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Results for “directed evolution”

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At least 829 records · Page 46Linked to original sources
PubMed2004

Colorimetric high-throughput assay for alkene epoxidation catalyzed by cytochrome P450 BM-3 variant 139-3.

Cytochrome P450 BM-3 variant 139-3 is highly active in the hydroxylation of alkanes and fatty acids (AGlieder, ET Farinas, and FH Arnold, Nature Biotech 2002;20:1135-1139); it also epoxidizes various alkenes, including styrene. Here the authors describe a colorimetric, high-throughput assay suitable for optimizing this latter activity by directed evolution. The product of styrene oxidation by 139-3, styrene oxide, reacts with the nucleophile gamma-(4-nitrobenzyl)pyridine (NBP) to form a purple-colored precursor dye, which can be monitored spectrophotometrically in cell lysates. The sensitivity limit of this assay is 50-100 microM of product, and the detection limit for P450 BM-3 139-3 is ~0.2 microM of enzyme. To validate the assay, activities in a small library of random mutants were compared to those determined using an NADPH depletion assay for initial turnover rates.

Alkenes↗
PubMed2001

Enzymes which are stable in the presence of organic solvents.

There are numerous advantages of employing enzymes as catalysts in organic solvents or aqueous solutions containing organic solvents instead of water. A few natural enzymes which are stable in the presence of organic solvents have been discovered. However, almost all natural enzymes are easily denatured and inactivated in the presence of organic solvents. Therefore, several physical and chemical methods, such as immobilization, modification, and entrapment, for stabilizing enzymes in the presence of organic solvents were developed. Protein engineering using site directed mutagenesis and directed evolution are useful for clarifying why organic solvent-stable enzymes are stable in the presence of organic solvents and for developing organic solvent-stable mutant enzymes.

Journal Article↗
PubMed2004

DNA delivery to cells in culture: generation of adenoviral libraries for high-throughput functional screening.

In functional genomics, the use of expression libraries of DNA variants in combination with potent screening techniques is a powerful tool for gene discovery. They allow study of gene and protein function, generation of peptide variants with novel properties, as well as identification of functional short DNA and RNA motifs. In proteomics, generation of large expression libraries of protein variants with random substitutions ("directed evolution") and further screening for novel or improved functions has been commonly used for isolation of proteins with novel characteristics, for improving enzymes, for rapid isolation of antibodies, and for functional protein studies. Most commonly, peptide libraries are expressed and screened in prokaryotic systems. Such systems have the advantage of rapid and simple generation of clones expressing single variants, allow high diversity (up to 10(11)), and can be combined with phage- or cell-surface display technique (2). The main disadvantage of bacterial systems is the absence of posttranslational modifications and native folding of many mammalian proteins, leading to limited applications, particularly when enzyme-substrate-, protein-protein, or protein-RNA interactions are to be studied.

Adenoviridae↗
PubMed2004

Flow cytometric screening of yeast surface display libraries.

A method to screen and isolate antigen specific clones from a library of single-chain antibodies expressed on the surface of yeast cells is presented. Two rounds of magnetic bead enrichment before flow cytometric sorting enables one to screen libraries of far greater diversity than can be screened by just flow cytometry. The strength of flow cytometric sorting is the ability to follow the selection in real time and to isolate easily the highest affinity antigen-specific clones. A major strength of yeast display as a discovery platform is the ability to characterize the binding properties, the affinity of a clone without the need for subcloning, expression, and purification of the scFv. The methodology for directed evolution of single-chain antibodies to increase the affinity of a clone is also described.

Agar↗
PubMedDate not supplied

Engineering cytochrome P-450s: chimeric enzymes.

Cytochrome P-450 isozymes represent a critical component of nature's spectrum of detoxification catalysts that could be exploited for bioremediation. The ethanol-inducible human cytochrome P-450 2E1 serves as a model eukaryotic P-450 that complements the bacterial P-450 cam in dehalogenation and detoxification of environmental pollutants. We explored the construction of novel chimeric P-450s using cytochrome P-450 camC and 2E1 genes. For construction of chimera 1 (478 amino acids, 55.14 kDa), 145 amino acids from the N-terminus of P-450 2E1 protein (493 amino acids, 56.84 kDa) were replaced with 130 amino acids from the N-terminus of P-450 camC protein (415 amino acids, 46.66 kDa). In chimera 2 (525 amino acids, 60.24 kDa) the strategy involves replacement of 28 amino acids in the C-terminus of chimera 1 with 75 amino acids from the C-terminus of P-450 camC gene. Homology models of both the chimeric proteins were developed using SWISS-MODEL based on the known crystal structure of cytochrome P-450 camC, BM-3, 1DT6A, and 2C17A. The models indicated that the proposed heme-binding site was intact, which is inevitable for catalytic activity of cytochrome P-450s. The expression of chimera 1 and 2 genes in Escherichia coli DH5alpha was evident from light-pink cell pellets, protein band in sodium dodecyl sulfate polyacrylamide gel electrophoresis, and diagnostic carbon monoxide-difference spectra. Our studies show that strategies can be developed to exploit the natural diversity of the P-450 superfamily to generate chimeric biocatalysts that would provide new templates amenable to directed evolution.

