichia pastoris was successful when using their native signal sequences with yields of 371 U·L−1 for AxPDH and 35 U·L−1 for AcPDH. The pure enzymes were characterized biochemically and tested for applications in carbohydrate conversion reactions of industrial relevance. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Open AccessArticle Lipases Immobilization for Effective Synthesis of Biodiesel Starting from Coffee Waste Oils
Biomolecules 2013, 3(3), 514-534; doi:10.3390/biom3030514
Received: 28 June 2013 / Revised: 4 August 2013 / Accepted: 6 August 2013 / Published: 13 August 2013
Cited by 5 | PDF Full-text (860 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Immobilized lipases were applied to the enzymatic conversion of oils from spent coffee ground into biodiesel. Two lipases were selected for the study because of their conformational behavior analysed by Molecular Dynamics (MD) simulations taking into account that immobilization conditions affect conformational [...] Read more.
Immobilized lipases were applied to the enzymatic conversion of oils from spent coffee ground into biodiesel. Two lipases were selected for the study because of their conformational behavior analysed by Molecular Dynamics (MD) simulations taking into account that immobilization conditions affect conformational behavior of the lipases and ultimately, their efficiency upon immobilization. The enzymatic synthesis of biodiesel was initially carried out on a model substrate (triolein) in order to select the most promising immobilized biocatalysts. The results indicate that oils can be converted quantitatively within hours. The role of the nature of the immobilization support emerged as a key factor affecting reaction rate, most probably because of partition and mass transfer barriers occurring with hydrophilic solid supports. Finally, oil from spent coffee ground was transformed into biodiesel with yields ranging from 55% to 72%. The synthesis is of particular interest in the perspective of developing sustainable processes for the production of bio-fuels from food wastes and renewable materials. The enzymatic synthesis of biodiesel is carried out under mild conditions, with stoichiometric amounts of substrates (oil and methanol) and the removal of free fatty acids is not required. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessArticle Enantiocomplementary Yarrowia lipolytica Oxidoreductases: Alcohol Dehydrogenase 2 and Short Chain Dehydrogenase/Reductase
Biomolecules 2013, 3(3), 449-460; doi:10.3390/biom3030449
Received: 3 July 2013 / Revised: 31 July 2013 / Accepted: 2 August 2013 / Published: 12 August 2013
Cited by 2 | PDF Full-text (302 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Enzymes of the non-conventional yeast Yarrowia lipolytica seem to be tailor-made for the conversion of lipophilic substrates. Herein, we cloned and overexpressed the Zn-dependent alcohol dehydrogenase ADH2 from Yarrowia lipolytica in Escherichia coli. The purified enzyme was characterized in vitro. [...] Read more.
Enzymes of the non-conventional yeast Yarrowia lipolytica seem to be tailor-made for the conversion of lipophilic substrates. Herein, we cloned and overexpressed the Zn-dependent alcohol dehydrogenase ADH2 from Yarrowia lipolytica in Escherichia coli. The purified enzyme was characterized in vitro. The substrate scope for YlADH2 mediated oxidation and reduction was investigated spectrophotometrically and the enzyme showed a broader substrate range than its homolog from Saccharomyces cerevisiae. A preference for secondary compared to primary alcohols in oxidation direction was observed for YlADH2. 2-Octanone was investigated in reduction mode in detail. Remarkably, YlADH2 displays perfect (S)-selectivity and together with a highly (R)-selective short chain dehydrogenase/ reductase from Yarrowia lipolytica it is possible to access both enantiomers of 2-octanol in >99% ee with Yarrowia lipolytica oxidoreductases. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessArticle Enzyme-Catalyzed Synthesis of Unsaturated Aliphatic Polyesters Based on Green Monomers from Renewable Resources
Biomolecules 2013, 3(3), 461-480; doi:10.3390/biom3030461
Received: 15 July 2013 / Revised: 31 July 2013 / Accepted: 1 August 2013 / Published: 12 August 2013
Cited by 20 | PDF Full-text (1232 KB) | HTML Full-text | XML Full-text
Abstract
Bio-based commercially available succinate, itaconate and 1,4-butanediol are enzymatically co-polymerized in solution via a two-stage method, using Candida antarctica Lipase B (CALB, in immobilized form as Novozyme® 435) as the biocatalyst. The chemical structures of the obtained products, poly(butylene succinate) (PBS) and [...] Read more.
