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Biocatalysis

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https://www.readbyqxmd.com/read/28523096/biocatalysis-in-the-pharmaceutical-industry-the-need-for-speed
#1
Matthew D Truppo
The use of biocatalysis in the pharmaceutical industry continues to expand as a result of increased access to enzymes and the ability to engineer those enzymes to meet the demands of industrial processes. However, we are still just scratching the surface of potential biocatalytic applications. The time pressures present in pharmaceutical process development are incompatible with the long lead times required for engineering a suitable biocatalyst. Dramatic increases in the speed of protein engineering are needed to deliver on the ever increasing opportunities for industrial biocatalytic processes...
May 11, 2017: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28514852/separated-immobilization-of-incompatible-enzymes-on-polymer-substrate-via-visible-light-induced-living-photografting-polymerization
#2
Xing Zhu, Bin He, Changwen Zhao, Yuhong Ma, Wantai Yang
The use of the mixed catalytic system with several enzymes can provide multiple benefits in terms of the costs, simplification of a multi-steps reaction, and the effectiveness of the complex chemical reactions. Although study of different enzymes co-immobilization system has attracted increasing attention in recent years, separately immobilizing enzymes which can not coexist on one support is still one of the great challenges. In this paper, a simple and effective strategy was introduced to separately encapsulate incompatible trypsin and transglutaminase (TGase) into different poly(ethylene glycol) (PEG) network layer grafted on low-density polyethylene (LDPE) film via visible light induced living photografting polymerization...
May 17, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28514518/a-retrosynthesis-approach-for-biocatalysis-in-organic-synthesis
#3
Uwe Bornscheuer, Rodrigo O M A de Souza, Leandro S M Miranda
Lead-In: For the planning of an organic synthesis route, the disconnection approach guided by retrosynthetic analysis of possible intermediates and the chemical reactions involved, back to ready available starting materials, is well established. In contrast, such concepts just get developed for biocatalytic routes. In this review we highlight functional group interconversions catalyzed by enzymes. The article is organized rather by chemical bonds formed - exemplified for C-N, C-O- and C-C-bonds - and not by enzyme classes, covering a broad range of reactions to incorporate the desired functionality in the target molecule...
May 17, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28500946/pa-tb-cu-mof-as-luminescent-nanoenzyme-for-catalytic-assay-of-hydrogen-peroxide
#4
Zewan Qi, Li Wang, Qi You, Yang Chen
Metal organic frameworks (MOFs) with flexible structures and components have aroused great interest in designing functional materials. In this work, we designed and made a kind of PA-Tb-Cu MOF nanoenzyme capable of emitting fluorescence for the catalytic reaction of hydrogen peroxide (H2O2). Luminescent Tb(3+), catalytic Cu(2+) and bridging ligand were assembled and integrated into a single material nanoenzyme. This PA-Tb-Cu MOF nanoenzyme not only possessed excellent catalytic activity comparable to horseradish peroxidase but also can real-time fluorescently indicate the concentration of H2O2 as low as 0...
May 6, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28498544/metabolic-engineering-of-cofactor-flavin-adenine-dinucleotide-fad-synthesis-and-regeneration-in-escherichia-coli-for-production-of-%C3%AE-keto-acids
#5
Ying Hou, Gazi Sakir Hossain, Jianghua Li, Hyun-Dong Shin, Guocheng Du, Jian Chen, Long Liu
Cofactor flavin adenine dinucleotide (FAD) plays a vital role in many FAD-dependent enzymatic reactions; therefore, how to efficiently accelerate FAD synthesis and regeneration is an important topic in biocatalysis and metabolic engineering. In this study, a system involving the synthesis pathway and regeneration of FAD was engineered in Escherichia coli to improve α-keto acid production-from the corresponding L-amino acids-catalyzed by FAD-dependent L-amino acid deaminase (L-AAD). First, key genes, ribH, ribC, and ribF, were overexpressed and fine-tuned for FAD synthesis...
May 12, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28497966/large-scale-analysis-of-hydrogen-bond-interaction-patterns-in-protein-ligand-interfaces
#6
Eva Nittinger, Therese Inhester, Stefan Bietz, Agnes Meyder, Karen T Schomburg, Gudrun Lange, Robert Klein, Matthias Rarey
Protein-ligand interactions are the fundamental basis for molecular design in pharmaceutical research, biocatalysis, and agrochemical development. Especially hydrogen bonds are known to have special geometric requirements and therefore deserve a detailed analysis. In modeling approaches a more general description of hydrogen bond geometries, using distance and directionality, is applied. A first study of their geometries was performed based on 15 protein structures in 1982. Currently there are about 95 000 protein-ligand structures available in the PDB, providing a solid foundation for a new large-scale statistical analysis...
May 12, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28497961/evaluating-the-development-of-biocatalytic-technology-for-the-targeted-removal-of-perchlorate-from-drinking-water
#7
Justin M Hutchison, Jeremy S Guest, Julie L Zilles
Removing micropollutants is challenging in part because of their toxicity at low concentrations. A biocatalytic approach could harness the high affinity of enzymes for their substrates to address this challenge. The potential of biocatalysis relative to mature (non-selective ion exchange, selective exchange, and whole-cell biological reduction) and emerging (catalysis) perchlorate-removal technologies was evaluated through a quantitative sustainable design framework, and research objectives were prioritized to advance economic and environmental sustainability...