Amino Acid Sequence↗
PubMed2003

Automated filter paper assay for determination of cellulase activity.

Recent developments in molecular breeding and directed evolution have promised great developments in industrial enzymes as demonstrated by exponential improvements in beta-lactamase and green fluorescent protein (GFP). Detection of and screening for improved enzymes are relatively easy if the target enzyme is expressible in a suitable high-throughput screening host and a clearly defined and usable screen or selection is available, as with GFP and beta-lactamase. Fungal cellulases, however, are difficult to measure and have limited expressibility in heterologous hosts. Furthermore, traditional cellulase assays are tedious and time-consuming. Multiple enzyme components, an insoluble substrate, and generally slow reaction rates have plagued cellulase researchers interested in creating cellulase mixtures with increased activities and/or enhanced biochemical properties. Although the International Union of Pure and Applied Chemists standard measure of cellulase activity, the filter paper assay (FPA), can be reproduced in most laboratories with some effort, this method has long been recognized for its complexity and susceptibility to operator error. Our current automated FPA method is based on a Cyberlabs C400 robotics deck equipped with customized incubation, reagent storage, and plate-reading capabilities that allow rapid evaluation of cellulases acting on cellulose and has a maximum throughput of 84 enzyme samples per day when performing the automated FPA.

Automation↗
PubMed2004

Redistribution of gene frequency and changes of genetic variation following a bottleneck in population size.

Although the distribution of frequencies of genes influencing quantitative traits is important to our understanding of their genetic basis and their evolution, direct information from laboratory experiments is very limited. In theory, different models of selection and mutation generate different predictions of frequency distributions. When a large population at mutation-selection balance passes through a rapid bottleneck in size, the frequency distribution of genes is dramatically altered, causing changes in observable quantities such as the mean and variance of quantitative traits. We investigate the gene frequency distribution of a population at mutation-selection balance under a joint-effect model of real stabilizing and pleiotropic selection and its redistribution and thus changes of the genetic properties of metric and fitness traits after the population passes a rapid bottleneck and expands in size. If all genes that affect the trait are neutral with respect to fitness, the additive genetic variance (VA) is always reduced by a bottleneck in population size, regardless of their degree of dominance. For genes that have been under selection, VA increases following a bottleneck if they are (partially) recessive, while the dominance variance increases substantially for any degree of dominance. With typical estimates of mutation parameters, the joint-effect model can explain data from laboratory experiments on the effect of bottlenecking on fitness and morphological traits, providing further support for it as a plausible mechanism for maintenance of quantitative genetic variation.

Gene Frequency↗
PubMed2006

Heat-inducible autolytic vector for high-throughput screening.

In directed evolution, a high-throughput screening system is often a prerequisite for sampling the enzyme variants. When the target enzyme is expressed intracellularly, for example when Escherichia coli is used as the host, chemical or enzymatic disruption of cell membrane is often required in many cases, which can be tedious, time-consuming, and costly. In this study, a set of heat-inducible autolytic vectors were constructed to solve this problem, in which the SRRz lysis gene cassette from bacteriophage lambda was placed downstream of heat-inducible promoters, lambda cI857/pR promoter and its mutant, c1857/pR(M). The artificial autolytic units were inserted into the backbone of pUC18 (away from the multiple cloning sites). For the wild promoter; cI857/pR, the SRRz lysis cassette was expressed by temperature up-shift from 28 degrees to 38 degrees C, and the lysis efficiency of transformed bacterial cells was found to be consistent and could reach 96.3% as measured by the reporter beta3-galactosidase assay. In order to obtain a higher cell growth rate, the mutant promoter cI857/pR(M) was utilized to allow bacteria growth at 35 degrees C and lysis at 42 degrees C. However; this heat-inducible system showed significant inconsistency in terms of lysis efficiency. Bacillus subtilis 168 lipase A gene was further inserted into the multiple cloning sites of the autolytic vector containing cI857/pR, and 93.7% of the expressed lipase activity was found in the culture medium upon heat induction, demonstrating the utility of the vector for expression and rapid extracellular assay of heterologous enzymes.

Bacillus subtilis↗
PubMed2000

Automated purification of His6-tagged proteins allows exhaustive screening of libraries generated by random mutagenesis.