Bio-based commercially available succinate, itaconate and 1,4-butanediol are enzymatically co-polymerized in solution via a two-stage method, using Candida antarctica Lipase B (CALB, in immobilized form as Novozyme® 435) as the biocatalyst. The chemical structures of the obtained products, poly(butylene succinate) (PBS) and poly(butylene succinate-co-itaconate) (PBSI), are confirmed by 1H- and 13C-NMR. The effects of the reaction conditions on the CALB-catalyzed synthesis of PBSI are fully investigated, and the optimal polymerization conditions are obtained. With the established method, PBSI with tunable compositions and satisfying reaction yields is produced. The 1H-NMR results confirm that carbon-carbon double bonds are well preserved in PBSI. The differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA) results indicate that the amount of itaconate in the co-polyesters has no obvious effects on the glass-transition temperature and the thermal stability of PBS and PBSI, but has significant effects on the melting temperature. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Review

Jump to: Research

Open AccessReview Microbial Enzymes: Tools for Biotechnological Processes
Biomolecules 2014, 4(1), 117-139; doi:10.3390/biom4010117
Received: 5 November 2013 / Revised: 2 January 2014 / Accepted: 2 January 2014 / Published: 16 January 2014
Cited by 46 | PDF Full-text (310 KB) | HTML Full-text | XML Full-text
Abstract
Microbial enzymes are of great importance in the development of industrial bioprocesses. Current applications are focused on many different markets including pulp and paper, leather, detergents and textiles, pharmaceuticals, chemical, food and beverages, biofuels, animal feed and personal care, among others. Today [...] Read more.
Microbial enzymes are of great importance in the development of industrial bioprocesses. Current applications are focused on many different markets including pulp and paper, leather, detergents and textiles, pharmaceuticals, chemical, food and beverages, biofuels, animal feed and personal care, among others. Today there is a need for new, improved or/and more versatile enzymes in order to develop more novel, sustainable and economically competitive production processes. Microbial diversity and modern molecular techniques, such as metagenomics and genomics, are being used to discover new microbial enzymes whose catalytic properties can be improved/modified by different strategies based on rational, semi-rational and random directed evolution. Most industrial enzymes are recombinant forms produced in bacteria and fungi. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Open AccessReview Research Applications of Proteolytic Enzymes in Molecular Biology
Biomolecules 2013, 3(4), 923-942; doi:10.3390/biom3040923
Received: 15 October 2013 / Revised: 4 November 2013 / Accepted: 6 November 2013 / Published: 8 November 2013
Cited by 5 | PDF Full-text (659 KB) | HTML Full-text | XML Full-text
Abstract
Proteolytic enzymes (also termed peptidases, proteases and proteinases) are capable of hydrolyzing peptide bonds in proteins. They can be found in all living organisms, from viruses to animals and humans. Proteolytic enzymes have great medical and pharmaceutical importance due to their key [...] Read more.
Proteolytic enzymes (also termed peptidases, proteases and proteinases) are capable of hydrolyzing peptide bonds in proteins. They can be found in all living organisms, from viruses to animals and humans. Proteolytic enzymes have great medical and pharmaceutical importance due to their key role in biological processes and in the life-cycle of many pathogens. Proteases are extensively applied enzymes in several sectors of industry and biotechnology, furthermore, numerous research applications require their use, including production of Klenow fragments, peptide synthesis, digestion of unwanted proteins during nucleic acid purification, cell culturing and tissue dissociation, preparation of recombinant antibody fragments for research, diagnostics and therapy, exploration of the structure-function relationships by structural studies, removal of affinity tags from fusion proteins in recombinant protein techniques, peptide sequencing and proteolytic digestion of proteins in proteomics. The aim of this paper is to review the molecular biological aspects of proteolytic enzymes and summarize their applications in the life sciences. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Open AccessReview Biophysical Insights into the Inhibitory Mechanism of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors
Biomolecules 2013, 3(4), 889-904; doi:10.3390/biom3040889
Received: 18 September 2013 / Revised: 22 October 2013 / Accepted: 22 October 2013 / Published: 1 November 2013
PDF Full-text (425 KB) | HTML Full-text | XML Full-text
Abstract
HIV-1 reverse transcriptase (RT) plays a central role in HIV infection. Current United States Federal Drug Administration (USFDA)-approved antiretroviral therapies can include one of five approved non-nucleoside RT inhibitors (NNRTIs), which are potent inhibitors of RT activity. Despite their crucial clinical role [...] Read more.