May 12, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28495560/characterization-of-two-cryptic-plasmids-from-kocuria-palustris-ipufs-1-and-construction-of-novel-escherichia-coli-kocuria-shuttle-vector-for-biocatalysis
#8
Hiroshi Toda, Takashi Koyanagi, Toshiki Enomoto, Nobuya Itoh
Two cryptic plasmids, designated pKPAL1 and pKPAL2, were identified from the gram-positive bacterium Kocuria palustris IPUFS-1, which was isolated from a fish source. The 2251-bp and 2488-bp circular genomes of pKPAL1 and pKPAL2, respectively, were sequenced. Subsequent open reading frame (ORF) and homology search analyses suggested that pKPAL1 and pKPAL2 possess two and three ORFs, respectively, and encode the putative replication proteins, RepA and RepB, like the genomes of several plasmids in gram-positive bacteria...
May 8, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28489346/metal-organic-frameworks-at-the-biointerface-synthetic-strategies-and-applications
#9
Christian Doonan, Raffaele Riccò, Kang Liang, Darren Bradshaw, Paolo Falcaro
Many living organisms are capable of producing inorganic materials of precisely controlled structure and morphology. This ubiquitous process is termed biomineralization and is observed in nature from the macroscale (e.g., formation of exoskeletons) down to the nanoscale (e.g., mineral storage and transportation in proteins). Extensive research efforts have pursued replicating this chemistry with the overarching aims of synthesizing new materials of unprecedented physical properties and understanding the complex mechanisms that occur at the biological-inorganic interface...
May 10, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28474899/liquefaction-of-biopolymers-solvent-free-liquids-and-liquid-crystals-from-nucleic-acids-and-proteins
#10
Kai Liu, Chao Ma, Robert Göstl, Lei Zhang, Andreas Herrmann
Biomacromolecules, such as nucleic acids, proteins, and virus particles, are persistent molecular entities with dimensions that exceed the range of their intermolecular forces hence undergoing degradation by thermally induced bond-scission upon heating. Consequently, for this type of molecule, the absence of a liquid phase can be regarded as a general phenomenon. However, certain advantageous properties usually associated with the liquid state of matter, such as processability, flowability, or molecular mobility, are highly sought-after features for biomacromolecules in a solvent-free environment...
May 5, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28470047/beyond-iron-iridium-containing-p450-enzymes-for-selective-cyclopropanations-of-structurally-diverse-alkenes
#11
Hanna M Key, Paweł Dydio, Zhennan Liu, Jennifer Y-E Rha, Andrew Nazarenko, Vida Seyedkazemi, Douglas S Clark, John F Hartwig
Enzymes catalyze organic transformations with exquisite levels of selectivity, including chemoselectivity, stereoselectivity, and substrate selectivity, but the types of reactions catalyzed by enzymes are more limited than those of chemical catalysts. Thus, the convergence of chemical catalysis and biocatalysis can enable enzymatic systems to catalyze abiological reactions with high selectivity. Recently, we disclosed artificial enzymes constructed from the apo form of heme proteins and iridium porphyrins that catalyze the insertion of carbenes into a C-H bond...
April 26, 2017: ACS Central Science
https://www.readbyqxmd.com/read/28466867/enzyme-discovery-beyond-homology-a-unique-hydroxynitrile-lyase-in-the-bet-v1-superfamily
#12
Elisa Lanfranchi, Tea Pavkov-Keller, Eva-Maria Koehler, Matthias Diepold, Kerstin Steiner, Barbara Darnhofer, Jürgen Hartler, Tom Van Den Bergh, Henk-Jan Joosten, Mandana Gruber-Khadjawi, Gerhard G Thallinger, Ruth Birner-Gruenberger, Karl Gruber, Margit Winkler, Anton Glieder
Homology and similarity based approaches are most widely used for the identification of new enzymes for biocatalysis. However, they are not suitable to find truly novel scaffolds with a desired function and this averts options and diversity. Hydroxynitrile lyases (HNLs) are an example of non-homologous isofunctional enzymes for the synthesis of chiral cyanohydrins. Due to their convergent evolution, finding new representatives is challenging. Here we show the discovery of unique HNL enzymes from the fern Davallia tyermannii by coalescence of transcriptomics, proteomics and enzymatic screening...
May 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28466644/development-of-halogenase-enzymes-for-use-in-synthesis
#13
Jonathan Latham, Eileen Brandenburger, Sarah A Shepherd, Binuraj R K Menon, Jason Micklefield
Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo...