In the course of site-directed mutagenesis or directed evolution experiments, large numbers of protein variants are often generated. To characterize functional properties of individual mutant proteins in vitro, a rapid and reliable protein purification system is required. We have developed an automated method for the parallel purification of 96 different protein variants that takes about two hours. Using a 96-well format, the whole process can be performed automatically by a pipetting robot. Coupled with a suitable assay, again using a 96-well format, all variants can be functionally characterized within a few hours. The protein purification procedure described here is based on the interaction between His6-tagged proteins and Ni-NTA-coated microplates. Typical yields are 3-8 pmol purified protein/well, which is sufficient to analyze most enzymatic activities. Using this procedure, we have purified and characterized variants of the restriction endonuclease EcoRV, which were produced in an effort to enhance the selectivity of this enzyme. For this purpose, three amino acid residues were randomized in a region known from the co-crystal structure to be located at the protein-DNA interface. From a library of about 1200 variants, predominantly single and double mutants, more than 1000 variants were purified and characterized in parallel, which corresponds to an almost complete screening of the library.

Automation↗
PubMed1997

Generation of large libraries of random mutants in Bacillus subtilis by PCR-based plasmid multimerization.

We describe a PCR-based method for the generation of plasmid multimers that can be directly transformed into Bacillus subtilis with very high efficiency. This technique is particularly useful for the generation of large libraries of randomly mutagenized genes, which are required for the optimization of enzymes by directed evolution. We subjected the gene coding for the protease subtilisin to six consecutive rounds of PCR at three different levels of mutagenicity. The resulting 18 populations were cloned using our PCR multimerization protocol, and the mutation frequencies were determined by DNA sequencing. The resulting data demonstrate that the mutation frequency during PCR can be controlled by adding varying concentrations of manganese chloride to the reaction mixture. We observed a bias in the type of base pair changes with A and T being mutated much more frequently than C and G. We determined the fraction of active clones in all populations and found that its natural logarithm is proportional to the average mutation frequency of the populations. These data reveal that a fraction of about 0.27 of all possible mutations leads to the inactivation of the subtilisin gene, which provides a measure for its structural plasticity.

Bacillus subtilis↗
PubMed2002

Designing proteins that work using recombinant technologies.

Therapeutic proteins have been engineered for a variety of purposes including reduced antigenicity, longer half-life, simplified process development, and increased affinity. Fusion proteins bring together functions from two different molecules creating therapeutics with completely novel activities. Protein engineering technologies have relied on rational design, directed evolution, DNA shuffling, RNA-peptide fusion, phage and ribosomal display methods to select out candidate protein forms with the desired therapeutic properties. Engineered site-specific pegylation and glycosylation strategies have improved circulation half-life, reduced immunogenicity and increased protein therapeutic stability. In this review we describe how protein engineering techniques have been used to select out, improve stability and clinical efficacy of protein therapeutics.

Animals↗
PubMed2010

AAV's anatomy: roadmap for optimizing vectors for translational success.

Adeno-Associated Virus based vectors (rAAV) are advantageous for human gene therapy due to low inflammatory responses, lack of toxicity, natural persistence, and ability to transencapsidate the genome allowing large variations in vector biology and tropism. Over sixty clinical trials have been conducted using rAAV serotype 2 for gene delivery with a number demonstrating success in immunoprivileged sites, including the retina and the CNS. Furthermore, an increasing number of trials have been initiated utilizing other serotypes of AAV to exploit vector tropism, trafficking, and expression efficiency. While these trials have demonstrated success in safety with emerging success in clinical outcomes, one benefit has been identification of issues associated with vector administration in humans (e.g. the role of pre-existing antibody responses, loss of transgene expression in non-immunoprivileged sites, and low transgene expression levels). For these reasons, several strategies are being used to optimize rAAV vectors, ranging from addition of exogenous agents for immune evasion to optimization of the transgene cassette for enhanced therapeutic output. By far, the vast majority of approaches have focused on genetic manipulation of the viral capsid. These methods include rational mutagenesis, engineering of targeting peptides, generation of chimeric particles, library and directed evolution approaches, as well as immune evasion modifications. Overall, these modifications have created a new repertoire of AAV vectors with improved targeting, transgene expression, and immune evasion. Continued work in these areas should synergize strategies to improve capsids and transgene cassettes that will eventually lead to optimized vectors ideally suited for translational success.

Cystic Fibrosis↗
PubMed1999

Hirudin display on the surface of bacteriophage M13.

Hirudin was fused to the N terminus of M13 minor protein gp3 (197-406) through a linker GGGS by inserting both the hirudin gene and the gp8 signal sequence into the modified phagemid vector pCANTAB 5V to construct pCANTAB 5G8-Hir. The expressed fusion protein was directed by gp8 signal peptide into the periplasm and assembled to the phage particle to form the hirudin-phage. The fusion protein and fusion phage were detected with biotin-thrombin by Western blotting analysis. Antithrombin activity analysis confirmed that the hirudin portion in the fusion protein and fusion phage bear similar native conformation. The successful display of hirudin on the surface of M13 phage laid a sound foundation for the further study on directed evolution of antithrombotic proteins with altered properties.