HIV-1 reverse transcriptase (RT) plays a central role in HIV infection. Current United States Federal Drug Administration (USFDA)-approved antiretroviral therapies can include one of five approved non-nucleoside RT inhibitors (NNRTIs), which are potent inhibitors of RT activity. Despite their crucial clinical role in treating and preventing HIV-1 infection, their mechanism of action remains elusive. In this review, we introduce RT and highlight major advances from experimental and computational biophysical experiments toward an understanding of RT function and the inhibitory mechanism(s) of NNRTIs. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Open AccessReview Biotechnological Applications of Transglutaminases
Biomolecules 2013, 3(4), 870-888; doi:10.3390/biom3040870
Received: 12 September 2013 / Revised: 10 October 2013 / Accepted: 11 October 2013 / Published: 22 October 2013
Cited by 12 | PDF Full-text (764 KB) | HTML Full-text | XML Full-text
Abstract
In nature, transglutaminases catalyze the formation of amide bonds between proteins to form insoluble protein aggregates. This specific function has long been exploited in the food and textile industries as a protein cross-linking agent to alter the texture of meat, wool, and [...] Read more.
In nature, transglutaminases catalyze the formation of amide bonds between proteins to form insoluble protein aggregates. This specific function has long been exploited in the food and textile industries as a protein cross-linking agent to alter the texture of meat, wool, and leather. In recent years, biotechnological applications of transglutaminases have come to light in areas ranging from material sciences to medicine. There has also been a substantial effort to further investigate the fundamentals of transglutaminases, as many of their characteristics that remain poorly understood. Those studies also work towards the goal of developing transglutaminases as more efficient catalysts. Progress in this area includes structural information and novel chemical and biological assays. Here, we review recent achievements in this area in order to illustrate the versatility of transglutaminases. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessReview Biocatalysis for Biobased Chemicals
Biomolecules 2013, 3(4), 812-847; doi:10.3390/biom3040812
Received: 3 September 2013 / Revised: 8 October 2013 / Accepted: 8 October 2013 / Published: 17 October 2013
Cited by 11 | PDF Full-text (674 KB) | HTML Full-text | XML Full-text
Abstract
The design and development of greener processes that are safe and friendly is an irreversible trend that is driven by sustainable and economic issues. The use of Biocatalysis as part of a manufacturing process fits well in this trend as enzymes are [...] Read more.
The design and development of greener processes that are safe and friendly is an irreversible trend that is driven by sustainable and economic issues. The use of Biocatalysis as part of a manufacturing process fits well in this trend as enzymes are themselves biodegradable, require mild conditions to work and are highly specific and well suited to carry out complex reactions in a simple way. The growth of computational capabilities in the last decades has allowed Biocatalysis to develop sophisticated tools to understand better enzymatic phenomena and to have the power to control not only process conditions but also the enzyme’s own nature. Nowadays, Biocatalysis is behind some important products in the pharmaceutical, cosmetic, food and bulk chemicals industry. In this review we want to present some of the most representative examples of industrial chemicals produced in vitro through enzymatic catalysis. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessReview Improvement of Biocatalysts for Industrial and Environmental Purposes by Saturation Mutagenesis
Biomolecules 2013, 3(4), 778-811; doi:10.3390/biom3040778
Received: 21 August 2013 / Revised: 22 September 2013 / Accepted: 23 September 2013 / Published: 8 October 2013
Cited by 4 | PDF Full-text (1286 KB) | HTML Full-text | XML Full-text
Abstract
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and [...] Read more.
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Open AccessReview Biocatalytic Synthesis of Chiral Alcohols and Amino Acids for Development of Pharmaceuticals
Biomolecules 2013, 3(4), 741-777; doi:10.3390/biom3040741
Received: 23 August 2013 / Revised: 22 September 2013 / Accepted: 23 September 2013 / Published: 2 October 2013
Cited by 20 | PDF Full-text (3082 KB) | HTML Full-text | XML Full-text
Abstract
Chirality is a key factor in the safety and efficacy of many drug products and thus the production of single enantiomers of drug intermediates and drugs has become increasingly important in the pharmaceutical industry. There has been an increasing awareness of the [...] Read more.