May 3, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28465211/catalytically-active-inclusion-bodies-carrier-free-protein-immobilizates-for-application-in-biotechnology-and-biomedicine
#14
Ulrich Krauss, Vera D Jäger, Martin Diener, Martina Pohl, Karl-Erich Jaeger
Bacterial inclusion bodies (IBs) consist of unfolded protein aggregates and represent inactive waste products often accumulating during heterologous overexpression of recombinant genes in Escherichia coli. This general misconception has been challenged in recent years by the discovery that IBs, apart from misfolded polypeptides, can also contain substantial amounts of active and thus correctly or native-like folded protein. The corresponding catalytically-active inclusion bodies (CatIBs) can be regarded as a biologically-active sub-micrometer sized biomaterial or naturally-produced carrier-free protein immobilizate...
April 29, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28464607/oriented-coimmobilization-of-oxidase-and-catalase-on-tailor-made-ordered-mesoporous-silica
#15
Juan M Bolivar, Victoria Gascon, Carlos Marquez-Alvarez, Rosa M Blanco, Bernd Nidetzky
Mesoporous silica materials are promising carriers for enzyme immobilization in heterogeneous biocatalysis applications. By tailoring their pore structural framework, these materials are designable for appropriate enzyme binding capacity and internal diffusivity. To supply O2 efficiently to solid-supported immobilized enzymes represents a core problem of heterogeneously catalyzed oxidative biotransformations. In this study, therefore, we synthesized and compared three internally well-ordered and two amorphous silica materials as enzyme carriers, each of those with pore sizes of ≥10 nm, to enable the coimmobilization of d-amino-acid oxidase (79 kDa) and catalase (217 kDa)...
May 12, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28464370/enzymatic-halogenation-a-timely-strategy-for-regioselective-c-h-activation
#16
Christian Schnepel, Norbert Sewald
Halogenating enzymes increasingly attract attention for biocatalytic C-H functionalization. Despite the importance for synthetic chemistry, selective introduction of halogens using conventional approaches often remains challenging, whereas biocatalysis offers excellent catalyst-controlled selectivity without requiring protecting groups or hazardous reagents. Owing to the high prevalence of halogenated secondary metabolites, a still growing repertoire of halogenases has been identified. Recently, flavin-dependent tryptophan halogenases turned into focus for synthetic use...
May 2, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28455340/engineering-escherichia-coli-nicotinic-acid-mononucleotide-adenylyltransferase-for-fully-active-amidated-nad-biosynthesis
#17
Xueying Wang, Yongjin J Zhou, Lei Wang, Wujun Liu, Yuxue Liu, Chang Peng, Zongbao K Zhao
Nicotinamide adenine dinucleotide (NAD) and its reduced form NADH function as essential redox cofactors and have major roles in determining cellular metabolic features. NAD can be synthesized through deamidated and amidated pathway, of which the key reaction involves adenylylation of nicotinic acid mononucleotide (NaMN) and nicotinamide mononucleotide (NMN), respectively. In Escherichia coli, NAD de novo biosynthesis depends on the protein NadD-catalyzed adenylylation of NaMN to nicotinic acid adenine dinucleotide (NaAD), followed by NAD synthase-catalyzed amidation...
April 28, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28448715/acyl-carrier-protein-cyanylation-delivers-a-ketoacyl-synthase-carrier-protein-crosslink
#18
Grace Thiele, Conne Friedman, Kathleen Tsai, Joris Beld, Casey H Londergan, Louise K Charkoudian
Acyl carrier proteins (ACPs) are central hubs in polyketide and fatty acid biosynthetic pathways, but the fast motions of the ACP's phosphosphopantetheine (Ppant) arm make its conformational dynamics difficult to capture using traditional spectroscopic approaches. Here we report that converting the terminal thiol of E. coli ACP's Ppant arm into a thiocyanate activates this site to form a selective crosslink with the active site cys-teine of its partner ketoacyl synthase (KS; FabF). The reaction releases a cyanide anion, which can be detected by infrared spectroscopy...
April 27, 2017: Biochemistry
https://www.readbyqxmd.com/read/28446346/engineering-nanosized-organosilica-for-molecular-recognition-and-biocatalysis-applications
#19
M Rita Correro, Yves Dudal, Philippe F-X Corvini, Patrick Shahgaldian
A series of synthetic nanomaterials capable of molecular recognition and/or biocatalysis have been produced by exploiting the self-sorting, self-assembly and polycondensation of organosilane building blocks around protein templates. The established methodology allows for the production of thin organosilica layers of controlled thickness, down to nanometer precision. Fully synthetic virus recognition materials have been shown to specifically bind their target virus down to picomolar concentrations. The shielding of natural enzymes allowed producing nanobiocatalysts functioning under harsh operational conditions...
April 26, 2017: Chimia
https://www.readbyqxmd.com/read/28445435/microarray-selection-of-cooperative-peptides-for-modulating-enzyme-activities
#20
Jinglin Fu
Recently, peptide microarrays have been used to distinguish proteins, antibodies, viruses, and bacteria based on their binding to random sequence peptides. We reported on the use of peptide arrays to identify enzyme modulators that involve screening an array of 10,000 defined and addressable peptides on a microarray. Primary peptides were first selected to inhibit the enzyme at low μM concentrations. Then, new peptides were found to only bind strongly with the enzyme-inhibitor complex, but not the native enzyme...
April 26, 2017: Microarrays
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