Antithrombins↗
PubMedDate not supplied

[Adaptive types of prolamins--specialized proteins from cereal seeds (Poaceae Banrh.)].

Amino acid composition of prolamins and the whole seed in representatives of 52 cereal genera and 22 tribes, as well as amino acid composition of seed protein fractions in representatives of 9 cereal genera are presented. In terms of proposed directed evolution of the seed proteins and adaptive role of prolamins in evolution and distribution of cereals, generalized data on their content in seed protein complex, electrophoretic, immunochemical, and amino acid composition of the seeds, we develop the notion of prolamins biochemical specialization and their polyphyletic origin during evolution of cereal seed protein complex. Seven adaptive types of prolamins are recognized: Sasa, Molinia, Chloris, Zingeria, Poa, Triticum, and Panicum types. Adaptive types of prolamins were formed in response to an ecological request of the environment where taxon ancestors existed and a taxon appeared and in relation to phylogenetic history of a taxon and its assignment to particular tribe and subfamily.

Adaptation, Biological↗
PubMed2000

Enzyme Mechanisms for Polycyclic Triterpene Formation.

The mechanisms by which triterpene cyclases transform olefins into complex and biologically important polycyclic products have fueled nearly half a century of intense research. Recent chemical and biological studies, together with previous findings, provide intriguing new insights into the enzymatic mechanism of triterpene formation and form a surprisingly detailed picture of these elegant catalysts. It can be concluded that the role of the oxidosqualene cyclases involves protection of the intermediate carbocation against addition of water or deprotonation by base, thereby allowing the shift of the hydride and methyl groups along a thermodynamically and kinetically favorable cascade. Key questions in the areas of structural biology, site-directed mutagenesis, and directed evolution are apparent, now that the first structure of a triterpene cyclase is known.

Journal Article↗
PubMed2001

[Research on the school of Danxi of the Ming dynasty].

Zhu Danxi, the founder of Danxi School, one of the four major schools of the Jin - Yuan dynasties, was famous for its Yin - nourishing theory. Clinically, it was adept in treating miscellaneous disorders, with the "four - injury theory" as its theory for differentiation of Zheng. The medical thinking of Danxi is quite specific that it exerted its clinical and academic influence mostly in the Ming dynasty, with so many schools followed him. Though research on its origin and evolution, direct followers like Dai Sigong, Wang Lü, Lin Chung et al. not only totally inherited Danxi's medical idea, but also became the receiver of his academic experiences. Indirect followers(study perronally) reached its peak in the Ming dynasty. They inherited Danxi's experience and further developed to supplement his theory. For other physicians partly following Danxi's experience also emerged and applied his academy for further development of medical theory.

China↗
PubMed1992

Luminescent screens for general X-ray diagnostics.

This article gives the main parameters of amplifying screens manufactured in the USSR: the sensitivity, the resolution, the modulation depth, the noise. The technical level of Soviet screens is compared with the level of those manufactured by certain foreign companies. The measures taken to increase the technical level of today's products and the further evolution directions are discussed. Data are given on screen production in the USSR during the last 5 years and their supposed production up to 2000.

Evaluation Studies as Topic↗
PubMed2003

Homogeneous biocatalysis in organic solvents and water-organic mixtures.

Biocatalysis in non-aqueous media has undergone tremendous development during the last decade, and numerous reactions have been introduced and optimized for synthetic applications. In contrast to aqueous enzymology, biotransformations in organic solvents offer unique industrially attractive advantages, such as: drastic changes in the enantioselectivity of the reaction, the reversal of the thermodynamic equilibrium of hydrolysis reactions, suppression of water-dependent side reactions, and resistance to bacterial contamination. Currently, the field is dominated by heterogeneous biocatalysis based primarily on lyophilized enzyme powders, cross-linked crystals, and enzymes immobilized on inert supports that are mainly applied in enantioselective synthesis. However, low reaction rates are an inherent problem of the heterogeneous biocatalysis, while the homogeneous systems have the advantage that the elimination of diffusional barriers of substrates and products between organic and water phases results in an increase in the reaction rate. Here the discussion is focused on the correlation between activity and structure of the intact enzymes dissolved in neat organic solvents, as well as modifications of natural enzymes, which make them soluble and catalytically active in non-aqueous environment. Factors that influence conformation and stability of the enzymes are also discussed. Current developments in non-aqueous biocatalysts that combine advantages of protein modification and immobilization, i.e., HIP plastics, enzyme chips, ionic liquids, are introduced. Finally, engineering enzymes for biotransformations in non-conventional media by directed evolution is summarized.

Catalysis↗