Chirality is a key factor in the safety and efficacy of many drug products and thus the production of single enantiomers of drug intermediates and drugs has become increasingly important in the pharmaceutical industry. There has been an increasing awareness of the enormous potential of microorganisms and enzymes derived there from for the transformation of synthetic chemicals with high chemo-, regio- and enatioselectivities. In this article, biocatalytic processes are described for the synthesis of chiral alcohols and unntural aminoacids for pharmaceuticals. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessReview Quantum Mechanical Modeling: A Tool for the Understanding of Enzyme Reactions
Biomolecules 2013, 3(3), 662-702; doi:10.3390/biom3030662
Received: 6 August 2013 / Revised: 17 September 2013 / Accepted: 19 September 2013 / Published: 23 September 2013
Cited by 2 | PDF Full-text (1451 KB) | HTML Full-text | XML Full-text
Abstract
Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine [...] Read more.
Most enzyme reactions involve formation and cleavage of covalent bonds, while electrostatic effects, as well as dynamics of the active site and surrounding protein regions, may also be crucial. Accordingly, special computational methods are needed to provide an adequate description, which combine quantum mechanics for the reactive region with molecular mechanics and molecular dynamics describing the environment and dynamic effects, respectively. In this review we intend to give an overview to non-specialists on various enzyme models as well as established computational methods and describe applications to some specific cases. For the treatment of various enzyme mechanisms, special approaches are often needed to obtain results, which adequately refer to experimental data. As a result of the spectacular progress in the last two decades, most enzyme reactions can be quite precisely treated by various computational methods. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Open AccessReview Arming Technology in Yeast—Novel Strategy for Whole-cell Biocatalyst and Protein Engineering
Biomolecules 2013, 3(3), 632-650; doi:10.3390/biom3030632
Received: 23 July 2013 / Revised: 28 August 2013 / Accepted: 2 September 2013 / Published: 9 September 2013
Cited by 6 | PDF Full-text (704 KB) | HTML Full-text | XML Full-text
Abstract
Cell surface display of proteins/peptides, in contrast to the conventional intracellular expression, has many attractive features. This arming technology is especially effective when yeasts are used as a host, because eukaryotic modifications that are often required for functional use can be added [...] Read more.
Cell surface display of proteins/peptides, in contrast to the conventional intracellular expression, has many attractive features. This arming technology is especially effective when yeasts are used as a host, because eukaryotic modifications that are often required for functional use can be added to the surface-displayed proteins/peptides. A part of various cell wall or plasma membrane proteins can be genetically fused to the proteins/peptides of interest to be displayed. This technology, leading to the generation of so-called “arming technology”, can be employed for basic and applied research purposes. In this article, we describe various strategies for the construction of arming yeasts, and outline the diverse applications of this technology to industrial processes such as biofuel and chemical productions, pollutant removal, and health-related processes, including oral vaccines. In addition, arming technology is suitable for protein engineering and directed evolution through high-throughput screening that is made possible by the feature that proteins/peptides displayed on cell surface can be directly analyzed using intact cells without concentration and purification. Actually, novel proteins/peptides with improved or developed functions have been created, and development of diagnostic/therapeutic antibodies are likely to benefit from this powerful approach. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessReview Fungal Beta-Glucosidases: A Bottleneck in Industrial Use of Lignocellulosic Materials
Biomolecules 2013, 3(3), 612-631; doi:10.3390/biom3030612
Received: 23 July 2013 / Revised: 17 August 2013 / Accepted: 20 August 2013 / Published: 3 September 2013
Cited by 33 | PDF Full-text (294 KB) | HTML Full-text | XML Full-text
Abstract
Profitable biomass conversion processes are highly dependent on the use of efficient enzymes for lignocellulose degradation. Among the cellulose degrading enzymes, beta-glucosidases are essential for efficient hydrolysis of cellulosic biomass as they relieve the inhibition of the cellobiohydrolases and endoglucanases by reducing [...] Read more.
Profitable biomass conversion processes are highly dependent on the use of efficient enzymes for lignocellulose degradation. Among the cellulose degrading enzymes, beta-glucosidases are essential for efficient hydrolysis of cellulosic biomass as they relieve the inhibition of the cellobiohydrolases and endoglucanases by reducing cellobiose accumulation. In this review, we discuss the important role beta-glucosidases play in complex biomass hydrolysis and how they create a bottleneck in industrial use of lignocellulosic materials. An efficient beta-glucosidase facilitates hydrolysis at specified process conditions, and key points to consider in this respect are hydrolysis rate, inhibitors, and stability. Product inhibition impairing yields, thermal inactivation of enzymes, and the high cost of enzyme production are the main obstacles to commercial cellulose hydrolysis. Therefore, this sets the stage in the search for better alternatives to the currently available enzyme preparations either by improving known or screening for new beta-glucosidases. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessReview Microbial Enzymes with Special Characteristics for Biotechnological Applications
Biomolecules 2013, 3(3), 597-611; doi:10.3390/biom3030597
Received: 28 June 2013 / Revised: 6 August 2013 / Accepted: 15 August 2013 / Published: 23 August 2013
Cited by 14 | PDF Full-text (173 KB) | HTML Full-text | XML Full-text
Abstract
This article overviews the enzymes produced by microorganisms, which have been extensively studied worldwide for their isolation, purification and characterization of their specific properties. Researchers have isolated specific microorganisms from extreme sources under extreme culture conditions, with the objective that such isolated [...] Read more.
This article overviews the enzymes produced by microorganisms, which have been extensively studied worldwide for their isolation, purification and characterization of their specific properties. Researchers have isolated specific microorganisms from extreme sources under extreme culture conditions, with the objective that such isolated microbes would possess the capability to bio-synthesize special enzymes. Various Bio-industries require enzymes possessing special characteristics for their applications in processing of substrates and raw materials. The microbial enzymes act as bio-catalysts to perform reactions in bio-processes in an economical and environmentally-friendly way as opposed to the use of chemical catalysts. The special characteristics of enzymes are exploited for their commercial interest and industrial applications, which include: thermotolerance, thermophilic nature, tolerance to a varied range of pH, stability of enzyme activity over a range of temperature and pH, and other harsh reaction conditions. Such enzymes have proven their utility in bio-industries such as food, leather, textiles, animal feed, and in bio-conversions and bio-remediations. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessReview Decarboxylation of Pyruvate to Acetaldehyde for Ethanol Production by Hyperthermophiles
Biomolecules 2013, 3(3), 578-596; doi:10.3390/biom3030578
Received: 9 July 2013 / Revised: 2 August 2013 / Accepted: 15 August 2013 / Published: 21 August 2013
Cited by 4 | PDF Full-text (344 KB) | HTML Full-text | XML Full-text
Abstract
Pyruvate decarboxylase (PDC encoded by pdc) is a thiamine pyrophosphate (TPP)-containing enzyme responsible for the conversion of pyruvate to acetaldehyde in many mesophilic organisms. However, no pdc/PDC homolog has yet been found in fully sequenced genomes and proteomes of hyper/thermophiles. [...] Read more.
Pyruvate decarboxylase (PDC encoded by pdc) is a thiamine pyrophosphate (TPP)-containing enzyme responsible for the conversion of pyruvate to acetaldehyde in many mesophilic organisms. However, no pdc/PDC homolog has yet been found in fully sequenced genomes and proteomes of hyper/thermophiles. The only PDC activity reported in hyperthermophiles was a bifunctional, TPP- and CoA-dependent pyruvate ferredoxin oxidoreductase (POR)/PDC enzyme from the hyperthermophilic archaeon Pyrococcus furiosus. Another enzyme known to be involved in catalysis of acetaldehyde production from pyruvate is CoA-acetylating acetaldehyde dehydrogenase (AcDH encoded by mhpF and adhE). Pyruvate is oxidized into acetyl-CoA by either POR or pyruvate formate lyase (PFL), and AcDH catalyzes the reduction of acetyl-CoA to acetaldehyde in mesophilic organisms. AcDH is present in some mesophilic (such as clostridia) and thermophilic bacteria (e.g., Geobacillus and Thermoanaerobacter). However, no AcDH gene or protein homologs could be found in the released genomes and proteomes of hyperthermophiles. Moreover, no such activity was detectable from the cell-free extracts of different hyperthermophiles under different assay conditions. In conclusion, no commonly-known PDCs was found in hyperthermophiles. Instead of the commonly-known PDC, it appears that at least one multifunctional enzyme is responsible for catalyzing the non-oxidative decarboxylation of pyruvate to acetaldehyde in hyperthermophiles. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessReview Carbonic Anhydrases and Their Biotechnological Applications
Biomolecules 2013, 3(3), 553-562; doi:10.3390/biom3030553
Received: 4 July 2013 / Revised: 7 August 2013 / Accepted: 9 August 2013 / Published: 19 August 2013
Cited by 6 | PDF Full-text (139 KB) | HTML Full-text | XML Full-text
Abstract
The carbonic anhydrases (CAs) are mostly zinc-containing metalloenzymes which catalyze the reversible hydration/dehydration of carbon dioxide/bicarbonate. The CAs have been extensively studied because of their broad physiological importance in all kingdoms of life and clinical relevance as drug targets. In particular, human [...] Read more.
The carbonic anhydrases (CAs) are mostly zinc-containing metalloenzymes which catalyze the reversible hydration/dehydration of carbon dioxide/bicarbonate. The CAs have been extensively studied because of their broad physiological importance in all kingdoms of life and clinical relevance as drug targets. In particular, human CA isoform II (HCA II) has a catalytic efficiency of 108 M−1 s−1, approaching the diffusion limit. The high catalytic rate, relatively simple procedure of expression and purification, relative stability and extensive biophysical studies of HCA II has made it an exciting candidate to be incorporated into various biomedical applications such as artificial lungs, biosensors and CO2 sequestration systems, among others. This review highlights the current state of these applications, lists their advantages and limitations, and discusses their future development. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessReview Architecture of Amylose Supramolecules in Form of Inclusion Complexes by Phosphorylase-Catalyzed Enzymatic Polymerization
Biomolecules 2013, 3(3), 369-385; doi:10.3390/biom3030369
Received: 18 June 2013 / Revised: 27 June 2013 / Accepted: 28 June 2013 / Published: 11 July 2013
Cited by 11 | PDF Full-text (662 KB) | HTML Full-text | XML Full-text
Abstract
This paper reviews the architecture of amylose supramolecules in form of inclusion complexes with synthetic polymers by phosphorylase-catalyzed enzymatic polymerization. Amylose is known to be synthesized by enzymatic polymerization using α-d-glucose 1-phosphate as a monomer, by phosphorylase catalysis. When the phosphorylase-catalyzed enzymatic [...] Read more.
This paper reviews the architecture of amylose supramolecules in form of inclusion complexes with synthetic polymers by phosphorylase-catalyzed enzymatic polymerization. Amylose is known to be synthesized by enzymatic polymerization using α-d-glucose 1-phosphate as a monomer, by phosphorylase catalysis. When the phosphorylase-catalyzed enzymatic polymerization was conducted in the presence of various hydrophobic polymers, such as polyethers, polyesters, poly(ester-ether), and polycarbonates as a guest polymer, such inclusion supramolecules were formed by the hydrophobic interaction in the progress of polymerization. Because the representation of propagation in the polymerization is similar to the way that a vine of a plant grows, twining around a rod, this polymerization method for the formation of amylose-polymer inclusion complexes was proposed to be named “vine-twining polymerization”. To yield an inclusion complex from a strongly hydrophobic polyester, the parallel enzymatic polymerization system was extensively developed. The author found that amylose selectively included one side of the guest polymer from a mixture of two resemblant guest polymers, as well as a specific range in molecular weights of the guest polymers poly(tetrahydrofuran) (PTHF) in the vine-twining polymerization. Selective inclusion behavior of amylose toward stereoisomers of chiral polyesters, poly(lactide)s, also appeared in the vine-twining polymerization. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Open AccessReview Angling for Uniqueness in Enzymatic Preparation of Glycosides
Biomolecules 2013, 3(2), 334-350; doi:10.3390/biom3020334
Received: 4 May 2013 / Revised: 23 May 2013 / Accepted: 3 June 2013 / Published: 13 June 2013
Cited by 4 | PDF Full-text (348 KB) | HTML Full-text | XML Full-text
Abstract
In the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays the enzyme can be engineered to be suitable for the process requirements. This is a general bird’s-eye view and as such cannot be specific for articulated situations [...] Read more.
In the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays the enzyme can be engineered to be suitable for the process requirements. This is a general bird’s-eye view and as such cannot be specific for articulated situations found in different classes of enzymes or for selected enzymatic processes. As far as the enzymatic preparation of glycosides is concerned, recent scientific literature is awash with examples of uniqueness related to the features of the biocatalyst (yield, substrate specificity, regioselectivity, and resistance to a particular reaction condition). The invention of glycosynthases is just one of the aspects that has thrust forward the research in this field. Protein engineering, metagenomics and reaction engineering have led to the discovery of an expanding number of novel enzymes and to the setting up of new bio-based processes for the preparation of glycosides. In this review, new examples from the last decade are compiled with attention both to cases in which naturally present, as well as genetically inserted, characteristics of the catalysts make them attractive for biocatalysis. Full article
(This article belongs to the Special Issue Enzymes and Their Biotechnological Applications) Print Edition available
Figures

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type of Paper: Review
Title: Angling for Uniqueness in Enzymatic Preparation of Glycosides
Author: Antonio Trincone
Affiliation: Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei, 34, 80078 Pozzuoli, Naples, Italy; E-Mail: antonio.trincone@icb.cnr.it
Abstract: In the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays, enzymes can be engineered to be suitable for the process requirements. However, this is a general bird’s-eye view and cannot be specific for articulated situations found in different class of enzymes or for selected enzymatic processes. As far as the enzymatic preparation of glycosides is concerned, recent scientific literature is crowded with examples of uniqueness related to the features of the biocatalyst (yield, substrate specificity, regioselectivity, resistance to particular reaction condition). The invention of glycosynthases is just one of the aspects that burst forth the research in this field; protein engineering, metagenomics and reaction engineering led to the discovery of an expanding number of novel enzymes and to the setting up of new bio-based processes for the preparation of glycosides. In this review, new examples from last decade are compiled with attention both to cases in which naturally present and genetically inserted characteristic of the catalysts make them attractive for biocatalysis.

Type of Paper: Article
Title: The Effect of Culture Conditions on Lipase Production by Geotrichum Candidum 4013
Authors: Jana Brabcová 1,2 and Marie Zarevúcka 2,*
Affiliations: 1 Institute of Chemical Technology Prague, Faculty of Food and Biochemical Technology, Technická 5, 160 28 Prague 6, Czech Republic
2 Institute of Organic Chemistry and Biochemistry AS CR, Flemingovo n. 2, 166 10 Prague 6, Czech Republic; E-Mail: zarevucka@uochb.cas.cz (M.Z.)
Abstract: The interest in microbial lipase production has increased in the last decades, because of its large potential in a wide range of industrial applications as additives in food processing, fine chemicals, detergents, waste water treatment, diagnostic, cosmetics, pharmaceuticals and medical. Moreover the lipases from Geotrichum candidum are currently the subject of investigation and industrial interest because it shows a strong preference for unsaturated fatty acids. Till now, the studies on lipolytic enzymes produced by Geotrichum sp. were generally focused on increasing or decreasing of their activity reflecting composition of culture media, but not on effects on the production of particular enzymes. Lipases with different specificities can be produced altering the medium composition. Some components of the culture medium can stimulate lipase production while others can act as repressors. The most common stimulators are long chain fatty acids and organic nitrogen sources, while common repressors are glucose and glycerol. The fungus Geotrichum candidum 4013 produces three extracellular lipases (Lip45kDa, Lip59kDa and Lip61kDa). The effect of culture conditions for maximum individual lipase production by Geotrichum candidum 4013 was studied in connection with composition of culture medium, time and temperature of lipase production. The enzymes were tested for their hydrolytic ability to p-nitrophenyl esters and compounds having a structure similar to the original substrate (triacylglycerols).

Type of Paper: Review
Title:
Biocatalyst Engineering for Improving Catalytic Performance in Neat Organic Solvents
Authors:
Munishwar Nath Gupta*, Joyeeta Mukherjee, Priyanka Dubey, Deepika Malhotra
Affiliation:
Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India; Email: munishwar@chemistry.iitd.ernet.in
Abstract: The use of enzymes in nearly anhydrous organic solvent generally results in low initial rates/percentage conversions. The current review focuses on some biocatalyst designs like immobilization on nanomaterials, enzyme precipitated and rinsed with organic solvents (EPROS), crosslinked enzyme crystals (CLEC), crosslinked enzyme aggregates (CLEA), protein coated microcrystals (PCMC) and crosslinked protein coated microcrystals (CLPCMC) which show much better catalytic efficiency in such media as compared to other kinds of biocatalyst preparations. The basic methodology and principle behind these efficient designs is described. The relatively recent results on catalytic promiscuity as seen in low water media as well have also been covered. It is hoped that this will further encourage wider biotechnological applications of enzymes in neat organic solvents.

Type of Paper: Article
Title: Morita-Baylis-Hillman Reaction of 4-Nitrobenzaldehyde with 2-Cyclohexenone Catalysed by Lipases in Aqueous-Organic Co-Solvent Mixtures
Authors: Manali Kapoor , Abir B. Majumder and Munishwar Nath Gupta*
Affiliation: Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India. *Email: munishwar@chemistry.iitd.ernet.in
Abstract: Lipases catalyzed the reaction between 4-nitrobenzaldehyde and 2-cyclohexen-1-one in aqueous-DMSO co-solvent mixtures to give Morita-Baylis-Hillman product and aldol product. Among lipases, Burkholderia cepacia lipase gave the best overall conversion of 96% in 50% (v/v) DMSO while Mucor javanicus lipase showed highest stereoselectivity in the formation of the aldol (79% ee) and Morita-Baylis-Hillman product (63% ee) with 30% (v/v) DMSO.

Type of Paper: Review
Title: Biocatalytic Applications of Transglutaminases
Authors: Natalie Rachel1, 2, 3 and Joelle N. Pelletier1a, 2, 3, 4 *
Affiliations: 1Département de chimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada; 2CGCC, the Center in Green Chemistry and Catalysis, Montréal, Canada; PROTEO, the Québec Network for Protein Function, Structure and Engineering, Québec, Canada; 4Département de biochimie, Université de Montréal, Montréal, Québec H3C 3J7, Canada; Email: joelle.pelletier@umontreal.ca
Abstract: In nature, transglutaminases catalyze the formation of amide bonds between proteins to form insoluble protein aggregates. They have long been applied in the food and textile industries as a protein cross-linking agent to alter the texture of meat, wool and leather. In recent years, novel applications of transglutaminases in areas ranging from materials sciences to medicine have come to light. There has also been a substantial effort to further investigate the fundamentals of transglutaminases, as there are many characteristics that remain poorly understood. These studies also work towards the goal of developing these enzymes as more efficient tools. Progress in this area includes additional structural information and novel chemical and biological assays. We review these recent biocatalytic achievements in order to illustrate the versatility of transglutaminases.

Type of Paper: Article
Title: Total Biosynthesis of Andrastins
Authors: Yudai Matsuda, Takayoshi Awakawa, Ikuro Abe*
Affiliations: Graduate School of Pharmaceutical Sciences, The University of Tokyo; *Email: abei@mol.f.u-tokyo.ac.jp
Abstract: Andrastins (andrastin A-D), produced by several Penicillium species, exhibits an inhibitory activity against the protein farnesyltransferase, and thus can be the leads for antitumor agents. They are the members of the fungal meroterpenoids derived from 3,5-dimethylorsellinic acid (DMOA), which comprise an especially large number of structurally diverse compounds. Here, we report the identification of the biosynthetic gene cluster for andrastins in the genome of Penicillium chrysogenum, and the reconstitution of the biosynthesis of andrastins in a heterologous fungal expression system. In this study, we characterized five enzymes involved in the biosynthesis of andrastins, which are unique to the biosynthetic pathway of andrastins, and succeeded in the heterologous production of andrastin A by expressing nine genes from the biosynthetic gene cluster.

Journal Contact

MDPI AG
Biomolecules Editorial Office
St. Alban-Anlage 66, 4052 Basel, Switzerland
biomolecules@mdpi.com
Tel. +41 61 683 77 34
Fax: +41 61 302 89 18
Editorial Board
Contact Details Submit to Biomolecules
Back to Top